[PyMOL] Automatic modification of structures in PyMOL
Hi everyone, I am trying to find a way, in Pymol, to remove an amino acid from a peptide and insert any other amino acid. I have been able to do this for one residue at a time using the command editor.attach_fragment(‘pk1′,’my_fragment_name’,11,0) but I have to do this in two parts so that the new amino acid binds at both ends. I was wondering if there is a way in which Pymol can “swap” an existing side chain at position N on the peptide for any other side chain in an automated fashion? Any help much appreciated. Angela -- Angela Gray -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] Automatic modification of structures in PyMOL
I think what you're asking for is one of the examples included in the PyMol source code. You can do this manually using the mutagenesis wizard, but it is possible to drive this wizard through scripts. The two examples can be found at: http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/mutate01.pml?view=markup and http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/mutate02.py?view=markup On Mon, Apr 19, 2010 at 8:15 AM, Angela Gray angela.gray...@googlemail.com wrote: Hi everyone, I am trying to find a way, in Pymol, to remove an amino acid from a peptide and insert any other amino acid. I have been able to do this for one residue at a time using the command editor.attach_fragment(‘pk1′,’my_fragment_name’,11,0) but I have to do this in two parts so that the new amino acid binds at both ends. I was wondering if there is a way in which Pymol can “swap” an existing side chain at position N on the peptide for any other side chain in an automated fashion? Any help much appreciated. Angela -- Angela Gray -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] Automatic modification of structures in PyMOL
Hi everyone, I am trying to find a way, in Pymol, to remove an amino acid from a peptide and insert any other amino acid. I have been able to do this for one residue at a time using the command editor.attach_fragment(‘pk1′,’my_fragment_name’,11,0) but I have to do this in two parts so that the new amino acid binds at both ends. I was wondering if there is a way in which Pymol can “swap” an existing side chain at position N on the peptide for any other side chain in an automated fashion? Any help much appreciated. Angela -- Angela Gray -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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
