From: Jorgen R. <jor...@gm...> - 2010-10-05 12:58:43
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Hello, I have loaded two PDB files in PyMol to pair fit some of their amino acids. When using the wizard, I'm getiing the following error. Does anyone has an idea how to solve this? _seeker and not _pf_s_* Editor-Error: Invalid input. Traceback (most recent call last): File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\wizard\pair_fit.py", line 147, in do_select cmd.edit(name + " and not " + sele_prefix + "*") # note, using new object name wildcards File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\editing.py", line 851, in edit if _self._raising(r,_self): raise pymol.CmdException CmdException: <pymol.CmdException instance at 0x0379D378> Jorgen Ravoet Molecular biologist |
From: Jason V. <jas...@sc...> - 2010-10-05 21:23:00
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Hi Jorgen, I cannot reproduce this. Can you please give me the PDBs (or PDB IDs) and commands to reproduce this error? Thanks, -- Jason On Tue, Oct 5, 2010 at 8:58 AM, Jorgen Ravoet <jor...@gm...> wrote: > Hello, > I have loaded two PDB files in PyMol to pair fit some of their amino acids. > When using the wizard, I'm getiing the following error. Does anyone has an > idea how to solve this? > _seeker and not _pf_s_* > Editor-Error: Invalid input. > Traceback (most recent call last): > File "C:\Program Files (x86)\DeLano > Scientific\PyMOL/modules\pymol\wizard\pair_fit.py", line 147, in do_select > cmd.edit(name + " and not " + sele_prefix + "*") # note, using new > object name wildcards > File "C:\Program Files (x86)\DeLano > Scientific\PyMOL/modules\pymol\editing.py", line 851, in edit > if _self._raising(r,_self): raise pymol.CmdException > CmdException: <pymol.CmdException instance at 0x0379D378> > Jorgen Ravoet > Molecular biologist > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2010-10-06 15:16:16
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Hi Jorgen, I just tried pair fitting some atoms from your PyMOL session and was able to reproduce what you found. Pair fitting is done between atoms, so please show lines or sticks, not just cartoons, when pair fitting. You can turn off the lines later if you don't need them. In this way, you can select just one atom at a time and PyMOL will be happy. The error begins when one selects an entire residue for pair fitting; PyMOL doesn't know how to pair fit an entire residue--though, maybe it should. If you choose a single atom, sometimes PyMOL will output, Selector: selection "sele" defined with 1 atoms. sele and not _pf_s_* but this should not break the fitting of the Pair Fitting wizard. If the error occurs, please either click "Clear" in the wizard or restart the Pair Fitting wizard altogether, while ensuring that you select just one atom a time. Cheers, -- Jason On Tue, Oct 5, 2010 at 8:58 AM, Jorgen Ravoet <jor...@gm...> wrote: > Hello, > I have loaded two PDB files in PyMol to pair fit some of their amino acids. > When using the wizard, I'm getiing the following error. Does anyone has an > idea how to solve this? > _seeker and not _pf_s_* > Editor-Error: Invalid input. > Traceback (most recent call last): > File "C:\Program Files (x86)\DeLano > Scientific\PyMOL/modules\pymol\wizard\pair_fit.py", line 147, in do_select > cmd.edit(name + " and not " + sele_prefix + "*") # note, using new > object name wildcards > File "C:\Program Files (x86)\DeLano > Scientific\PyMOL/modules\pymol\editing.py", line 851, in edit > if _self._raising(r,_self): raise pymol.CmdException > CmdException: <pymol.CmdException instance at 0x0379D378> > Jorgen Ravoet > Molecular biologist > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |