[PyMOL] Finding parameter settings in old PyMol session

Hi all, I need to make a set of figures with a protein having different ligands bound to the active site. I already have a few of them finished and now I want to make the rest in a similar (identical) way. Unfortunately, I have forgotten how I set sphere_scale, stick_radius and the like for

Re: [PyMOL] Finding parameter settings in old PyMol session

Hey Wulf, after firing up your old session, you should be able to extract any setting by typing 'get setting', e.g. 'get stick_radius' or 'get sphere_scale'. Also, think about saving important PyMOL work as pml scripts. I find them much easier to handle. Andreas Wulf Blankenfeldt

[PyMOL] Exporting a selection to file

Hello, is it possible to generate a list of all residues within 5A of another (or whatever you need) and then save this list to a file/clipboard? Thanks a lot for the help, Luca begin:vcard fn:Luca Varani n:Varani;Luca org:Institute for Research in Biomedicine adr:;;Via Vela

Re: [PyMOL] Exporting a selection to file

Hi! Try with: select selection name, name of the object to which the selection belongs w. 5 of other object select other selection name, br. selection name save name.pdb, other selection name The first command select the atoms at 5 Angstroms from other object; the second select the whole

[PyMOL] how to resolve the error

Friends, Someone please write to me how to resolve the following error. OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.3-devel) Traceback (most recent call last): File /usr/lib/python2.5/site-packages/pymol/__init__.py, line

[PyMOL] special bond in pymol

Hi, Can anyone help thierry ? http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149 I would like to ask to make a special bond in pymol. Actually in my protein I have a real covalent bond between an Asn and a Lys.. Obviously, Pymol doesn’t know how to draw it. Can you help me ?

Re: [PyMOL] special bond in pymol

Hi Nir, Pymol just draws bonds based on distances, not based on topological information. If atoms are within contact distance, a bond will be drawn, whatever the atoms are. If one feels need for an additional bond, it is possible to add them using: bond selection1, selection2 This will draw

Re: [PyMOL] special bond in pymol

Obviously that should read 'resn asn' in stead of 'resn asp'. Sorry for that. Tsjerk On Tue, Mar 31, 2009 at 9:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Nir, Pymol just draws bonds based on distances, not based on topological information. If atoms are within contact distance, a

[PyMOL] get_dihedral bottleneck

Hi PyMol-Community, I have been looking for a PyMOL command to calculate the ribose sugar pucker information (in DNA) but have not found anything. Thus, I began writing a simple Python script that is supposed to take a selection, determine whether or not it contains a ribose sugar ring, and