From owner-chemistry@ccl.net Wed Apr 4 10:53:00 2012 From: "David A Case case ~~ biomaps.rutgers.edu" To: CCL Subject: CCL: Announcement: release of Amber12 and AmberTools12 Message-Id: <-46629-120404104140-1079-jmeW+r7UxV3mQ+3l9g1ExQ#%#server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 4 Apr 2012 10:41:31 -0400 Mime-Version: 1.0 Sent to CCL by: David A Case [case%a%biomaps.rutgers.edu] I am pleased to announce the release Amber12 and AmberTools12. Amber is a suite of programs designed for molecular dynamics simulations of biomolecules. For full information on what is new in Amber 12, and how to order it, please visit: http://ambermd.org/#Amber12 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. Key facilities allow the preparation of systems for MD simulations, and analysis of trajectories. The suite can also be used to carry out complete molecular dynamics investigations, employing explicit, generalized Born, Poisson-Boltzmann or 3D-RISM solvent models. AmberTools is released under the GNU General Public License (GPL), with some components using other open source licenses. For more information, and to download AmberTools12, please visit: http://ambermd.org/#AmberTools ...dave case (For the Amber development team: http://ambermd.org/contributors.html ) From owner-chemistry@ccl.net Wed Apr 4 11:47:01 2012 From: "shamsa alina shamsa.pakistan ~~ yahoo.com" To: CCL Subject: CCL: single/multiview mode in gaussviw Message-Id: <-46630-120404090945-4318-ilHWKDfyBKXNUDg+wVYJ8A.:.server.ccl.net> X-Original-From: "shamsa alina" Date: Wed, 4 Apr 2012 09:09:42 -0400 Sent to CCL by: "shamsa alina" [shamsa.pakistan . yahoo.com] I want to ask how i can see various molecule in a single gaussview window? as i have read help menu its saying " Clicking on the small triangle to the right of the single view/multiview icon reveals a small menu containing these items " next option then multiview option , but i could not find this " multiview option " where is it ? please anyone cane guide me about this? From owner-chemistry@ccl.net Wed Apr 4 15:34:00 2012 From: "Vale Cofer-Shabica dylan_cofer-shabica,,brown.edu" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46631-120404110911-4293-MxLSiwNFRbfdn+O/mYfVwA[]server.ccl.net> X-Original-From: Vale Cofer-Shabica Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 4 Apr 2012 11:08:27 -0400 MIME-Version: 1.0 Sent to CCL by: Vale Cofer-Shabica [dylan_cofer-shabica|brown.edu] You might start with the pdftotext program. It will extract text from pdf files, which you could then parse with another utility. The program is included with many GNU/Linux distributions in the poppler or poppler-utils package. The source code can also be obtained from: http://poppler.freedesktop.org/. I hope that helps, vale --------------------------------- Vale Cofer-Shabica Department of Chemistry, Brown University Dylan_Cofer-Shabica%%brown.edu On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=-=llnl.gov wrote: > > Sent to CCL by: "Brian  Bennion" [bennion1=llnl.gov] > Hello, > > Does anyone have/know of code to parse pdf tables for chemical structure and activity data? > > Searching the web did not result in much so I may not be searching with the correct terms.  One interesting hit was the clide code from simbiosis. > > Has anyone used this for pulling structures out of pdf files? > > I want to populate a repository with chemical structures and annotate the entries with the activity data given in an associated table located in the same pdf document. > > Thanks > Brian>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Wed Apr 4 16:09:00 2012 From: "Flick Coleman wcoleman__wellesley.edu" To: CCL Subject: CCL: single/multiview mode in gaussviw Message-Id: <-46632-120404125620-18922-Q273KA54uBemTnHAVaNKSg]=[server.ccl.net> X-Original-From: Flick Coleman Content-Type: multipart/alternative; boundary=f46d04182558d7d03e04bcdd4c35 Date: Wed, 4 Apr 2012 12:55:29 -0400 MIME-Version: 1.0 Sent to CCL by: Flick Coleman [wcoleman_-_wellesley.edu] --f46d04182558d7d03e04bcdd4c35 Content-Type: text/plain; charset=ISO-8859-1 You can see multiple molecules if all of them are a part of the same molecule group. When you have more than one molecule in a group, there will be some new icons that show up. One is a green button that moves through the molecules in an animation; one is an up/down arrow that allows you to move through the molecules; the last, on the right of the set of new icons, shows either a single or double molecule icon. Clicking on the single molecule icon (the default) should enable you to see two molecules in the frame. to the right of the now double molecule icon should be a down triangle. At least on all of my systems this is partially hidden and looks like just a partial triangle. Clicking on this brings up a menu that allows you to change the settings for displaying multiple members of the same molecule group. Hope this helps. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html www.flicksstuff.com/photos/pictures.html new galleries coming soon On Wed, Apr 4, 2012 at 9:09 AM, shamsa alina shamsa.pakistan ~~ yahoo.com < owner-chemistry~!~ccl.net> wrote:> > > > --f46d04182558d7d03e04bcdd4c35 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You can see multi= ple molecules if all of them are a part of the same molecule group.=A0 When= you have more than one molecule in a group, there will be some new icons t= hat show up.=A0 One is a green button that moves through the molecules in a= n animation; one is an up/down arrow that allows you to move through the mo= lecules; the last, on the right of the set of new icons, shows either a sin= gle or double molecule icon.=A0 Clicking on the single molecule icon (the d= efault) should enable you to see two molecules in the frame.=A0 to the righ= t of the now double molecule icon should be a down triangle.=A0 At least on= all of my systems this is partially hidden and looks like just a partial t= riangle.=A0 Clicking on this brings up a menu that allows you to change the= settings for displaying multiple members of the same molecule group.

Hope this helps.


Cheers,

F= lick

_______________
William= F. Coleman
Professor of Chemistry
Wellesl= ey College
Wellesley MA 02481

www.wellesle= y.edu/Chemistry/colemanw.html
www.= flicksstuff.com/photos/pictures.html new galleries coming soon




On Wed, Apr 4, 2012 at 9:09 AM, shamsa a= lina shamsa.pakistan ~~ yahoo.com <owner-chemistry~!~cc= l.net> wrote:


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--f46d04182558d7d03e04bcdd4c35-- From owner-chemistry@ccl.net Wed Apr 4 16:44:00 2012 From: "Billy McCann bwm0005-,-tigermail.auburn.edu" To: CCL Subject: CCL: single/multiview mode in gaussviw Message-Id: <-46633-120404133240-17742-1ov4XEH3BiEQ1rxOGHMZOw]|[server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 4 Apr 2012 17:32:27 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005{=}tigermail.auburn.edu] Hi Shamsa. If you select File -> New -> Add to molecule group, the icon will appear. Hope that helps. +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu . ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu . ccl.net] On Behalf Of shamsa alina shamsa.pakistan ~~ yahoo.com Sent: Wednesday, April 04, 2012 8:10 AM To: Billy McCann Subject: CCL: single/multiview mode in gaussviw Sent to CCL by: "shamsa alina" [shamsa.pakistan . yahoo.com] I want to ask how i can see various molecule in a single gaussview window? as i have read help menu its saying " Clicking on the small triangle to the right of the single view/multiview icon reveals a small menu containing these items " next option then multiview option , but i could not find this " multiview option " where is it ? please anyone cane guide me about this?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 Wed Apr 4 17:18:01 2012 From: "Aniko Simon aniko[]simbiosys.ca" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46634-120404164149-19031-ozbKPj+hPPU8JvLVWHrDrQ[-]server.ccl.net> X-Original-From: "Aniko Simon" Date: Wed, 4 Apr 2012 16:41:46 -0400 Sent to CCL by: "Aniko Simon" [aniko .. simbiosys.ca] Hello Brian, As you suggested, CLiDE can process structures from tables (PDF is one of the supported input formats). More information and screen-shots on this topic here: http://www.simbiosys.com/clide/gallery_clide.html CLiDE can produce an SDF output file with the chemical structures from the document, which then can be merged via Unix scripts with an output of a tool such as pdftotext (free). So in essence using 2 tools plus some scripting this can be achieved. Let me know if you need more help. Best wishes, Aniko ps. regarding other people using CLiDE please see some of the recent customer quotes under: http://www.simbiosys.com/support/index.html#quotes -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 | http://www.simbiosys.com/ From owner-chemistry@ccl.net Wed Apr 4 18:11:00 2012 From: "TJ O Donnell tjo*o*acm.org" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46635-120404171521-25068-GFR7IfsmgSo561jOhS5xdg%server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 4 Apr 2012 14:09:36 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo-*-acm.org] You might also try openbabel. The babel program can convert pdb to other formats that might be more helpful. You can also write python scripts using openbabel to read a pdb file. TJ O'Donnell On Wed, Apr 4, 2012 at 8:08 AM, Vale Cofer-Shabica dylan_cofer-shabica,,brown.edu wrote: > > Sent to CCL by: Vale Cofer-Shabica [dylan_cofer-shabica|brown.edu] > You might start with the pdftotext program. It will extract text from > pdf files, which you could then parse with another utility. The > program is included with many GNU/Linux distributions in the poppler > or poppler-utils package. The source code can also be obtained from: > http://poppler.freedesktop.org/. > > I hope that helps, > vale > > --------------------------------- > Vale Cofer-Shabica > Department of Chemistry, Brown University > Dylan_Cofer-Shabica[*]brown.edu > > > On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=-=llnl.gov > wrote: >> >> Sent to CCL by: "Brian  Bennion" [bennion1=llnl.gov] >> Hello, >> >> Does anyone have/know of code to parse pdf tables for chemical structure and activity data? >> >> Searching the web did not result in much so I may not be searching with the correct terms.  One interesting hit was the clide code from simbiosis. >> >> Has anyone used this for pulling structures out of pdf files? >> >> I want to populate a repository with chemical structures and annotate the entries with the activity data given in an associated table located in the same pdf document. >> >> Thanks >> Brian>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> >