From: Spyros C. <s.c...@gm...> - 2012-08-31 15:22:00
|
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 |