From owner-chemistry@ccl.net Thu Dec 8 04:12:01 2005 From: "Yao-Yinng Chien chieny|,|msu.edu" To: CCL Subject: CCL: seek NMR mailing list similar to CCL Message-Id: <-30226-051208040905-14882-uPSrglVASLnVtrhide2IKA[*]server.ccl.net> X-Original-From: "Yao-Yinng Chien" Sent to CCL by: "Yao-Yinng Chien" [chieny:_:msu.edu] Hi, I am looking for NMR mailing list similar to CCL. I googled by the key word "NMR mailing list", but not quite satisfied. Could you please help me out? The question I wish to ask at NMR mailing list is : The time required for 2 nuclei remained in close contact for NOE (Nuclear Overhauser Enhancement) transfer to occur? Some background: NOESY spectrum of 2-octanone in aqueous humic acids solution (HA). Several cross peaks of 2-octanone are observed. The one puzzled me is the cross peak between the Hydrogens at position 1 and 8 of carbons (H18). Assuming H18 is due to intermolecular interaction, how long these 2 nuclei (of two separate 2-octanone molecules) need to be in close contact (5 A?) for NOE transfer to occur? Most NMR biochemists tell me "milliseconds", but cannot provide me references. Help in references are deeply appreciated. Notice that H at position 1 is polar, whereas position 8 is a non-polar end. Usually polar end and nonpolar end does not like each other. What forces them together, trapped in a pocket? Assuming H18 is due to intrAmolecular interaction. This implies 2-octanone is bent like a V-shape, so that polar and non-polar ends can meet. Seems requires an even smaller pocket. Then again, how long these 2 nuclei (of the same 2-octanone molecule) need to be in close contact (5 A?) for NOE transfer to occur? Notice: Formation of 2-octanone micelles in HA solution would make 2-octanone linear and pulls polar and non-polar ends further apart. Humic acids (HA) is one of the dark brown organic material on the top of soils, mixtures of decomposed compounds from plant and animals. Lignin is one of its precursors. On sandy soil, it's the only protection to keep organic contaminants from leaching to groundwater. To simplify the system, you can assume it's a polysaccharide with 1000 atoms. From owner-chemistry@ccl.net Thu Dec 8 08:20:01 2005 From: "Gilles Marcou gilles.marcou!^!pharma.u-strasbg.fr" To: CCL Subject: CCL: seek NMR mailing list similar to CCL Message-Id: <-30227-051208063307-9596-Fv+6OpthzZlI0xc86DQKNg++server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 8 Dec 2005 11:49:13 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou%pharma.u-strasbg.fr] Hi, > The time required for 2 nuclei remained in close contact for NOE (Nuclear > Overhauser Enhancement) transfer to occur? It may be a good idea to make a molecular mechanics simulation and try to extract from it, possible NOE enhancement. You can do that with the program NOEProm, if you manage to get your calculations in macromodel format. http://desoft03.usc.es/mmartin/rmnweb/rmnexp_software.html You will be able then to put in relation NOE intensities and relative potential energies of your conformers. Hope this helps. Ciao, -- Gilles Marcou Université Louis Pasteur de Strasbourg Faculté de Pharmacie Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR7081 74, Route du Rhin, BP24 67401 Illkirch tel.:(0033)(0)3.90.24.42.21 eMail: marcou a pharma.u-strasbg.fr From owner-chemistry@ccl.net Thu Dec 8 08:55:01 2005 From: "Dr. Seth Olsen s.olsen1^^^uq.edu.au" To: CCL Subject: CCL:G: Visualization Software Options? Message-Id: <-30228-051208080919-22445-03mAG6gF/d1xZLt3CHWgYQ||server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 Dec 2005 22:32:19 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1^^uq.edu.au] Hi CCLers, For reasons unknown MOLEKEL has been quite prone to sudden crashes on my new notebook machine (FC4). I've tried to relink it, but that is getting nowhere for reasons I have yet to work out. In the meantime, I'm on the lookout for programs that have similar capability. I already have ghemical (good, but doesn't seem to take gaussian cube files) and molden (only good if opengl version is used, and that's a bit of a pain b/c you can't load things and manipulate them as well as with MOLEKEL). I have two questions: 1. has anyone else had trouble with MOLEKEL on Fedora 4 machines? Has anyone had trouble with linking it? 2. does anyone know of some good visualization software that I haven't mentioned above? I suspect the linking problems are due to my own ignorance in the dark arts. I've tried gcc v.4, gcc 2.95.3 and icc, so I'm pretty sure that the problem is either me or so deep that I won't solve it in reasonable time. I'm particularly looking for software that does isodensity surfaces and/or electrostatic potential surfaces well (preferably from gaussian cube files, though that's not strictly necessary). Cheers, Seth From owner-chemistry@ccl.net Thu Dec 8 09:30:01 2005 From: "Wang Yang yangwang2008:_:gmail.com" To: CCL Subject: CCL: Short code to generate carbon and BN nanotubes Message-Id: <-30229-051208090435-16234-4GyjGPRYmQSs2J3RR2gdPQ-$-server.ccl.net> X-Original-From: Wang Yang Content-Type: multipart/alternative; boundary="----=_Part_8809_266936.1134050673353" Date: Thu, 8 Dec 2005 22:04:33 +0800 MIME-Version: 1.0 Sent to CCL by: Wang Yang [yangwang2008],[gmail.com] ------=_Part_8809_266936.1134050673353 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All, Here I propose a rather short code written in FORTRAN 77 to generate coordinates of carbon and boron-nitrogen single-walled nanotubes. The basic idea is to screen out atoms in the 2D graphene plane with a rectangle formed by two rolling vectors and two axial vectors. The source code is given as follows. PROGRAM Nanotube INTEGER GCD, n, m, n_, m_, NumL, c_bn, gcd_nm, i, j, k, l, $ st1, st2, stm REAL a, c, t, radius, p, theta, x, y, z PARAMETER(PI =3D 3.14159265359, BND_LEN =3D 1.420) WRITE(*,*) 'Please enter n, m, l, c_bn:' READ(*,*) n, m, NumL, c_bn gcd_nm =3D GCD(n, m) n_ =3D (2*m + n)/gcd_nm m_ =3D -(2*n + m)/gcd_nm IF((MOD((n-m), 3) .EQ. 0 .AND. m .NE. 0) THEN n_ =3D n_ / 3 m_ =3D m_ / 3 END IF a =3D BND_LEN * SQRT(3.0) c =3D SQRT(REAL(n*n + m*m + n*m)) t =3D SQRT(REAL(n_*n_ + m_*m_ + n_*m_)) radius =3D c * a / (2 * PI) p =3D a / (2 * c * radius) stm =3D m * n_ - n * m_ DO i =3D 1, n + n_ -1 DO j =3D m_ + 1, m st1 =3D m * i - n * j st2 =3D n_ * j - m_ * i IF( (st1 .GE. 0) .AND. (st1 .LT. stm) .AND. $ (st2 .GE. 0) .AND. (st2 .LE. stm) ) THEN st1 =3D (2*n_ + m_)*i + (2*m_ + n_)*j st2 =3D (2*n + m)*i + (2*m + n)*j DO l =3D 0, NumL -1 DO k =3D 0, 1 z =3D (REAL(st1 - k*(n_ + m_)) $ / (2*t) + REAL(l)*t) * a theta =3D REAL(st2 - k*(n + m)) * p x =3D radius * COS(theta) y =3D radius * SIN(theta) IF(c_bn .EQ. 0) THEN WRITE(*, 100) 'C', x, y, z ELSE IF(k .EQ. 0) THEN WRITE(*, 100) 'B', x, y, z ELSE WRITE(*, 100) 'N', x, y, z END IF END IF END DO END DO END IF END DO END DO 100 FORMAT(1X, A2, 3F12.6) END FUNCTION GCD(n, m) INTEGER GCD, n, m, b, s, r b =3D MAX(n, m) s =3D MIN(n, m) IF(s .EQ. 0) THEN GCD =3D b RETURN END IF r =3D MOD(b,s) DO WHILE(r .NE. 0) b =3D s s =3D r r =3D MOD(b,s) END DO GCD =3D s END Any constructive comments are welcome! Thank you for noticing these matters. -- Yang Wang Department of Chemistry, Beijing Normal University, Beijing, China 100875 TEL: 86-10-5880-1456 FAX: 86-10-5880-2075 EMAIL: yangwang2008\a/gmail.com WEB SITE: http://202.112.86.128/studentspace/aqyw/ ------=_Part_8809_266936.1134050673353 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All,

    Here I propose a rather short code writ= ten in FORTRAN 77 to generate coordinates of carbon and boron-nitrogen single-walled nanotubes.
    The basic idea is to screen = out atoms in the 2D graphene plane with a rectangle formed by two rolling vectors and two axial vectors.
    The source code is given as follows.

 &n= bsp;    PROGRAM Nanotube
     &n= bsp;  INTEGER GCD, n, m, n_, m_, NumL, c_bn, gcd_nm, i, j, k, l,
&= nbsp;    $        &n= bsp; st1, st2, stm
        REAL a, c,= t, radius, p, theta, x, y, z=20
        PARAMETER(PI =3D 3.141592653= 59, BND_LEN =3D 1.420)
        WRITE(= *,*) 'Please enter n, m, l, c_bn:'
      &= nbsp; READ(*,*) n, m, NumL, c_bn
      &nb= sp; gcd_nm =3D GCD(n, m)
        n_ = =3D (2*m + n)/gcd_nm
        m_ =3D -= (2*n + m)/gcd_nm
        IF((MOD((n-m), 3) .EQ. 0 .AN= D. m .NE. 0) THEN
         = n_ =3D n_ / 3
          m_= =3D m_ / 3
        END IF
 &= nbsp;      a =3D BND_LEN * SQRT(3.0)
 &nbs= p;      c =3D SQRT(REAL(n*n + m*m + n*m))
 = ;       t =3D SQRT(REAL(n_*n_ + m_*m_ + n_*m_= ))
        radius =3D c * a / (2 * PI)<= br>       p =3D  a / (2 * c * radius)        stm =3D m * n_ - n * m_
&nbs= p;       DO i =3D 1, n + n_ -1
  = ;        DO j =3D m_ + 1, m
 &nb= sp;         st1 =3D m * i - n * j           st2 =3D n_ *= j - m_ * i
           IF( (st1 .= GE. 0) .AND. (st1 .LT. stm) .AND.
     $  = ;        (st2 .GE. 0) .AND. (st2 .LE. st= m) ) THEN
          &n= bsp;  st1 =3D (2*n_ + m_)*i + (2*m_ + n_)*j
    = ;         st2 =3D (2*n + m)*i + (2*= m + n)*j
            &nb= sp; DO l =3D 0, NumL -1
        =         DO k =3D 0, 1
  &nb= sp;            =    z     =3D (REAL(st1 - k*(n_ + m_))
&nb= sp;    $        &nbs= p;           / (2*t) + RE= AL(l)*t) * a
          = ;        theta =3D REAL(st2 - k*(n + m))= * p            = ;            &n= bsp;=20
            = ;      x     =3D radius * COS(= theta)
           = ;       y     =3D radius = * SIN(theta)
          = ;      IF(c_bn .EQ. 0) THEN
   &= nbsp;           &nbs= p;    WRITE(*, 100) 'C', x, y, z
    =             &nb= sp; ELSE
          &nb= sp;       IF(k .EQ. 0) THEN
            = ;          WRITE(*, 100) 'B', = x, y, z
          &nbs= p;       ELSE
    &nbs= p;            &= nbsp;    WRITE(*, 100) 'N', x, y, z
   &nb= sp;            =   END IF
         &nbs= p;      END IF
     &n= bsp;          END DO
 =              EN= D DO
           END IF
=           END DO
 &nbs= p;      END DO
100     FORM= AT(1X, A2, 3F12.6)
        END
&nb= sp;
        FUNCTION GCD(n, m)
&nb= sp;         INTEGER GCD, n, m, b, s= , r
          b =3D MAX(n, = m)
          s =3D MIN(n, m= )
          IF(s .EQ. 0) THE= N
            GCD= =3D b
           = ; RETURN
          END IF          r =3D MOD(b,s)
=           DO WHILE(r .NE. 0)            b =3D = s
            s = =3D r
           = r =3D MOD(b,s)
          END DO
 =          GCD =3D s
  &= nbsp;     END
       <= br>
    Any constructive comments are welcome!
 &= nbsp;  Thank you for noticing these matters.

-- <= br>Yang Wang

Department of Chemistry,
Beijing Normal University, Beijing, China 100875
TEL: 86-10-5880-145= 6
FAX: 86-10-5880-2075
EMAIL: yangwang2008\a/gmail.com
WEB SITE: http://202.112.86.128/studentspace/aqyw/
------=_Part_8809_266936.1134050673353-- From owner-chemistry@ccl.net Thu Dec 8 10:05:01 2005 From: "Axel Mathieu AMathieu\a/tranzyme.com" To: CCL Subject: CCL: seek NMR mailing list similar to CCL Message-Id: <-30230-051208090316-12734-+gA8Eam0qFCSFnFgsNmH1Q*server.ccl.net> X-Original-From: "Axel Mathieu" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 8 Dec 2005 09:03:55 -0500 MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu++tranzyme.com] Yao-Yinng, I'm also part of the "Association of Managers in Magnetic Resonance Laboratories" (AMMRL) newsgroup at http://chemnmr.colorado.edu/ammrl/; you need to be an NMR "manager" of some sort to be able to post on this newsgroup or you can ask someone who is already on the list. Your question would fit in the realm of the newsgroup. Unfortunately I do not know the answer to your question ... APM -----Original Message----- > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net] Sent: 8 décembre, 2005 04:45 To: Axel Mathieu Subject: CCL: seek NMR mailing list similar to CCL Sent to CCL by: "Yao-Yinng Chien" [chieny:_:msu.edu] Hi, I am looking for NMR mailing list similar to CCL. I googled by the key word "NMR mailing list", but not quite satisfied. Could you please help me out? The question I wish to ask at NMR mailing list is : The time required for 2 nuclei remained in close contact for NOE (Nuclear Overhauser Enhancement) transfer to occur? Some background: NOESY spectrum of 2-octanone in aqueous humic acids solution (HA). Several cross peaks of 2-octanone are observed. The one puzzled me is the cross peak between the Hydrogens at position 1 and 8 of carbons (H18). Assuming H18 is due to intermolecular interaction, how long these 2 nuclei (of two separate 2-octanone molecules) need to be in close contact (5 A?) for NOE transfer to occur? Most NMR biochemists tell me "milliseconds", but cannot provide me references. Help in references are deeply appreciated. Notice that H at position 1 is polar, whereas position 8 is a non-polar end. Usually polar end and nonpolar end does not like each other. What forces them together, trapped in a pocket? Assuming H18 is due to intrAmolecular interaction. This implies 2-octanone is bent like a V-shape, so that polar and non-polar ends can meet. Seems requires an even smaller pocket. Then again, how long these 2 nuclei (of the same 2-octanone molecule) need to be in close contact (5 A?) for NOE transfer to occur? Notice: Formation of 2-octanone micelles in HA solution would make 2-octanone linear and pulls polar and non-polar ends further apart. Humic acids (HA) is one of the dark brown organic material on the top of soils, mixtures of decomposed compounds from plant and animals. Lignin is one of its precursors. On sandy soil, it's the only protection to keep organic contaminants from leaching to groundwater. To simplify the system, you can assume it's a polysaccharide with 1000 atoms.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Dec 8 10:42:00 2005 From: "Ben Sattelle ben.sattelle===postgrad.manchester.ac.uk" To: CCL Subject: CCL:G: Visualization Software Options? Message-Id: <-30231-051208104051-9413-PJt8ydCk2WxgzvfEA1Aeog!^!server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format="flowed" Date: Thu, 8 Dec 2005 15:40:37 +0000 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle!=!postgrad.manchester.ac.uk] chemcraft is useful (freeware version does have some annoying limitations), ben. http://www.chemcraftprog.com/ > Sent to CCL by: "Dr. Seth Olsen" [s.olsen1^^uq.edu.au] > > Hi CCLers, > > For reasons unknown MOLEKEL has been quite prone to sudden crashes on my > new notebook machine (FC4). I've tried to relink it, but that is > getting nowhere for reasons I have yet to work out. In the meantime, > I'm on the lookout for programs that have similar capability. I already > have ghemical (good, but doesn't seem to take gaussian cube files) and > molden (only good if opengl version is used, and that's a bit of a pain > b/c you can't load things and manipulate them as well as with > MOLEKEL). I have two questions: > > 1. has anyone else had trouble with MOLEKEL on Fedora 4 machines? Has > anyone had trouble with linking it? > 2. does anyone know of some good visualization software that I haven't > mentioned above? > > I suspect the linking problems are due to my own ignorance in the dark > arts. I've tried gcc v.4, gcc 2.95.3 and icc, so I'm pretty sure that > the problem is either me or so deep that I won't solve it in reasonable > time. > > I'm particularly looking for software that does isodensity surfaces > and/or electrostatic potential surfaces well (preferably from gaussian > cube files, though that's not strictly necessary). > > Cheers, > > Seth------------------------------------------------------------ Mr B.M. Sattelle, Room B8, Jackson's Mill, School of Chemical Engineering and Analytical Science (CEAS), The University of Manchester, PO Box 88, Sackville Street, Manchester, M60 1QD, UK. Tel: [+44] (0)161 306 8857 http://neon.ce.umist.ac.uk/ http://www.manchester.ac.uk/ceas ------------------------------------------------------------ From owner-chemistry@ccl.net Thu Dec 8 11:21:01 2005 From: "Joslyn Y Kravitz jyudenfr]_[umich.edu" To: CCL Subject: CCL:G: Visualization Software Options? Message-Id: <-30232-051208111125-29558-rrywwblmWNfTIHntHQ+4RQ---server.ccl.net> X-Original-From: Joslyn Y Kravitz Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 8 Dec 2005 10:18:40 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Joslyn Y Kravitz [jyudenfr\a/umich.edu] Try gOpenMol. I have only used it on Windows machines and SGIs but in both cases it has been great. It does take cube files. Joslyn On Thu, 8 Dec 2005, Dr. Seth Olsen s.olsen1^^^uq.edu.au wrote: > Sent to CCL by: "Dr. Seth Olsen" [s.olsen1^^uq.edu.au] > > Hi CCLers, > > For reasons unknown MOLEKEL has been quite prone to sudden crashes on my > new notebook machine (FC4). I've tried to relink it, but that is > getting nowhere for reasons I have yet to work out. In the meantime, > I'm on the lookout for programs that have similar capability. I already > have ghemical (good, but doesn't seem to take gaussian cube files) and > molden (only good if opengl version is used, and that's a bit of a pain > b/c you can't load things and manipulate them as well as with > MOLEKEL). I have two questions: > > 1. has anyone else had trouble with MOLEKEL on Fedora 4 machines? Has > anyone had trouble with linking it? > 2. does anyone know of some good visualization software that I haven't > mentioned above? > > I suspect the linking problems are due to my own ignorance in the dark > arts. I've tried gcc v.4, gcc 2.95.3 and icc, so I'm pretty sure that > the problem is either me or so deep that I won't solve it in reasonable > time. > > I'm particularly looking for software that does isodensity surfaces > and/or electrostatic potential surfaces well (preferably from gaussian > cube files, though that's not strictly necessary). > > Cheers, > > Seth> > > > > > From owner-chemistry@ccl.net Thu Dec 8 14:45:01 2005 From: "Sengen Sun sengensun%a%yahoo.com" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30233-051208143737-3670-A43uUxcmGxbtseM5yHeKIg%a%server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 8 Dec 2005 11:37:34 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun%x%yahoo.com] Dear college and graduate school educational workers: In the last January when we were in the hot debate, one of you wrote me something like this: ["My friend, orbitals will be observed again and again and again..., first in Nature, then in Science, then in JACS, then in JPC, JOC, JIC...... The images will be very very pretty. I want to see by then how well you like those images....."] My current questions are directed to those who teach something like ["orbitals not physically real; orbitals not observable; objections to that orbitals observable"....] How do you folks explain to an average student when he argues with you with copies of the Natture papers, Science papers, C&EN news reports... that all have positively confirmed orbitals are observed? Do you have to say ["Nature papers are wrong, Science papers are wrong, C&EN news reports are wrong, Angew Chem is wrong..... Please trust me, my rationale is right because Hoffmann said something like orbitals are both real and unreal. And Hoffmann also said that PES tells us the ways orbitals interact..."]? Do you also have to tell your student finally that he cannot understand this until he drinks and digests all deeplyu of the Pyrean (sic) spring? What else could you say? I am really curious. We are facing an unbearable disaster and dilemma in scientific education and research on this issue. This why I have stood up to support Dr. Eric Scerri who raised such an very important issue initially at CCL years ago. I am offering a possible solution. That is, Hoffmann, the authority in this field, makes a clear statement that every one can understand on this issue. And then we all follow that. This attacker will disappear and this ox will not be grinning any more if any one can offer a better and feasible solution! Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Dec 8 15:50:00 2005 From: "ramesh r ramesh_ass]_[yahoo.co.in" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30234-051208134602-32420-xwYU9akaCAHdj+I8/tekIQ|a|server.ccl.net> X-Original-From: ramesh r Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-41187699-1134060055=:97686" Date: Thu, 8 Dec 2005 16:40:55 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] --0-41187699-1134060055=:97686 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I have two questions to ask related to how to create a animation and movie: 1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file. 2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file. At this point, Could you please suggest any program do that task. Thanks in advance sincerely, ramesh --------------------------------- Yahoo! India Matrimony: Find your partner now. --0-41187699-1134060055=:97686 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi CCLers,
I have two questions to ask related to how to create a animation and movie:
1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file.
2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file.
 
At this point, Could you please suggest any program do that task.
 
Thanks in advance
                    sincerely,
                     ramesh 


Yahoo! India Matrimony: Find your partner now. --0-41187699-1134060055=:97686-- From owner-chemistry@ccl.net Thu Dec 8 16:25:00 2005 From: "himanshu khandelia hkhandel%%cems.umn.edu" To: CCL Subject: CCL: Linux Cluster Building Workshops Message-Id: <-30235-051208153451-32557-WeuvjBIBao9I3DhAA3qbAw/a\server.ccl.net> X-Original-From: "himanshu khandelia" Sent to CCL by: "himanshu khandelia" [hkhandel- -cems.umn.edu] Is anyone aware of any cluster building workshops that might be useful for engineers and scientists who are not system administrators, but are trying to build their own machines ? From owner-chemistry@ccl.net Thu Dec 8 17:00:00 2005 From: "Sengen Sun sengensun],[yahoo.com" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30236-051208142531-2594-w0OTmlK8tzb5w6a91DEmag^server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 8 Dec 2005 10:25:22 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun|yahoo.com] Dear college and graduate school educational workers: In the last January when we were in the hot debate, one of you wrote me saying something like this: ["My friend, orbitals will be observed again and again and again..., first in Nature, then in Science, then in JACS, then in JPC, JOC, JIC...... The images will be very very pretty. I want to see by then how well you like those images....."] My current questions are directed to those who teach something like ["orbitals not physically real; orbitals not observable; objections to that orbitals observable"....] How do you folks explain to an average student when he argues with you with copies of the Nature papers, Science papers, C&EN news reports... that all have positively confirmed orbital orbservations? Do you have to say ["Nature papers are wrong, Science papers are wrong, C&EN news reports are wrong, Angew Chem is wrong..... Please trust me, my rationale is right because Hoffmann said something like orbitals are both real and unreal. And Hoffmann also said that PES tells us the ways orbitals interact..."]? Do you also have to tell the student finally that you cannot understand this until you drink and digest all deeplyu of the Pyrean (sic) spring? What else could you say? I am really curious. We are facing an unbearable disaster and dilemma in scientific education and research on this issue. This why I have stood up to support Dr. Eric Scerri who raised such an very important issue initially at CCL years ago. I have received a private e-mail I like the most so far, which says: ["You attacker are too naive if you think all drivers are free of alcohol"]. How wanderful such a metaphor! The quote by Hoffmann has a clear language word-by-word no matter how you read it. There has not been so far a second person who dare to say explicitly TRUE or FALSE to it in the public. How interesting it is in the modern age of human civilization in science and philosophy! Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Dec 8 17:34:00 2005 From: "Peter Burger chburger**aci.unizh.ch" To: CCL Subject: CCL: crystal field & ligand field theory & MO theory Message-Id: <-30237-051208162816-22105-P+NpLih0kZzmMg6NnFTzLA^-^server.ccl.net> X-Original-From: "Peter Burger" Sent to CCL by: "Peter Burger" [chburger . aci.unizh.ch] Dear CCLers recently I faced a problem while teaching, i.e. the discrepancy of ligand field splitting and qualitative MO theory for e.g. d8-configured square planar complexes ML4 with pure sigma donors, e.g. [PdH4]2- (D4h symmetry). Is there any way to bridge the gap between the square planar ligand field splitting shown in every textbook (order dxz, dyz, then dxy or dz2 followed by dx2-y2)) and MO theory? The qualitiative MO (first order pertubation) treatment leaves the obviously symmetrically non-degenerate dxy (b2g) and dxz and dyz (eg) at albeit nevertheless _energetically_ identical orbital energies (all three are non-bonding in the absence of pi-acceptors). Is there a good way to get out of this while teaching qualitative MO theory? The obvious problem is that students have memorized the ligand field splitting in previous lectures. Best regards Peter From owner-chemistry@ccl.net Thu Dec 8 18:09:01 2005 From: "Gustavo Seabra gustavo.seabra=-=gmail.com" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30238-051208155648-4989-PmuDXEsP2dHa15nOPEhx7w]=[server.ccl.net> X-Original-From: Gustavo Seabra Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 8 Dec 2005 15:49:54 -0500 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra/a\gmail.com] Hi Sengen, I haven't posted yet, but have been following this discussion very closely. May I suggest that that are interested in this issue read the related articles, especially the experimentals who claim to "see" the orbitals, and then go back to the discussion? Maybe then we could all start building an answer. For that matter, could you post the references here? Thanks. Gustavo. From owner-chemistry@ccl.net Thu Dec 8 18:44:00 2005 From: "Loan Huynh huynhkl2000[#]yahoo.ca" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30239-051208171345-30091-Qo8RhBzxYQwMkd5zxp92gQ^server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-990960829-1134080015=:54878" Date: Thu, 8 Dec 2005 17:13:35 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000###yahoo.ca] --0-990960829-1134080015=:54878 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Ramesh,you may want to used VMD and VideoMach, it can take the PDB files. You can down load the free version from the internet, http://www.ks.uiuc.edu/Research/vmd/ http://gromada.com/videomach.html cheers LH "ramesh r ramesh_ass]_[yahoo.co.in" wrote: Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] --0-41187699-1134060055=:97686 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I have two questions to ask related to how to create a animation and movie: 1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file. 2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file. At this point, Could you please suggest any program do that task. Thanks in advance sincerely, ramesh --------------------------------- Yahoo! India Matrimony: Find your partner now. --0-41187699-1134060055=:97686 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I have two questions to ask related to how to create a animation and movie: 1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file. 2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file. At this point, Could you please suggest any program do that task. Thanks in advance sincerely, ramesh --------------------------------- Yahoo! India Matrimony: Find your partner now. --0-41187699-1134060055=:97686--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Find your next car at Yahoo! Canada Autos --0-990960829-1134080015=:54878 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi Ramesh,you may want to used VMD and VideoMach, it can take the PDB files.  You can down load the free version from the internet,
 
 
cheers
LH
"ramesh r ramesh_ass]_[yahoo.co.in" <owner-chemistry**ccl.net> wrote:
Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in]
--0-41187699-1134060055=:97686
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi CCLers,
I have two questions to ask related to how to create a animation and movie:
1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file.
2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file.

At this point, Could you please suggest any program do that task.

Thanks in advance
sincerely,
ramesh




---------------------------------
Yahoo! India Matrimony: Find your partner now.
--0-41187699-1134060055=:97686
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi CCLers,
I have two questions to ask related to how to create a animation and movie:
1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file.
2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file.
 
At this point, Could you please suggest any program do that task.
 
Thanks in advance
                    sincerely,
                     ramesh 




Yahoo! India Matrimony: Find your partner now.
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http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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Find your next car at Yahoo! Canada Autos --0-990960829-1134080015=:54878-- From owner-chemistry@ccl.net Thu Dec 8 19:19:00 2005 From: "Andrew D. Fant fant(~)pobox.com" To: CCL Subject: CCL: Linux Cluster Building Workshops Message-Id: <-30240-051208174021-24024-S1sQQce0T8Zp8BRk/PXGFg(!)server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 Dec 2005 17:40:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant/./pobox.com] himanshu khandelia hkhandel%%cems.umn.edu wrote: > Sent to CCL by: "himanshu khandelia" [hkhandel- -cems.umn.edu] > Is anyone aware of any cluster building workshops that might be useful > for engineers and scientists who are not system administrators, but are > trying to build their own machines ? The Linux Clusters Institute at http://www.linuxclustersinstitute.org/ has seminars on cluster building, although they do tend to dive rather heavily into theory. The MIT press has published "How To Build A Beowulf" by Stirling, et al on the subject, as well as a followup volume entitled "Beowulf Cluster Computing" in versions for Linux and Windows. O'Reilly, whose titles are usually the last work for IT topics like this, has published 2 disappointing volumes for this as well. The first was simply Building Linux Clusters and has been withdrawn from the market. The follow-on "Building High-Performance Linux Clusters" is better, but still is less that one might help. If you simply want to put together 4-8 PCs to run a single application for you or a single research group, I would suggest looking at Rocks ( http://www.rocksclusters.org) as a simple way to get something up and running. Oscar or Warewulf ( http://oscar.openclustergroup.org or http://warewulf-cluster.org ) are more complex options that require greater familiarity with Linux and systems administration. My biggest bit of advice, however, comes from a bumper sticker that the electrician's union hands out around here. "Wiring Is Not A Hobby". If you are going to be running multiple applications from multiple sources/vendors, going above about 10 systems, having users from more than one fairly tight-knit and cooperative research group, or making the results from this cluster the basis of your research plans, you probably want to get an IT professional involved. While many researchers keep clusters running on a part-time basis with either their time or that of their grad students, this can rapidly become a time sink. If your institution provides internal consulting services, or has a central research computing facility, I would check with them about what facilities and support they provide. The word on the street is that NIH and NSF are both being fussier about funding one-off clusters for researchers. Hope this helps, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant[a]pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Thu Dec 8 19:55:01 2005 From: "john furr john.furr^_^gmail.com" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30241-051208161147-15564-/5skQuMtzqQRhsvn7AvhcQ]*[server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_14153_15231443.1134076302787" Date: Thu, 8 Dec 2005 16:11:42 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr%x%gmail.com] ------=_Part_14153_15231443.1134076302787 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline My personal opinion is that PyMol is the best tool for this Job. Sincerely, John Furr http://www.dynamol.com Dynamol Inc. On 12/8/05, ramesh r ramesh_ass]_[yahoo.co.in wrote: > > Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] > --0-41187699-1134060055=3D:97686 > Content-Type: text/plain; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit > > Hi CCLers, > I have two questions to ask related to how to create a animation and > movie: > 1. I may want to create a animation of a molecular model protein like > rotation, translation and save it as file. > 2. I have a docked complexes contains ligands and proteins. With this, = I > may want to create a movie showing docking of a ligand into the active si= te > and save it in file. > > At this point, Could you please suggest any program do that task. > > Thanks in advance > sincerely, > ramesh > > > > > --------------------------------- > Yahoo! India Matrimony: Find your partner now. > --0-41187699-1134060055=3D:97686 > Content-Type: text/html; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit > >
Hi CCLers,
I have two questions to ask > related to how to create a animation and movie:
1. I may want= to > create a animation of a molecular model protein like rotation, translatio= n > and save it as file.
2. I have a docked complexes contai= ns > ligands and proteins. With this, I may want to create a movie > showing docking of a ligand into the active site and save it in > file.
 
At this point, Could you please sugg= est > any program do that task.
 
Thanks in > advance
         = ;           > sincerely,
        &n= bsp;            = ;ramesh 


>

> Yahoo! India Matrimony: Find your > partner now. > --0-41187699-1134060055=3D:97686-- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_14153_15231443.1134076302787 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline My personal opinion is that PyMol is the best tool for this Job.

Sincerely,
John Furr
http://www.dynamol.com
Dynamol Inc.

On 12/8/05, ramesh r ramesh_ass]_[= yahoo.co.in <owner-ch= emistry:_:ccl.net > wrote:
Sent to CCL by: ramesh r [ramesh_ass : = yahoo.co.in ]
--0-41187699-1134060055=3D:97686
Content-Type: text/plain; char= set=3Diso-8859-1
Content-Transfer-Encoding: 8bit

Hi CCLers,
&n= bsp; I have two questions to ask related to how to create a animation = and movie:
  1. I may want to create a animation of a molecular model pr= otein like rotation, translation and save it as file.
  2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file.

  At this point, Could you pleas= e suggest any program do that task.

  Thanks in advance            &n= bsp;         sincerely,
&nb= sp;            =           ramesh




---------------------------------
Yahoo! Indi= a Matrimony: Find your partner now.
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= Content-Type: text/html; charset=3Diso-8859-1
Content-Transfer-Encoding:= 8bit

<DIV id=3DRTEContent>Hi CCLers,</DIV>  <DIV>I have two questions to ask related to how to create a animation and movie:</DIV>  <DIV>1. I may want to create a animation of a molecular model protein like rotation, translation and save it as file.</DIV>  <DIV>2.&nbsp;I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing&nbsp;docking of a ligand into&nbsp;the active site and save it in file.</DIV>  <DIV>&nbsp;</DIV>  &= lt;DIV>At this point, Could you please suggest any program do that task.</DIV>  <DIV>&nbsp;</DIV>  &= lt;DIV>Thanks in advance</DIV>  <DIV>&nbsp;&nbsp;&nbsp;&am= p;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs= p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&am= p;nbsp; sincerely,</DIV>  <DIV>&nbsp;&nbsp;&nbsp;= &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&= nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;= &nbsp;&nbsp;&nbsp;ramesh&nbsp;</DIV><BR><BR&= gt;<p>
            = ;    <hr size=3D1>
<a href=3Dhttp://yahoo.shaadi.com>Yahoo! India Matrimony= </a>: Find your partner now.
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------=_Part_14153_15231443.1134076302787-- From owner-chemistry@ccl.net Thu Dec 8 20:30:01 2005 From: "Brian Salter-Duke b_duke,octa4.net.au" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30242-051208163325-23973-8MgItknarIFhMJAWgI97qg!=!server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 9 Dec 2005 08:33:11 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke{=}octa4.net.au] On Thu, Dec 08, 2005 at 03:01:49PM -0500, Sengen Sun sengensun%a%yahoo.com wrote: > Sent to CCL by: Sengen Sun [sengensun%x%yahoo.com] > Dear college and graduate school educational workers: > > In the last January when we were in the hot debate, > one of you wrote me something like this: > > ["My friend, orbitals will be observed again and again > and again..., first in Nature, then in Science, then > in JACS, then in JPC, JOC, JIC...... The images will > be very very pretty. I want to see by then how well > you like those images....."] > > My current questions are directed to those who teach > something like ["orbitals not physically real; > orbitals not observable; objections to that orbitals > observable"....] > > How do you folks explain to an average student when he > argues with you with copies of the Natture papers, > Science papers, C&EN news reports... that all have > positively confirmed orbitals are observed? > > Do you have to say ["Nature papers are wrong, Science > papers are wrong, C&EN news reports are wrong, Angew > Chem is wrong..... Please trust me, my rationale is > right because Hoffmann said something like orbitals > are both real and unreal. And Hoffmann also said that > PES tells us the ways orbitals interact..."]? > > Do you also have to tell your student finally that he > cannot understand this until he drinks and digests all > deeplyu of the Pyrean (sic) spring? > > What else could you say? I am really curious. > I think you are confused. I am certainly in the camp of those who say that orbitals (i.e. molecular orbitals in many electron molecules) are not real, but I still use them. In fact I have spent time this year writing code to get orbitals in a form that they can be displayed by visualisation codes. In PES, for example, the main educational point is to stress that the experiment tells us about molecular states. That is the key. We can then go on to say that we can approximate the state in the molecular orbital theory and use this to get some understanding. However, we should also remember that we are using an approximation, that it does not always work even roughly, and that orbitals are not real because they are part of the approximation. In education we use models and approximations all the time. The important thing is to not confuse them with observable facts. Use them well. Put them in their place. > We are facing an unbearable disaster and dilemma in > scientific education and research on this issue. This > why I have stood up to support Dr. Eric Scerri who > raised such an very important issue initially at CCL > years ago. I am happy for Eric to raise this issue, but you exaggerate. There is no unbearable disaster and there is no real dilemma. > I am offering a possible solution. That is, Hoffmann, > the authority in this field, makes a clear statement > that every one can understand on this issue. And then > we all follow that. Absolutely not! Even if Hoffmann made a clear statement, which he did not, we should not decide science or education on what an authority says. > This attacker will disappear and this ox will not be > grinning > any more if any one can offer a better and feasible > solution! > > Sengen > > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com> > > -- Brian Salter-Duke (Brian Duke) b_duke]-[octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Thu Dec 8 21:05:01 2005 From: "=?iso-8859-1?Q?V=EDctor_Manuel_Medel_Ju=E1rez?= vmedel:-:cinvestav.mx" To: CCL Subject: CCL: molden format to tinker Message-Id: <-30243-051208183107-15999-GquqI7/oWw6SJulhkwRSVg\a/server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Manuel_Medel_Ju=E1rez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 8 Dec 2005 16:36:39 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Manuel_Medel_Ju=E1rez?= [vmedel*o*cinvestav.mx] Hola a todos I am trying to convert a structure that I saved in molden with the Tinker format, but it is saved for the mm2. So I want to convert to charmm format. Is something inside of the tinker package that do it? If it is not, Is there others package for to do it? I would appreciate to hear how to do it ? Thanks a lot From owner-chemistry@ccl.net Thu Dec 8 21:39:01 2005 From: "Elaine Meng meng- -cgl.ucsf.edu" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30244-051208195758-4414-AhxrOTrHxYM8iqwE37C6/w]![server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 8 Dec 2005 16:57:51 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Elaine Meng [meng*_*cgl.ucsf.edu] > Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] > > Hi CCLers, > I have two questions to ask related to how to create a animation > and movie: > 1. I may want to create a animation of a molecular model protein > like rotation, translation and save it as file. > 2. I have a docked complexes contains ligands and proteins. With > this, I may want to create a movie showing docking of a ligand into > the active site and save it in file. > > At this point, Could you please suggest any program do that task. > > Thanks in advance > sincerely, > ramesh Hi Ramesh, In Chimera, the Movie Recorder tool allows you to save image frames and automatically assemble them into a movie file (MPEGs or Quicktime). Once you have displayed the molecule(s) as desired (ribbons, colors, background color, etc.), you can start recording frames, then move the structures, then stop recording frames, and finally encode into a movie file. The start, stop, and encode are each a single click on the graphical interface of the Movie Recorder. Probably the more difficult part is how to set up what happens during recording. Although you could just move molecules by hand with the mouse, the nicer way is to have a script specifying rotations, translations, etc. The Movie Recorder is also implemented as the "movie" command so that you can start and stop recording within the script. Chimera can be downloaded free for noncommercial use from http:// www.cgl.ucsf.edu/chimera/ Movie Recorder man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ recorder.html movie command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Here is an example script that fetches a structure from the PDB (1gfl) and shows it in various ways. You would put these lines below in a text file named something.com and open it with File... Open in Chimera. That would execute the script, including recording image frames and assembling them into a Quicktime movie file (you'd probably have to change the output file pathname to something that works on your system). The movie command has many options; mostly defaults are used in this example. # # Chimera command script showing green fluorescent protein (PDB 1gfl) # movie record open 1gfl; del ~ :.a; window; linewidth 3; scale 1.6; rainbow; wait sleep 3 chain #,#n,ca,c,o; wait 1 sleep 3 ~disp; ribbon roll y 1 180; wait ribrepr edged roll y 1 180; wait ribrepr smooth roll y 1 80; wait ribbackbone repr sphere :1.a,230.a#,#ca color white,a :1.a,230.a#,#ca;disp :1.a,230.a#,#ca roll y 1 90; wait scale 1.015 20; wait disp :65-67.a; color byatom :65-67.a; repr cpk :65-67.a; wait 1 clip hither -1 20; wait sleep 5 clip hither 1 20; wait scale 0.98 10; wait sleep 2 roll y 1 180; wait movie stop movie encode mformat mov output /users/meng/Desktop/gfp.mov # end of script There is a learning curve for the commands, but that also means you can do a lot of things! Best, Elaine ----- Elaine C. Meng, Ph.D. meng#,#cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Thu Dec 8 22:15:02 2005 From: "Dr. N. SUKUMAR nagams]![rpi.edu" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30245-051208185149-467-+TjqmewJBQNzeb9ynCiOgQ.:.server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 08 Dec 2005 18:51:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams]_[rpi.edu] On Thu, 08 Dec 2005 14:50:18 EST "Sengen Sun sengensun%a%yahoo.com" wrote: ... > I am offering a possible solution. That is, Hoffmann, the authority in this field, makes a clear statement that every one can understand on this issue. And then we all follow that. ... Sengen ===========End of original message text=========== That is not how science works and you know it. Hoffmann is not the Oracle and his words are not Scripture. Nor do our unsupported opinions one way or the other matter; we are not voting in an election. What matters are the logical consistency of our arguments -- and many here have expressed these very clearly --- and the experimental facts. I donot have the specific quote or reference that concerns you available to me now and I will avoid repeating my own arguments from last January. There are many textbook errors and J.Chem.Educ.has a regular column devoted to these. Journal errors are customarily refuted in the journals themselves. ==============Original message text=============== On Fri, 02 Dec 2005 14:02:30 EST "Sengen Sun sengensun\a/yahoo.com" wrote: > If an experimental quantity A tells something or some actions about B, B then can be measured through A... Sengen ===========End of original message text=========== Experimental measurement A (typically an intensity) tells us something about object B in theory/model C. However theory C' may interpret the same experimental result in terms of object B' (for instance orbitals or bonds). Often C and C' are approximate models (like the independent-particle model and the Born-Oppenheimer approximation), each applicable within a limited domain of validity. Push the model beyond this domain and you get UNREAL answers. This is all I understand by real and unreal. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Thu Dec 8 22:50:02 2005 From: "Sengen Sun sengensun() yahoo.com" To: CCL Subject: CCL: some clarifications Message-Id: <-30246-051208221626-28483-kt2YMBDyE0MtFOL8fZ67Ng,server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 8 Dec 2005 19:16:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun{=}yahoo.com] First, I apologize that a draft of my post (with Date: Thu, 8 Dec 2005 10:25:22) went through CCL by accident. The one with Date: Thu, 8 Dec 2005 11:37:34) is the final one I wanted to post. I thank Brian Salter-Duke for his contributions of solid science and clear languages to support this discussion. See my comments below: > I think you are confused. I am certainly in the > camp > of those who say > that orbitals (i.e. molecular orbitals in many > electron molecules) are > not real, but I still use them. In fact I have > spent > time this year > writing code to get orbitals in a form that they > can > be displayed by > visualisation codes. > In PES, for example, the main educational point is > to > stress that the > experiment tells us about molecular states. That is > the key. We can then > go on to say that we can approximate the state in > the > molecular orbital > theory and use this to get some understanding. > However, we should also > remember that we are using an approximation, that > it > does not always > work even roughly, and that orbitals are not real > because they are part > of the approximation. > In education we use models and approximations all > the > time. The > important thing is to not confuse them with > observable facts. Use them > well. Put them in their place. Sorry, Brian. I am not confused here. Orbitals are very useful to me too. But the current problem is that orbitals have been exaggerated too much in the literature. I may get back this point later (maybe next year). I am trying to exit for now for the holiday season. > > We are facing an unbearable disaster and dilemma > in > > scientific education and research on this issue. > This > > why I have stood up to support Dr. Eric Scerri > who > > raised such an very important issue initially at > CCL > > years ago. > I am happy for Eric to raise this issue, but you > exaggerate. There is > no unbearable disaster and there is no real > dilemma. You probably right here. It does look like that I exaggerated. I meant that we do currently have an unresolvable logical conflict. > > I am offering a possible solution. That is, > Hoffmann, > > the authority in this field, makes a clear > statement > > that every one can understand on this issue. And > then > > we all follow that. > Absolutely not! Even if Hoffmann made a clear > statement, which he did > not, we should not decide science or education on > what an authority > says. Brian is right. But, I meant that a Nobel Laureate has a quite high impact on the directions how science can evolve. Therefore, a clear and concise language from the Nobel Laureate is extremely important. It would be a terrible thing that every one writes to him in order to understand him. Thank you again, Brian Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com