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

[PyMOL] Missing residues in PDB

Hi. We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically? -- Andrey ---

Re: [PyMOL] missing residues

Selam Ahmet, I cordially suggest to have a look at http://catb.org/~esr/faqs/smart-questions.html to phrase your question more effectively, such that we can provide more tailored help. It would have been nice to have an example that we could try ourselves. I find that as preparation for MD simula

Re: [PyMOL] missing residues

Thanks Michael, How can I overcome using Pymol? 14 Ekim 2011 23:05 tarihinde Michael Zimmermann yazdı: > The easiest way to model in the missing loops is to make a homology model > of the full sequence using the incomplete structure as a template. ( > http://swissmodel.expasy.org or I-TASSER) >

Re: [PyMOL] missing residues

The easiest way to model in the missing loops is to make a homology model of the full sequence using the incomplete structure as a template. ( http://swissmodel.expasy.org or I-TASSER) Alternatively, you can use Modeller to model in the loop and refine it. 2011/10/14 ahmet yıldırım > Dear use

[PyMOL] missing residues

Dear users, There are 7 missing residues in xxx.pdb file. xxx.pdb consist of chain a and chain b. In chain b there are only 7 missing residues. chain a is complete. I fitted the complete chain onto the one with missing residues, wrote the new coordinates for the fitted chain and put them in the br