Re: [PyMOL] Missing residues in PDB

I found a solution! With openbabel a pdb without residue names and numbers can be easily fixed: 1. babel file.pdb file.mol 2. babel file.mol file.pdb Et voila! Now you have a pdb with repaired residue names! 2012/1/31 Андрей Гончар : > Thanks! > > 2012/1/31 Thomas Holder : >> I put a script on th

Re: [PyMOL] Missing residues in PDB

Thanks! 2012/1/31 Thomas Holder : > I put a script on the PyMOLWiki that does renumbering based connectivity: > > http://pymolwiki.org/index.php/Renumber > > Cheers, >  Thomas > > > On 01/30/2012 02:52 PM, Thomas Holder wrote: >> >> On 01/30/2012 02:24 PM, gontchar andrey wrote: >>> >>> Thanks a l

Re: [PyMOL] Missing residues in PDB

I put a script on the PyMOLWiki that does renumbering based connectivity: http://pymolwiki.org/index.php/Renumber Cheers, Thomas On 01/30/2012 02:52 PM, Thomas Holder wrote: > On 01/30/2012 02:24 PM, gontchar andrey wrote: >> Thanks a lot! >> A very useful script, but not exactly that I need.

Re: [PyMOL] Missing residues in PDB

Thanks! I'll try it! On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote: > Hi Andrey, > > I have a script that updates the sequence based on residue numbering > (resi). See attachment. > > Usage: set_sequence sequence [, selection [, start ]] > > Example: > > # import script > run se

Re: [PyMOL] Missing residues in PDB

On 01/30/2012 02:24 PM, gontchar andrey wrote: Thanks a lot! A very useful script, but not exactly that I need... In my pdb file residues are not numbered. I think that I have to determine amino acids only by atom sequence and connetcions... This problem is a little more complicated than assign

Re: [PyMOL] Missing residues in PDB

Thanks a lot! A very useful script, but not exactly that I need... In my pdb file residues are not numbered. I think that I have to determine amino acids only by atom sequence and connetcions... This problem is a little more complicated than assigning names to numbered residues, I think... Do y

Re: [PyMOL] Missing residues in PDB

Hi Andrey, I have a script that updates the sequence based on residue numbering (resi). See attachment. Usage: set_sequence sequence [, selection [, start ]] Example: # import script run setseq.py # create a poly-ala peptide fab A, myobj # set new sequence set_sequence CDEFGHIKL, m