RE: [PyMOL] combine align and rms_cur to calculate rms for complexes

Andrea, PyMOL really can't do this job generally well because you'd need to specify an atom-by-atom correspondance between the two ligands. Unless the ligands are identical and have identical atom names, the numbers you get will be misleading. If that is in fact the case, then I think you're o

RE: [PyMOL] Light source questions

Chris, Multiple light sources will be in the next release -- the code is currently in CVS. For future reference: set light_count, 4 and modify the light, light2, and light3 vectors (if necessary) light0 is fixed along Z and has no default specular component. The Z axis light intensity is con

RE: [PyMOL] Transparent background

Yes, in recent builds (http://delsci.com/beta). set opaque_background, off then draw or ray and then save the image. NOTE: Some graphics cards support this in OpenGL (draw command), other systems can only do transparent backgrounds via the ray-tracer (ray command). Cheers, Warren -- Warren

RE: [PyMOL] displaying protein with propeptide

I'm not sure how version-dependent this is, but setting connect_mode to 1 before loading the PDB should disable distance-based connectivity determination. set connect_mode, 1 load CONECT_only_pdb.pdb -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC

Re: [PyMOL] displaying protein with propeptide

Is there a similar command to force PyMOL to use only CONECT lines in the pdb file instead of generating connectivity by distance? Eric Warren DeLano wrote: A quick fix is to use the "retain_order" setting. set retain_order which will force PyMOL to honor the order of ATOMs in the PDB file o

RE: [PyMOL] displaying protein with propeptide

A quick fix is to use the "retain_order" setting. set retain_order which will force PyMOL to honor the order of ATOMs in the PDB file over the numeric ordering of residue identifiers. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC

[PyMOL] combine align and rms_cur to calculate rms for complexes

Hi all, could someone confirm this: I have some complexes protein+ligand and I'd like to perform rms calculation for the position of the ligand. This what I have done: load reference.pdb select proteinreference, segi A select ligreference, segi B load compare.pdb select proteincomapre, segi A sele

Re: [PyMOL] displaying protein with propeptide

Hi Ann, I would change the chain id of the propeptide in a text editor, to say P and remove the P from after the residue numbers. J Anne Mølgaard wrote: Hi, I am having problems displaying proteins with unusual residue numbering, such as proteins with propeptides. An example is 1cs8, which

[PyMOL] Transparent background

Hi pymol users, I'd like to make a figure with a transparent background. Is it possible with pymol? Thanks for your help. Fred

[PyMOL] displaying protein with propeptide

Hi, I am having problems displaying proteins with unusual residue numbering, such as proteins with propeptides. An example is 1cs8, which starts off like this: ATOM 1 N SER A 1P-32.762 23.978 22.929 0.00 34.26 N ATOM 2 CA SER A 1P-32.360 24.645 21.660 0.00 34.08