From owner-chemistry@ccl.net Tue May 29 10:32:00 2007 From: "Zuccotto, Fabio Nervianoms Fabio.Zuccotto]*[nervianoms.com" To: CCL Subject: CCL: Binding site Message-Id: <-34362-070529102927-1288-hFgECIwWDYZP0MXN2RoY9w_._server.ccl.net> X-Original-From: "Zuccotto, Fabio [Nervianoms]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7A1F8.D7BB19E0" Date: Tue, 29 May 2007 15:54:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Zuccotto, Fabio [Nervianoms]" [Fabio.Zuccotto#nervianoms.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7A1F8.D7BB19E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCL - I was wondering if there is a good quality software = (possibly free) that allows to: - identify cavities on a protein surface - calculate the volume of the cavities =20 Thank you =20 Fabio ------_=_NextPart_001_01C7A1F8.D7BB19E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello=20 CCL - I was wondering if there is a good quality software (possibly = free) that=20 allows to:
-=20 identify cavities on a protein surface
-=20 calculate the volume of the cavities
 
Thank=20 you
 
Fabio
------_=_NextPart_001_01C7A1F8.D7BB19E0-- From owner-chemistry@ccl.net Tue May 29 12:50:00 2007 From: "Jeff Nauss jnauss^^accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for June and July Message-Id: <-34363-070529003149-26623-xgQerptwZafiYhuM//eGFg*o*server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Mon, 28 May 2007 20:53:36 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss{:}accelrys.com] Accelrys Inc. are holding the following training workshops during June and July. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. For the on-line presentations, the price is $175 per three hour session for all customers. ON-LINE Introduction to Materials Studio 4 June (4pm BST) QSAR in Materials Studio 5 June (4pm BST) Catalyst Migration 6 June (4pm BST) Introduction to Discovery Studio 11 June (4pm BST) Insight II to Discovery Studio Migration 12 June (4pm BST) Protein -Protein Docking with InsightII 14 June (4pm BST) Introduction to Discovery Studio 3 July (4pm BST) Insight II to Discovery Studio Migration 6 July (4pm BST) Sequence Analysis for Homology Modeling 10 July (4pm BST) Protein Homology Modeling in Discovery Studio 11 July (4pm BST) Simulations in Discovery Studio (Part 1) 12 July (4pm BST) Simulations in Discovery Studio (Part 2) 13 July (4pm BST) Solvation Models in CHARMm 18 July (7am PDT) Docking & Scoring in Discovery Studio 23 July (4pm BST) De Novo Design with Discovery Studio 24 July (4pm BST) Catalyst to Discovery Studio Migration 25 July (4pm BST) Pharmacophore Modeling with Discovery Studio (Part 1) 26 July (4pm BST) Pharmacophore Modeling with Discovery Studio (Part 2) 27 July (4pm BST) Note that BST denotes local time in the United Kingdom and PDT denotes Pacific daylight time (Los Angeles, CA). Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Please visit http://www.accelrys.com/services/training/ for a complete list of available workshops and opportunities. Questions regarding scheduling and content should be directed to workshops[*]accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Tue May 29 13:25:00 2007 From: "Maurizzio m.argonni]![gmail.com" To: CCL Subject: CCL: Binding site Message-Id: <-34364-070529131327-10399-MPAhSLEouPjNNFECenVanA()server.ccl.net> X-Original-From: Maurizzio Content-Type: multipart/alternative; boundary="----=_Part_267375_7243465.1180458774241" Date: Tue, 29 May 2007 13:12:54 -0400 MIME-Version: 1.0 Sent to CCL by: Maurizzio [m.argonni(!)gmail.com] ------=_Part_267375_7243465.1180458774241 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, The Castp server: http://sts.bioengr.uic.edu/castp/ and the program Surfnet from Roman Laskowski at: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html will allow you to do what you want. Maurizzio On 5/29/07, Zuccotto, Fabio Nervianoms Fabio.Zuccotto]*[nervianoms.com < owner-chemistry[-]ccl.net> wrote: > > Hello CCL - I was wondering if there is a good quality software (possibly > free) that allows to: > - identify cavities on a protein surface > - calculate the volume of the cavities > > Thank you > > Fabio > ------=_Part_267375_7243465.1180458774241 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello,
 
The Castp server:
 
 
and the program Surfnet from Roman Laskowski at:
 
 
will allow you to do what you want.
 
Maurizzio

 
On 5/29/07, Zuccotto, Fabio Nervianoms Fabio.Zuccotto]*[nervianoms.com <owner-chemistry[-]ccl.net > wrote:
Hello CCL - I was wondering if there is a good quality software (possibly free) that allows to:
- identify cavities on a protein surface
- calculate the volume of the cavities
 
Thank you
 
Fabio

------=_Part_267375_7243465.1180458774241-- From owner-chemistry@ccl.net Tue May 29 14:00:00 2007 From: "Chelsey Crosse cmcrosse*_*mtu.edu" To: CCL Subject: CCL: show ruler in VMD Message-Id: <-34365-070529100202-32396-+YVzjECyFSU3Z2bx3YfBcw,server.ccl.net> X-Original-From: Chelsey Crosse Content-Type: multipart/alternative; boundary=Apple-Mail-1-274721236 Date: Tue, 29 May 2007 09:29:44 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Chelsey Crosse [cmcrosse#,#mtu.edu] --Apple-Mail-1-274721236 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Yubo, The only way that I know of to put a ruler in VMD by opening the Tcl console and drawing it in yourself. However, I'm not positive about how accurate you can make it. Chelsey On 25 May 2007, at 10:17, Yubo Fan yubofan(0)mail.chem.tamu.edu wrote: > Hello, > > A quick question about VMD. Is there any way to show ruler (ie > angstroms in unit) in VMD window? > > Thanks, > > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan^^^mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ > --Apple-Mail-1-274721236 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Yubo,

The only way that I know of = to put a ruler in VMD by opening the Tcl console and drawing it in = yourself.=A0 However, I'm not positive about how accurate you can make = it.

Chelsey

On 25 May 2007, at 10:17, Yubo Fan yubofan(0)mail.chem.tamu.edu = wrote:

=A0
=A0
Thanks,
=A0
Dr. Yubo Fan=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 Email: Department of = Chemistry=A0=A0=A0 Tel:=A0=A0 1-979-845-5237
College Station, TX 77843

= --Apple-Mail-1-274721236-- From owner-chemistry@ccl.net Tue May 29 18:20:01 2007 From: "Jeff Nauss jnauss(!)accelrys.com" To: CCL Subject: CCL: Binding site Message-Id: <-34366-070529131507-11129-hO+zlrHtAbyNg4QYPPGUzw..server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Tue, 29 May 2007 10:14:42 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss#%#accelrys.com] owner-chemistry[A]ccl.net wrote on 05/29/2007 06:54:14 AM: > Hello CCL - I was wondering if there is a good quality software > (possibly free) that allows to: > - identify cavities on a protein surface > - calculate the volume of the cavities A similar question was asked recently. You could search the CCL archives for the answers at that time. The binding site analysis functionality in Discovery Studio and InsightII will identify and report a surface cavity volume. The same algorithm is available in Cerius2 but will not report a volume. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Tue May 29 21:45:00 2007 From: "Mustafa Hussein mustafa.hussein86===yahoo.com" To: CCL Subject: CCL: A Comprehensive book on theoretical chemistry Message-Id: <-34367-070529211123-28913-ZHHJcmgC3+9rAcbpENCHvg .. server.ccl.net> X-Original-From: "Mustafa Hussein" Date: Tue, 29 May 2007 21:11:19 -0400 Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86---yahoo.com] Hi, I am a senior pharmacy undergrad, Minia, Egypt. I am studting theoretical chemistry independently as I hope I pursue my PhD research in it. I am currently studying books like Introduction to Computational Chemistry, Frank Jensen, Essentials of Computational Chemistry, Christopher Cramer, and some web material. I am really looking for a book that provides a comprehensive view on computational techniques and methods, including essentials of theory and formalism, in addition to exercises and worked examples, meaningly, a book that helps me teach myself the subjet. Noteworthy, I have already get a good knowledge base in math, Computer Science and quantum mechanics, in addition to the fundamentals of the electronic structure theory. thanks in advance Mustafa Hussein mustafa.hussein86|,|yahoo.com Faculty of Pharmacy, Minia University Minia 61511, Egypt From owner-chemistry@ccl.net Tue May 29 22:48:00 2007 From: "Alexandr Isayev alex(!)ccmsi.us" To: CCL Subject: CCL: A Comprehensive book on theoretical chemistry Message-Id: <-34368-070529223817-22567-9zUnCXGfQDLavvFBqBypyA[]server.ccl.net> X-Original-From: Alexandr Isayev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 29 May 2007 21:36:42 -0500 MIME-Version: 1.0 Sent to CCL by: Alexandr Isayev [alex#%#ccmsi.us] Dear Mustafa, One of the most comprehensive book on subject that I've ever read is "Molecular Electronic-Structure Theory" by Trygve Helgaker, Poul Jorgensen and Jeppe Olsen. It practically covers all aspects theory (HF, MBPT, CI, CC, etc) but DFT. Sincerely, Alexandr Tuesday, May 29, 2007, 8:11:19 PM, you wrote: MHmhyc> Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86---yahoo.com] MHmhyc> Hi, MHmhyc> I am a senior pharmacy undergrad, Minia, Egypt. I am studting MHmhyc> theoretical chemistry independently as I hope I pursue my PhD research in it. MHmhyc> I am currently studying books like Introduction to MHmhyc> Computational Chemistry, Frank Jensen, Essentials of MHmhyc> Computational Chemistry, Christopher Cramer, and MHmhyc> some web material. MHmhyc> I am really looking for a book that provides a comprehensive MHmhyc> view on computational techniques and methods, including MHmhyc> essentials of theory and formalism, MHmhyc> in addition to exercises and worked examples, meaningly, a MHmhyc> book that helps me teach myself the subjet. Noteworthy, I have already get a good knowledge MHmhyc> base in math, Computer Science and quantum mechanics, in MHmhyc> addition to the fundamentals of the electronic structure theory. MHmhyc> thanks in advance MHmhyc> Mustafa Hussein MHmhyc> mustafa.hussein86===yahoo.com MHmhyc> Faculty of Pharmacy, MHmhyc> Minia University MHmhyc> Minia 61511, Egypt MHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhyc> Conferences: MHmhyc> http://server.ccl.net/chemistry/announcements/conferences/ MHmhycMHmhycMHmhycMHmhycMHmhyc------------------------------------------------------- Alexandr Isayev, Graduate Research Assistant, and System Administrator -$- Computational Center for Molecular Structure and Interactions (CCMSI), Jackson State University, Jackson, MS USA Tel: +(601) 979-1134 e-mail: alex(at)ccmsi.us Web: http://www.ccmsi.us --------------------------------------------------------