Hello Ramesh,
Is it possible to do the labelling using single letter codes for the
amino acid residues rather than the three letter codes?
Yes.
1. Add this to your $HOME/.pymolrc file:
# start $HOME/.pymolrc modification
one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q',
Ezequiel H Panepucci wrote:
Hello Ramesh,
use:
label n. ca, one_letter[resn]
Cheers,
Zac
Thanks Zac. that was indeed very useful. But I have one more problem.
Doing thus gives me only the name of the aa, not its number. How to give
the label command in order to give the
andr...@biochem.utah.edu wrote:
Hey Ramesh,
for all sorts of labeling, image manipulation programs like photoshop or
the gimp are superior. Convince yourself how simple it is even to adjust
the z position of the label in a stereo picture by moving it (one partner
of the stereo pair)
I am wondering where I can find mesh represenation of protein surface in
PyMol API.
--
Bingding Huang
PhD student
Bioinformatics group
Biotec Department of Computing
Tazberg 47, 01307
TU Dresden, Germany
Tel:0049 351 46340064 (Office)
Tel:0049 351 4403368 (Home)
Fax:0049 351
1. Add this to your $HOME/.pymolrc file:
# start $HOME/.pymolrc modification
one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
Hi all:
I'd like to set a value for a selection of residues within an
object --- which I think might be tough given the docs on the set
command, but I'm open to suggestions. The particular case here is
setting cartoon_transparency, which I'd like to use to make a subset
of residues in a
I've been trying to generate an electrostatic potential map of the surface of
a protein using Pymol but haven't been successful. I'm working with the latest
version of pymol (0.98, windows version), which brings the APBS plugin (I have
as well installed the APBS plugin apbs_tools.py) that is
Hi,
I just checked the apbs download page and I couldn't find apbs binaries
available for windows. The only way I've seen (through previous mailing
lists posts) is to compile it using cygwin, but the performance is less
than optimal.
So if you or someone else has compiled apbs for windows, the
