From owner-chemistry@ccl.net Thu Oct 6 04:03:01 2005 From: "Dhaval R Mehta dhavalm99{=}gmail.com" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29506-051006023345-10924-8KEBgeDn31JA4BKZwj8G0A]|[server.ccl.net> X-Original-From: "Dhaval R Mehta" Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] Hie, I have the N,CA,C atom coordinate file in the PDB format of two proteins.Which software will allow the superposition of these proteins (without the sidechains)? Name:-Dhaval Mehta Email:-dhavalm99(!)gmail.com From owner-chemistry@ccl.net Thu Oct 6 08:34:00 2005 From: "andras.borosy:givaudan.com" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29507-051006044933-9008-Hp6hDAVydeF86+p5+KCpxw[-]server.ccl.net> X-Original-From: andras.borosy(_)givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0030772BC1257092_=" Date: Thu, 6 Oct 2005 10:49:21 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy^-^givaudan.com This is a multipart message in MIME format. --=_alternative 0030772BC1257092_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr. Mehta, There are many, like MOLOC (www.moloc.ch) free for academics and cheap for industry. Sybyl (www.tripos.com) MOE Insight (www.accelrys.com) etc. Best wishes, Dr. Andr=E1s Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D=FCbendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy_._givaudan.com owner-chemistry_._ccl.net wrote on 06.10.2005 10:18:02: >=20 > Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] > Hie, > I have the N,CA,C atom coordinate file in the PDB format of two=20 > proteins.Which software will allow the superposition of these=20 > proteins (without the sidechains)? >=20 > Name:-Dhaval Mehta > Email:-dhavalm99=3D-=3Dgmail.com >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D->=20> http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage >=20> http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage >=20 > Subscribe/Unsubscribe:=20 > http://www.ccl.net/chemistry/sub=5Funsub.shtml >=20>=20 > Job advertisements: http://www.ccl.net/jobs=20 >=20>=20>=20 >=20 --=_alternative 0030772BC1257092_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Mr. Mehta,

There are many, like

MOLOC (www.moloc.ch) free for academ= ics and cheap for industry.
Sybyl (www.tripos.com)
MOE
Insight (www.accelrys.com)
etc.

Best wishes,

Dr. Andr=E1s Borosy
Seniour Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz AG
Ueberlandstr. 138
8600 D=FCbendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy_._givaudan.com

owner-chemistry_._ccl.net wrote on 06.10.2005 10:18:02= : > > Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] > Hie, > I have the N,CA,C atom coordinate file in the PDB format of two > proteins.Which software will allow the superposition of these > proteins (without the sidechains)? > > Name:-Dhaval Mehta > Email:-dhavalm99=3D-=3Dgmail.com > > > > -=3D This is automatically added to each message by the mailing script =3D- > > > > > > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessa= ge > > > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessa= ge > > > http://www.ccl.net/chemistry/sub=5Funsub.shtml > >= > > > > > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+ > > --=_alternative 0030772BC1257092_=-- From owner-chemistry@ccl.net Thu Oct 6 09:09:00 2005 From: "Goedele Roos groos**vub.ac.be" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29508-051006063616-26241-xkixCz7+9YOc6dDPF7goJA%server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 6 Oct 2005 11:40:23 +0200 (MEST) Sent to CCL by: Goedele Roos [groos()vub.ac.be] Hi, I use PYMOL. It is free on the net Goedele >Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] >Hie, > I have the N,CA,C atom coordinate file in the PDB format of two proteins.Which software will allow the superposition of these proteins (without the sidechains)? > >Name:-Dhaval Mehta >Email:-dhavalm99=-=gmail.com> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Thu Oct 6 09:44:01 2005 From: "=?ISO-8859-1?Q?Tommi_Nyr=F6nen?= nyronen*_*csc.fi" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29509-051006061954-19236-guGctWNzJDAoUiM+Fqsi5w()server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Tommi_Nyr=F6nen?= Content-ID: Content-Type: MULTIPART/MIXED; BOUNDARY="-1497257471-818937201-1128591013=:9270" Date: Thu, 6 Oct 2005 12:33:33 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Tommi_Nyr=F6nen?= [nyronen^^csc.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---1497257471-818937201-1128591013=:9270 Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1; FORMAT=flowed Content-Transfer-Encoding: 8BIT Content-ID: Dear Dhaval, I recommend trying superposition features in Bodil http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil/about.php It's free of charge for academics. Features * Multi-view 3D graphics * Stereoscopic viewing using CrystalEyes goggles (or equivalent) is supported on both SGI Irix and Intel Linux. * Integration of sequence viewing and alignment editing with 3D molecular graphics * A hierarchichal tree view to chemical data * Molecular surface calculation and visualization * Visualization of electron density and Grid / AutoDock / DelPhi maps * Fully automatic protein structure superposition using a C-alpha packing profile correlation * Modular architecture: dynamically loaded plugin modules, application programming interface based on standard C++ rgds, -tommi- Tommi Nyrönen, Ph.D., Development Manager, Bioinformatics, CSC P.O.Box 405, 02101 ESPOO, Finland tel.+358-9-4572235 mob.+358-50-3819511 fax. +358-9-4572302 CSC is the Finnish IT Center for Science, http://www.csc.fi email: tommi.nyronen/./csc.fi On Thu, 6 Oct 2005, Dhaval R Mehta dhavalm99{=}gmail.com wrote: > > Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] > Hie, > I have the N,CA,C atom coordinate file in the PDB format of two proteins.Which software will allow the superposition of these proteins (without the sidechains)? > > Name:-Dhaval Mehta > Email:-dhavalm99=-=gmail.com> > > > Tommi Nyrönen, Ph.D., Development Manager, Bioinformatics, CSC P.O.Box 405, 02101 ESPOO, Finland tel.+358-9-4572235 mob.+358-50-3819511 fax. +358-9-4572302 CSC is the Finnish IT Center for Science, http://www.csc.fi email: tommi.nyronen/./csc.fi ---1497257471-818937201-1128591013=:9270-- From owner-chemistry@ccl.net Thu Oct 6 10:19:00 2005 From: "Dhurairaj Senthilnathan zenthil03.:.yahoo.co.in" To: CCL Subject: CCL: reactive intermediate labeling Message-Id: <-29510-051006084409-25311-C0Vm9+15bPTuy9HbyStPPg,server.ccl.net> X-Original-From: Dhurairaj Senthilnathan Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 6 Oct 2005 13:43:57 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Dhurairaj Senthilnathan [zenthil03:-:yahoo.co.in] when we model a reaction mechanism, so many reactive intermediates are involvede( such as carbocation, carbanion etc). how to label carbocation and carbanion in gaussview and how to implement its gaussian. reply me thank you D.senthilnathan ________________________________________________________________________ Mr.D.SENTHILNATHAN , Research Scholar, School of Chemistry, Bharathidasan University, TIRUCHIRAPPALLI - 620 024, TamilNadu, INDIA Phone : + 91 431 2407053(office) + 94 437 81355 (Mobile) E-mail: zenthil03{:}yahoo.co.in chemthilchem{:}gmail.com __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com From owner-chemistry@ccl.net Thu Oct 6 10:54:00 2005 From: "Isma Tejero Villagrasa ismael()klingon.uab.es" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29511-051006093649-25406-iZl89DEAgTRr054uam0rDA%a%server.ccl.net> X-Original-From: Isma Tejero Villagrasa Content-transfer-encoding: 8BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 06 Oct 2005 14:41:24 +0200 MIME-version: 1.0 Sent to CCL by: Isma Tejero Villagrasa [ismael-#-klingon.uab.es] You can get ProFit at http://www.bioinf.org.uk/software/profit/index.html hope this helps Isma Dhaval R Mehta dhavalm99{=}gmail.com wrote: >Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] >Hie, > I have the N,CA,C atom coordinate file in the PDB format of two proteins.Which software will allow the superposition of these proteins (without the sidechains)? > >Name:-Dhaval Mehta >Email:-dhavalm99=-=gmail.com> > > > > > > -- Ismael Tejero-Villagrasa Edifici Cn., Unitat Química Física Universitat Autònoma de Barcelona, 08193 - Bellaterra Catalonia, Spain Tel: +34 93-581.28.14 Fax: 581.29.20 ismael.:.klingon.uab.es http://klingon.uab.es/ismael From owner-chemistry@ccl.net Thu Oct 6 11:29:01 2005 From: "ReichertD|*|mir.wustl.edu" To: CCL Subject: CCL: W:Program for reading MOPAC output Message-Id: <-29512-051006110350-19441-Td697rzBLoPFb8NWq8Kibg]*[server.ccl.net> X-Original-From: ReichertD;;mir.wustl.edu Content-type: multipart/related; Boundary="0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD" Date: Thu, 6 Oct 2005 09:18:28 -0500 MIME-Version: 1.0 Sent to CCL by: ReichertD_-_mir.wustl.edu --0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: multipart/alternative; Boundary="1__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD" --1__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: quoted-printable Gustavo, Check out the program MOLDEN. -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd[A]wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 = "Gustavo L.C. = Moura = gustavo[-]mercury = To .chem.pitt.edu" "Reichert, David E. " = = ccl.net> = cc Sent by: = owner-chemistry[A]c Subj= ect cl.net CCL: W:Program for reading MOPAC= output = = 10/05/2005 03:59 = PM = = = Please respond to = "CCL Subscribers" = = = = Sent to CCL by: "Gustavo L.C. Moura" [gustavo~!~mercury.chem.pitt.edu] Dear CCL readers, I have a large number of molecules that I have optimized using the= MOPAC program. I would like to know if there is a graphical program tha= t can read the MOPAC output, draw the molecule on the screen and provide = an easy way of showing the charges over each one of the atoms. The program= could either show the charges as a label over the atoms or as a table beside the drawn molecule. I am really looking for a free for academia program, but any suggestions are welcome. The program should be for Windows or Linux operating systems. Thank you very much in advance for your help. Sincerely yours, Gustavo L.C. Moura -=3D This is automatically added to each message by the mailing script = =3D- To recover the email address of the author of the message, please chang= ehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: text/html; charset=US-ASCII Content-Disposition: inline Content-transfer-encoding: quoted-printable

Gustavo,
Check out the program MOLDEN.
-david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd[A]wustl.edu
voice: (314) 362-8461
fax: (314) 362-9940
3D"Inactive "Gustavo L.C. Moura gustavo[-]mercury.chem.pitt.edu" &l= t;owner-chemistry[A]ccl.net>

=

"Gustavo L.C. Moura gustavo[-]mercury.chem= .pitt.edu" <owner-chemistry[A]ccl.net>
Sent by: owner-chemistry[A]ccl.net
10/05/2005 03:59 PM =

Please respond to
"CCL Subscribers" <chemistry[A]ccl.net>

=

To
3D""
"Reichert, David E. " <reichertd[A]= mir.wustl.edu>

cc
3D""

Subject
3D""
CCL: W:Program for reading MOPAC output

=3D"" 3D"" <= /td>

Sent to CCL by: "Gustavo L.C. Moura" [gustavo~!~mercury.chem.= pitt.edu] Dear CCL readers, I have a large number of molecules that I have optimized= using the MOPAC program. I would like to know if there is a graphical = program that can read the MOPAC output, draw the molecule on the screen= and provide an easy way of showing the charges over each one of the at= oms. The program could either show the charges as a label over the atom= s or as a table beside the drawn molecule. I am really looking for a free for academia program, but= any suggestions are welcome. The program should be for Windows or Linu= x operating systems. Thank you very much in advance for your help. Sincerely yours, Gustavo L.C. Moura -=3D This is automatically added to each message by the mailing script = =3D- To recover the email address of the author of the message, please chang= e http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /tt> http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /tt> http://www.ccl.net/chemistry/sub_unsub.shtml Before posting check wait time for next message at: http://www.ccl.net Job advertisements: http:/= /www.ccl.net/jobs http://www.ccl.net/spammers.txt -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD-- --0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: image/gif; name="graycol.gif" Content-Disposition: inline; filename="graycol.gif" Content-ID: <10__=09BBFA01DFDD0CFD8f9e8a[A]msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAAQAKECAMzMzAAAAP///wAAACH5BAEAAAIALAAAAAAQABAAAAIXlI+py+0PopwxUbpu ZRfKZ2zgSJbmSRYAIf4fT3B0aW1pemVkIGJ5IFVsZWFkIFNtYXJ0U2F2ZXIhAAA7 --0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: image/gif; name="pic02368.gif" Content-Disposition: inline; filename="pic02368.gif" Content-ID: <20__=09BBFA01DFDD0CFD8f9e8a[A]msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhWABDALP/AAAAAK04Qf79/o+Gm7WuwlNObwoJFCsoSMDAwGFsmIuezf///wAAAAAAAAAA AAAAACH5BAEAAAgALAAAAABYAEMAQAT/EMlJq704682770RiFMRinqggEUNSHIchG0BCfHhOjAuh EDeUqTASLCbBhQrhG7xis2j0lssNDopE4jfIJhDaggI8YB1sZeZgLVA9YVCpnGagVjV171aRVrYR RghXcAGFhoUETwYxcXNyADJ3GlcSKGAwLwllVC1vjIUHBWsFilKQdI8GA5IcpApeJQt8L09lmgkH LZikoU5wjqcyAMMFrJIDPAKvCFletKSev1HBw8KrxtjZ2tvc3d5VyKtCKW3jfz4uMKmq3xu4N0nK BVoJQmx2LGVOmrqNjjJf2hHAQo/eDwJGTKhQMcgQEEAnEjFS98+RnW3smGkZU6ncCWav/4wYOnAI TihRL/4FEwbp28BXMMcoscQCVxlepL4IGDSCyJyVQOu0o7CjmLN50OZlqWmyFy5/6yBBuji0AxFR M00oQAqNIstqI6qKHUsWRAEAvagsmfUEAImyxgbmUpJk3IklNUtJOUAVLoUr1+wqDGTE4zk+T6FG uQb3SizBCwatiiUgCBN8vrz+zFjVyQ8FWkOlg4NQiZMB5QS8QO3mpOaKnL0Z2EKvNMSILEThKhCg zMKPVxYJh23qm9KNW7pArPynMqZDiErsTMqI+LRi3QAgkFUbXpuFKhSYZALd0O5RKa2z9EYKBbpb qxIKsjUPRgD7I2XYV6wyrOw92ykExP8NW4URhknC5dKGE4v4NENQj2jXjmfNgOZDaXb5glRmXQ33 YEWQYNcZFnrYcIQLNzyTFDQNkXIff0ExVlY4srziQk43inZgL4rwxxINMvpFFAz1KOODHiu+4aEw NEjFl5B3JIKWKF3k6I9bfUGp5ZZcdunll5IA4cuHvQQJ5gcsoCWOOUwgltIwAKRxJgbIkJAQZEq0 2YliZnpZZ4BH3CnYOXldOUOfQoYDqF1LFHbXCrO8xmRsfoXDXJ6ChjCAH3QlhJcT6VWE6FCkfCco CgrMFsROrIEX3o2whVjWDjoJccN3LdggSGXLCdLEgHr1lyU3O3QxhgohNKXJCWv8JQr/PDdaqd6w 2rj1inLiGeiCJoDspAoQlYE6QWLSECehcWIYxIQES6zhbn1iImTHEQyqJ4eIxJJoUBc+3CbBuwZE V5cJPPkIjFDdeEabQbd6WgICTxiiz0f5dBKquXF6k4senwEhYGnKEFJeGrxUZy8dB8gmAXI/sPvH ESfCwVt5hTgYiqQqtdRNHQIU1PJ33ZqmzgE90OwLaoJcnMop1WiMmgkPHQRIrwgFuNV90A3doNKT mrKIN07AnGcI9BQjhCBN4RfA1qIZnMqorJCogKfGQnxSCDilTVIA0yl5ciTovgLuBDKFUDE9aQcw 9SA+rjSNf9/M1gxrj6VwDTS0IUSElMzBfsj0NFXR2kwsV1A5IF1grLgLL/r1R40BZEnuBWgmQEyb jqRwSAt6bqMCOFkvKFN2GPPkUzIm/SCF8z8pVzpbjVnMsy0vOr1hw3SaSRUhpY09v0z0J1FnwzPl fmh+xl4WtR0zGu24I4KbMQm3lnVu2oNWxI9W/lcyzA+mCKF4DBikxb/+UWtOGRiFP8qEwAayIgIA Ow== --0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD Content-type: image/gif; name="ecblank.gif" Content-Disposition: inline; filename="ecblank.gif" Content-ID: <30__=09BBFA01DFDD0CFD8f9e8a[A]msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAABAIAAAAAAAP///yH5BAEAAAEALAAAAAAQAAEAAAIEjI8ZBQA7 --0__=09BBFA01DFDD0CFD8f9e8a93df938690918c09BBFA01DFDD0CFD-- From owner-chemistry@ccl.net Thu Oct 6 12:03:01 2005 From: "Prashanth Athri athriprashanth,yahoo.com" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29513-051006112349-21862-6wKlPeCehOBljORFADvong{=}server.ccl.net> X-Original-From: Prashanth Athri Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 6 Oct 2005 07:23:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Prashanth Athri [athriprashanth%yahoo.com] Hi, You can use VMD. VMD: Extensions > Analysis > RMSD calculator - then click "Backbone only", and whatever options you prefer. VMD is free for academics. -Prashanth --- "Goedele Roos groos**vub.ac.be" wrote: > > Sent to CCL by: Goedele Roos [groos()vub.ac.be] > > Hi, > I use PYMOL. It is free on the net > Goedele > > > >Sent to CCL by: "Dhaval R Mehta" > [dhavalm99(-)gmail.com] > >Hie, > > I have the N,CA,C atom coordinate file in the > PDB format of two proteins.Which software will allow > the superposition of these proteins (without the > sidechains)? > > > >Name:-Dhaval Mehta > >Email:-dhavalm99=-=gmail.com> > > > > > > > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17 > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the [#] > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST[#]ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From owner-chemistry@ccl.net Thu Oct 6 12:38:01 2005 From: "Pankaj Daga pdaga(-)olemiss.edu" To: CCL Subject: CCL: Reading the GAMESS outfile Message-Id: <-29514-051006100251-17685-cmSI1p9KDEyd+L43+lqKrA_-_server.ccl.net> X-Original-From: "Pankaj Daga" Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 06 Oct 2005 01:25:06 -1200 MIME-Version: 1.0 Sent to CCL by: "Pankaj Daga" [pdaga++olemiss.edu] Hi Sitha Why don't you try Molekel? Its free online and is to install. I know it works out well with G98, i dont know about GAMESS. But you should try that. PanDa > Sent to CCL by: Sanyasi Sitha [sitha|*|bc.edu] > Hi > I am a student from Boston college. I am using the GAMESS > program to do optimization and property calculations. I > tried to visualize my GAMESS output results with some of > the freely available visualization softwares like Facio, > gOpenMol----but till now I was not able to find a suitable > one. I will be grateful if some one can suggest me a > suitable program to visualize my GAMESS out file. > > thanking you > > Name: Sanyasi Sitha > Email: sitha=bc.edu > > > > -= This is automatically added to each message by the > mailing script =- To recover the email address of the > author of the message, please change the strange > characters on the top line to the [*] sign. You can also> > Before posting check wait time for next message at: > http://www.ccl.net> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+-+-+ > > > > From owner-chemistry@ccl.net Thu Oct 6 14:03:00 2005 From: "JINDAL SHAH shah.424!A!osu.edu" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29515-051006123730-26652-i6N9sMv1ARhkn/GUUfESZQ#server.ccl.net> X-Original-From: JINDAL SHAH Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 06 Oct 2005 12:01:30 -0400 MIME-Version: 1.0 Sent to CCL by: JINDAL SHAH [shah.424..osu.edu] Dhaval, Please have a look at LSQMAN. http://xray.bmc.uu.se/usf/lsqman_man.html Thanks for all those who responded to the query. I had only known about the above program. Regards, Jindal ----- Original Message ----- > From: "Isma Tejero Villagrasa ismael()klingon.uab.es" Date: Thursday, October 6, 2005 8:41 am Subject: CCL: W:Protein Superposition Software > > Sent to CCL by: Isma Tejero Villagrasa [ismael-#-klingon.uab.es] > You can get ProFit at > http://www.bioinf.org.uk/software/profit/index.html > hope this helps > > Isma > > Dhaval R Mehta dhavalm99{=}gmail.com wrote: > > >Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] > >Hie, > > I have the N,CA,C atom coordinate file in the PDB format of > two proteins.Which software will allow the superposition of these > proteins (without the sidechains)? > > > >Name:-Dhaval Mehta > >Email:-dhavalm99=-=gmail.com> > > > > > > > > > > > > > > > -- > > Ismael Tejero-Villagrasa > Edifici Cn., Unitat Química Física > Universitat Autònoma de Barcelona, 08193 - Bellaterra > Catalonia, Spain > Tel: +34 93-581.28.14 Fax: 581.29.20 > > ismael+/-klingon.uab.es > http://klingon.uab.es/ismael > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the {:} sign. You can > also> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Oct 6 15:55:00 2005 From: "Jason Gans jgans _ lanl.gov" To: CCL Subject: CCL: W:Protein Superposition Software Message-Id: <-29516-051006153632-2437-msACYujLPXHv0HDRzoPQhA#,#server.ccl.net> X-Original-From: Jason Gans Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 06 Oct 2005 12:37:24 -0600 Mime-Version: 1.0 Sent to CCL by: Jason Gans [jgans:-:lanl.gov] See QMol (windows only). http://www.mbg.cornell.edu/Shalloway_Lab_QMOL.cfm From the menu bar, "Molecule" -> "Align Molecules ...". Regards, Jason At 02:36 AM 10/6/2005, you wrote: >Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] >Hie, > I have the N,CA,C atom coordinate file in the PDB format of two > proteins.Which software will allow the superposition of these proteins > (without the sidechains)? > >Name:-Dhaval Mehta >Email:-dhavalm99=-=gmail.com From owner-chemistry@ccl.net Thu Oct 6 19:30:00 2005 From: "Caio Julio Martins Veloso cveloso^^^pucminas.br" To: CCL Subject: CCL: RES: W:Protein Superposition Software Message-Id: <-29517-051006183311-19869-MEAxJg+sxvq2MVgktdvekA/./server.ccl.net> X-Original-From: "Caio Julio Martins Veloso" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 6 Oct 2005 18:47:55 -0300 MIME-Version: 1.0 Sent to CCL by: "Caio Julio Martins Veloso" [cveloso-.-pucminas.br] I sugest TOPOFIT http://mozart.bio.neu.edu/topofit/topofit.html Regards, Caio Veloso. At 02:36 AM 10/6/2005, you wrote: >Sent to CCL by: "Dhaval R Mehta" [dhavalm99(-)gmail.com] >Hie, > I have the N,CA,C atom coordinate file in the PDB format of two > proteins.Which software will allow the superposition of these proteins > (without the sidechains)? > >Name:-Dhaval Mehta >Email:-dhavalm99=-=gmail.com