Re: [PyMOL] Editing of the pdb structure

2012-01-30 Thread Thomas Evangelidis
Is it a small organic molecule or a modified amino acid within the context of a protein? 2012/1/29 Tim Schulte > Dear James, > I agree with Joao, for fast and dirty minimisation you might try the > program Chimera or VegaZZ. If you just wanna have an energy-minimized small > molecule the Prodr

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-30 Thread Ramiro Téllez Sanz
I had exactly the same problem but under Gentoo Linux 64bits using KDE 4.7.4. In my case, I solved it by re-installing the package for chemical-mime-data (sci-chemistry/chemical-mime-data), which was missing since the removal of some Gnome chemical packages with all their dependencies I didn'

[PyMOL] Missing residues in PDB

2012-01-30 Thread gontchar andrey
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 in PDB

2012-01-30 Thread Thomas Holder
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

Re: [PyMOL] Missing residues in PDB

2012-01-30 Thread gontchar andrey
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

2012-01-30 Thread Thomas Holder
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

2012-01-30 Thread gontchar andrey
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

[PyMOL] list of polar contacts

2012-01-30 Thread Abhinav Verma
Hi, I am trying to get the list of hbonds formed using Apply-find-polarcontacts. I searched and found some scripts, but they never give me the same result as the one by default pymol. Any ideas how I can get the hbonds as a list. Thanks, Abhinav -

[PyMOL] To build protein structure model?

2012-01-30 Thread Hong ZHAN
Hi everyone, I am a new guy in this area.. And I just want to know how to build a structure model of my protein from homologues crystal structure and protein seq.??? Thx Hong Sincerely, -- Try before you buy = See our

Re: [PyMOL] To build protein structure model?

2012-01-30 Thread João Rodrigues
Try MODELLER. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style A

Re: [PyMOL] To build protein structure model?

2012-01-30 Thread Nat Echols
On Mon, Jan 30, 2012 at 6:05 AM, Hong ZHAN wrote: > I am a new guy in this area.. And I just want to know how to build a > structure model of my protein from homologues crystal structure and protein > seq.??? You probably want to try using a homology modeling server for this rather than PyMOL:

Re: [PyMOL] list of polar contacts

2012-01-30 Thread Thomas Evangelidis
Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use list_hbonds.py from: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ and set the cutoff and angle to the values you wish. Thomas On 30 January 2012 16:34, Abhinav Verma wrote: > Hi

[PyMOL] atom structure

2012-01-30 Thread nami sugiyama
Hi, We would like to visualize the protein structure at the atoms level, by visualizing atoms as "balls" and the bonds between them as "sticks". Is there a way?? Nami -- Try before you buy = See our experts in actio

Re: [PyMOL] atom structure

2012-01-30 Thread João Rodrigues
Hi, You can set something like this: set sphere_scale, 0.2 set stick_radius, 0.15 show spheres show sticks I usually use lines for the bonds though. Best, João -- Try before you buy = See our experts in action! The mo

Re: [PyMOL] list of polar contacts

2012-01-30 Thread Thomas Evangelidis
I think you can reproduce the results from "apply->find->polar contacts" option with the PyMOL built-in "distance" command. E.g. distance hbonds, all, all, 3.2, mode=2 The problem is that you cannot set the A-H-D angle which is important for the definition of the H-bond. On 30 January 2012 18:4

Re: [PyMOL] atom structure

2012-01-30 Thread Katherine Sippel
Hi Nami, You want http://www.pymolwiki.org/index.php/Ball_and_Stick Katherine On Mon, Jan 30, 2012 at 10:46 AM, nami sugiyama wrote: > Hi, > > We would like to visualize the protein structure at the atoms level, > by visualizing atoms as "balls" and the bonds between them as > "sticks". Is ther

Re: [PyMOL] Editing of the pdb structure

2012-01-30 Thread Thomas Evangelidis
I think you got your answers from the AMBER and GROMACS mailing list :) Just a comment about PRODRG server, it is not the best choice for geometry optimization and charge calculation. Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations for Building GROMOS-Compatible Small M