Hi Spyros, so you want to visualize how often each atom matches your GREP query? You could put that count number as b-factor and then do a spectrum coloring. Example:
python # load one of the homology models cmd.load('tem1_mod445.pdb') # set b-factor to zero for all atoms cmd.alter('all', 'b=0') # increment b-factor for each GREP line for line in open('output.txt'): line = line.split(':', 1)[-1] name = line[12:16] resi = line[22:26] cmd.alter('resi %s and name %s' % (resi, name), 'b=b+1') # show spheres, colored from yellow to red according to count cmd.show_as('spheres') cmd.spectrum('b', 'yellow_red', quiet=0) python end Cheers, Thomas Spyros Charonis wrote, On 08/31/12 17:21: > Dear PyMOL community, > > I have a python script that reads a directory of ~500 homology models > generated from a pipeline (I used a PDB file as a template to generate > the models). > It extracts residues that have charge-bearing atoms on them. When using > GREP/EGREP to query a specific coordinate (e.g. 29.010) against the dataset > and to determine which and in how many homology models it is present, > the output looks like so: > > ./tem1_mod445.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > ./tem1_mod446.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > ./tem1_mod461.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > > ./tem1_mod179.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 > > ./tem1_mod180.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 > > > and so forth..... > > The ./tem1_mod**** string refers to the specific homology model file > that contains the atom. > > QUESTION > Once I have collected all atoms that I possess z-coordinates values > within a range (29 - 54), Is there a way to map these onto a template PDB > structure (in my case 3NY8 - adrenergic receptor). In other words, > having collected hundreds of atomic coordinates (all from charged > residues and > all with z-values between 29.000 - 54.000 angstroms) across several > different homology models (my dataset contains ~500 models) > is there a way to visualize (using the z-coordinate spatial value as the > criterion) them on a single PDB file? > The reason I would like to do this is to observe any patterns in the > occurrence of charge throughout the transmembrane region of receptor > proteins. > > Many thanks in advance. > > Regards, > Spyros Charonis -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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