Hi Martin,
I think that Pymol indeed assumes PDB formatting, where the b-factor
and occupancy fields are float format %6.2f, whereas the PQR format
often uses %8.3f formatting in stead. That will make both approaches
fail. You'll have to do some scripting to get it right:
You can try the following function. Not tested though :p
def load_pqr(pqr,name=):
if not name:
name = name.replace(.pqr,)
pdb = []
for i in open(pqr):
if i.startswith(ATOM) or i.startswith(HETATM):
pdb.append(i[:54]+%6.2f%6.2f\n%(float(i[54:60]),float(i[60:66])))
else:
pdb.append(i)
cmd.read_pdbstr(.join(pdb),name=name)
cmd.extend(load_pqr,load_pqr)
Cheers,
Tsjerk
On Thu, Oct 13, 2011 at 9:12 AM, Martin Hediger ma@bluewin.ch wrote:
Thanks, Tsjerk
However, the first set of commands does not seem to have any effect (neither
produce an error). Is it supposed to be able to enter them at the PyMOL
prompt just as you wrote? The spectrum command seems to have an effect but
all atoms appear in red. One should be blue.
Is there a restriction on how the PQR file is to be formatted? I was reading
PQR is not as strict as PDB format, so I believe the file I posted should be
a valid PQR format.
Martin
Am 13.10.11 06:17, schrieb Tsjerk Wassenaar:
Hi Martin,
You can use b and q as selection keywords (help selections):
color red, b 0
color blue, b 0
Or you can use 'spectrum' (help spectrum):
spectrum b, red_white_blue
Hope it helps,
Tsjerk
On Oct 13, 2011 12:58 AM, Martin Hediger ma@bluewin.ch wrote:
Dear List
I have the below model of three charged atoms (as a PQR file).
ATOM 1 C ASP A 0.0 0.0 10.0 -2.0 4.0
ATOM 2 C ASP A 0.0 0.0 0.0 -2.0 4.0
ATOM 3 C ASP A 0.0 0.0 -10.0 2.0 4.0
The last two numbers are the charge and the radius, it's supposed to be
in pqr format.
Can PyMOL display the negative atoms blue and the positive one red (or
the other way around)?
Thanks for any help.
Martin
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Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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