Re: [PyMOL] Vacuum Electrostatics error
Hi Joel, This is unfortunately an oversight on my part. This fix unfortunately never made its way to a patched version. I will make sure it does for the next patch. In the meantime, if you ever do come across this issue, the workaround is to disable undo from the Edit menu. Best, Jarrett J On Tue, Nov 28, 2023 at 3:50 PM Joel Tyndall wrote: > Hi all, > > > > I tried to help Anna with her issue around the colour bar (which seemed > unusual) only to find that I cannot generate the electrostatic maps at all > on 2 different PCs running windows (10 I believe). > > > > The error is Pop-error: invalid source selection name ‘assign_tmp1’ > > > > Running 2.5.1 > > > > Joel > > > > > > Joel Tyndall | BSc(Hons) PhD > > Professor in Medicinal Chemistry > School of Pharmacy | He Rau Kawakawa > University of Otago | Te Whare Wānanga o Otāgo > > PO Box 56 9054 > > Dunedin | Ōtepoti > > New Zealand | Aotearoa > > Website | pharmacy.otago.ac.nz > > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Vacuum Electrostatics error
Hi all, I tried to help Anna with her issue around the colour bar (which seemed unusual) only to find that I cannot generate the electrostatic maps at all on 2 different PCs running windows (10 I believe). The error is Pop-error: invalid source selection name ‘assign_tmp1’ Running 2.5.1 Joel Joel Tyndall | BSc(Hons) PhD Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Website | pharmacy.otago.ac.nz ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Vacuum Electrostatics
Problem solved... next time I'll do a completely clean install. Sorry for the needless email. Ian On Mon, Jul 27, 2009 at 11:08 AM, Ian Berke ian.be...@yale.edu wrote: Hi, I'm getting this error still using a self-compiled version from the latest SVN and python 2.6.2. The error is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 In a previous post it was reported to be fixed. Is anyone still having this issue? Thanks, Ian Mark, Should be fixed now (in rev 3720). Cheers, Wawrren -Original Message- From: Mark Wehner [mailto:mark.weh...@ru...] Sent: Monday, May 11, 2009 12:11 PM To: pymol-us...@li... Subject: [PyMOL] Vacuum electrostatics Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing similar problems at the moment? Mark -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list pymol-us...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] vacuum electrostatics
Dear users I'm trying to compare the electrostatic charge surface of my protein with and without ligand, by using the command generate vacuum electrostatics. that's works fine for the protein without ATP but that doesn't work with the ligand.The surface obtaine doesn't take account the ligand thanks -- CHAIX Denis Centre de Biochimie Structurale INSERM U554/CNRS 5048 29 rue de Navacelles F-34090 Montpellier, France Tel: 33 4 67 41 77 21 Fax: 33 4 67 41 79 13 e-mail:denis.ch...@cbs.cnrs.fr http://www.cbs.cnrs.fr -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] vacuum electrostatics
Denis, Sorry, PyMOL only has protein charges coded at present. Perhaps the APBS project's pdb2pqr utility might be able to assign charges to canonoical ligands (such as ATP)? http://apbs.sourceforge.net Cheers, Warren -Original Message- From: Chaix Denis [mailto:denis.ch...@cbs.cnrs.fr] Sent: Monday, May 18, 2009 9:10 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] vacuum electrostatics Dear users I'm trying to compare the electrostatic charge surface of my protein with and without ligand, by using the command generate vacuum electrostatics. that's works fine for the protein without ATP but that doesn't work with the ligand.The surface obtaine doesn't take account the ligand thanks -- CHAIX Denis Centre de Biochimie Structurale INSERM U554/CNRS 5048 29 rue de Navacelles F-34090 Montpellier, France Tel: 33 4 67 41 77 21 Fax: 33 4 67 41 79 13 e-mail:denis.ch...@cbs.cnrs.fr http://www.cbs.cnrs.fr -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Vacuum electrostatics
Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing similar problems at the moment? Mark -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Vacuum electrostatics
Mark, Should be fixed now (in rev 3720). Cheers, Wawrren -Original Message- From: Mark Wehner [mailto:mark.weh...@rub.de] Sent: Monday, May 11, 2009 12:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Vacuum electrostatics Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing similar problems at the moment? Mark -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Vacuum electrostatics
Hi all, I had a problem calculating electrostatic surfaces for my pdb - identical to the problem detailed below: http://sourceforge.net/mailarchive/message.php?msg_id=36854260 In short, an electrostatic surface with green/blue/red patches that changes according to the colour of the underlying structure (and doesn't seem to bear an obvious relation to the 'correct' electrostatic surface generated as below). The get around/fix was to shorten the file name of the pdb -ie remove the refmac/coot additions to the original file name. Giving the input pdb an alias works equally well. I didn't see a reply to the above post, so hopefully this helps/narrows down the problem. Cheers, Robin
[PyMOL] vacuum electrostatics
Hi Shawn, As you can see when you select the generate electrostatic surface within PyMol - Warren has stated that it is unvalidated experimental code and the results should be viewed with skepticism. If you want publishable electrostatics calculated using more realistic estimates of dielectric constants then you should use eithe APBS, GRASp, or some other Poisson Boltzman solver. Personally I wouldn't put figures generated from PyMols internal electrostatics calculations any any publication. Scott On Apr 10, 2005, at 9:29 AM, Shawn Milano wrote: Hi, I want to show an electrostatic surface of my protein for publication. In Pymol, I believe I can use generate-vacuum electrostatics. However, I am not quite sure what the difference is between absolute and relative protein surface potential. Could you help me with this? Second, I have a question about the slider that appears after the surface is calculated. What do the numbers represent, and what is changing as you slide to the left and right. I want to use the figure for publication and make sure I understand how to explain it properly. Thanks, Shawn-
[PyMOL] vacuum electrostatics
Hi, I want to show an electrostatic surface of my protein for publication. In Pymol, I believe I can use generate-vacuum electrostatics. However, I am not quite sure what the difference is between absolute and relative protein surface potential. Could you help me with this? Second, I have a question about the slider that appears after the surface is calculated. What do the numbers represent, and what is changing as you slide to the left and right. I want to use the figure for publication and make sure I understand how to explain it properly. Thanks, Shawn-
