Re: [PyMOL] list of polar contacts

Hi Abhinav and Jason, > The underlying C-object for a measurement does not support > iterate/alter. This is rather silly; PyMOL should be able to tell you > what's in the object. As an ad-hoc hack, I wrote a Python script to access internal C-object of distance representation and convert it to at

[PyMOL] MacPyMOL Knowledge of Opened Structures

Hi PyMOLers, I noticed some strange behaviour when I do the following: 1) Load A.pdb into MacPyMOL via "pymol A.pdb"2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A" 3) Load a completely different structure (must have different number of atoms than A.pdb), B.pdb, into a

Re: [PyMOL] drawing and formating bonds between atoms

Gonzalo, The cartoon representation is a stylized representation of the structure using backbone atoms as guides. Setting stick_color or line_color on a cartoon won't help -- you need to show lines or sticks. If you need sticks/lines back just type: show lines, sele or show sticks, sele where

Re: [PyMOL] drawing and formating bonds between atoms

Sorry guys, it's me again. It worked while I was seeing the structure in lines style, but when I change the style to cartoon, the bonds that I set dissapear.. How can I prevent it? Thanks again, and sorry for beeing that noob. Gonzalo > From: jason.vertr...@schrodinger.com > Date: Tue, 31 Jan 20

Re: [PyMOL] drawing and formating bonds between atoms

Gonzalo, Just pick a bond and issue the following setting command to make colored lines: set_bond line_color, yourColor, sele You can also use set_bond stick_color, yourColor, sele for sticks. "sele" should be the two bound atoms. Cheers, -- Jason On Tue, Jan 31, 2012 at 1:51 PM, Gonzalo

[PyMOL] drawing and formating bonds between atoms

Hello everyone,I was trying to make a pymol script. I have to draw different lines in my pdb structure with different colors.So, I find the way to draw a bond between to atoms, for example."bond resi 234 and resn GLU and name CA, resi 259 and resn SER and name CA" But it always draw the bond wi

Re: [PyMOL] list of polar contacts

Hi Abhinav, The underlying C-object for a measurement does not support iterate/alter. This is rather silly; PyMOL should be able to tell you what's in the object. Please file a feature request on the open-source bug tracker and we'll be sure to look at this ASAP. Cheers, -- Jason On Tue, Jan

Re: [PyMOL] list of polar contacts

Hi thanks, still it is not the same.. But thanks.. I wish Jason can reply if there is any way to get the list from the apply command. thanks, Abhi On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis wrote: > I think you can reproduce the results from "apply->find->polar contacts" > option wit

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.