Re: [PyMOL] Cartoon visualization of per-residue txt data

Hi James, No, you can't set transparency based on b-factor. As for the selections, don't use selection keywords (ss) as names. Cheers, Tsjerk On Apr 12, 2015 3:25 PM, "James Starlight" wrote: > and also a question- > how it would be possible to do something with the selection based on > the b

Re: [PyMOL] Cartoon visualization of per-residue txt data

Hi James, "ss" is a reserved keyword of the selection language, so you should not use it as the name of an object or selection. Cheers, Thomas On 12 Apr 2015, at 09:24, James Starlight wrote: > and also a question- > how it would be possible to do something with the selection based on > the

Re: [PyMOL] Cartoon visualization of per-residue txt data

and also a question- how it would be possible to do something with the selection based on the b-factors e.g PyMOL>select ss, b < -0.2 Selector: selection "ss" defined with 119 atoms. than I've tried to make visualization of the residues within the ss to display residues names from the label co

Re: [PyMOL] Cartoon visualization of per-residue txt data

Hi Tsjerk, the interesting option for coloring which I found to set sensitivity of the visualization in my case: spectrum b, red_orange_white, minimum=-1, maximum=0.1 are there any same commands to set transparency level according to the B-factor value? Here the issue is with the proper select

Re: [PyMOL] Cartoon visualization of per-residue txt data

also to specify: I've already done this for one pdb and one dat file using just sequence command from the pymol with loaded protA.pdb inFile = open("./test.dat", 'r') # create the global, stored array stored.newB = [] # read the new B factors from file for line in inFile.readlines(): stored.new

Re: [PyMOL] Cartoon visualization of per-residue txt data

thanks for the information! Here I ask to provide me with some more help because I'm not a big expert in the python . For instance I have 2 folders- one with 10 pdb's corresponded to the 10 complexes of one receptor (289 residues) docked with 10 different ligands; the second one is the 10 the_same

Re: [PyMOL] Cartoon visualization of per-residue txt data

Hi James, I think what you want to do is to load your data to the b-factor column of the pdb file and then ask PyMol to color the protein according to the b-factor values. Try with this example from the PyMol wiki and let us know if you find som