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_name.dat files corresponded to the 10 logs having 1 column with the values per each residue (totally 289 values) of the receptor. I need to associate each pdb with each dat to exchange existing B-factors within each pdb onto the values taken from the corresponded.dat files and associate it's directly to the C-alpha atoms of each complex for instance. Will it be better to rewrite here the script from the PyMol Wiki or to use data2bfactor.py (here as I found I need to modify my dat logs including to them number of receptor residues and chainID). James 2015-04-08 19:00 GMT+02:00 Osvaldo Martin <aloctavo...@gmail.com>: > 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 some trouble. > > Regards, > Osvaldo. > > On Wed, Apr 8, 2015 at 1:47 PM, James Starlight <jmsstarli...@gmail.com> > wrote: >> >> Dear Pymol users! >> >> For better visualization of the MMGBSA outputs from MD performed for 10 >> ligands >> agains 1 receptor-target I wonder to map per-residue decomposition >> data from each of the systems onto the receptor's 3D structure. >> Eventually I'd like to produce 10 cartoon diagrams which would differs >> in the coloring according to the difference in the contribution of >> residues from the receptor's cavity to binding for different ligands. >> I will be very thankful if someone provide me with ideas of how such >> visualization could be done using receptors structure, decomposition >> logs as the inputs and/or pymol. Here some general idea whig came in >> mind- import column from the mmgbsa.log directly (with number of >> rows= number of receptors residues) to the receptor.pdb B-factors >> column (for instance making meaningful value for C-alpha atom and 0 >> for the rest). Will be very thankful for some examples of how it could >> be achieved e.g using combination of awk_sed if more trivial way is >> not exist. >> >> >> Thanks for help!! >> >> James >> >> >> ------------------------------------------------------------------------------ >> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >> Develop your own process in accordance with the BPMN 2 standard >> Learn Process modeling best practices with Bonita BPM through live >> exercises >> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- >> event?utm_ >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
