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
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