Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids
Thanks a lot! That helped! Carsten Siebenhaar - Am 24.05.2010 um 21:50 schrieb Folmer Fredslund: Dear Carsten, On 17 May 2010 14:39, Carsten Siebenhaar csie...@gwdg.de wrote: Hello, I'm new to this board. I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer). Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms: You clicked /11//A/HIS`509/CD2`A Selector: selection sele defined with 20 atoms. PyMol keeps on asking me to pick a residue. Is there a way to easily avoid this problem or could this be considered a real bug? Thanks a lot! Carsten Do you want to retain the double conformations? If not, then you could use PyMOL to delete the alternate conformations thus, just retaining one of them. # select remove all non A altlocs remove not (alt ''+A) # reset the PDB information alter all, alt='' taken from: http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations I hope this helps. Folmer Fredslund -- ___ 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-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
Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids
Hi Carsten, Welcome and sorry for the delayed response, I was away at a training camp last week. Unfortunately, PyMOL cannot handle alternate conformations in the mutagenesis wizard. You can pick other atoms, but not those with alternate locations. Cheers -- Jason On Mon, May 17, 2010 at 8:39 AM, Carsten Siebenhaar csie...@gwdg.de wrote: Hello, I'm new to this board. I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer). Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms: You clicked /11//A/HIS`509/CD2`A Selector: selection sele defined with 20 atoms. PyMol keeps on asking me to pick a residue. Is there a way to easily avoid this problem or could this be considered a real bug? Thanks a lot! Carsten -- ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ 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
Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids
Dear Carsten, On 17 May 2010 14:39, Carsten Siebenhaar csie...@gwdg.de wrote: Hello, I'm new to this board. I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer). Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms: You clicked /11//A/HIS`509/CD2`A Selector: selection sele defined with 20 atoms. PyMol keeps on asking me to pick a residue. Is there a way to easily avoid this problem or could this be considered a real bug? Thanks a lot! Carsten Do you want to retain the double conformations? If not, then you could use PyMOL to delete the alternate conformations thus, just retaining one of them. # select remove all non A altlocs remove not (alt ''+A) # reset the PDB information alter all, alt='' taken from: http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations I hope this helps. Folmer Fredslund -- ___ 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-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
