Hi Martin,
Try replacing
> (phi, psi) = cmd.phi_psi("br. first my_res")
with
(phi, psi) = cmd.phi_psi("br. first my_res").values()[0]
Here's what I have now, for the script (I fixed one more bug):
import pickle
rot_lib =
pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/si
Hi Jason and PyMOL users
I tried to run the script to get the number of rotamers, but I seem to
have something missing.
The script looks as follows:
import pickle
rot_lib =
pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
from pymol import st
Hi PyMOLers,
I think there is a bug in PyMOL regarding the "set cartoon_transparency"
setting. According to the PyMOL-Wiki, the arguments are:
set cartoon_transparency, value, selection
where the "value" ranges from 0.0-1.0 and the selection is optional. However,
selections that are not ent
Program Vasco can do it.
Sebastian Kruggel wrote:
> dear all,
>
> i am looking for a possibility to map lipophilic potential
> on pymol generated surfaces. i didn't find anything in the
> documentation and in the mailing list the question came up once
>
> http://www.mail-archive.com/pymol-users@
Thanks, Jason, it works. :)
Li
On Sun, Sep 12, 2010 at 5:40 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Li,
>
> I created a small python script "testAlign.py" with the following 3
> lines as its content:
>
> cmd.fetch("1cll 1ggz", async=0)
> rmsd = cmd.align("1cll", "1ggz")[
dear all,
i am looking for a possibility to map lipophilic potential
on pymol generated surfaces. i didn't find anything in the
documentation and in the mailing list the question came up once
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg03459.html
but there was no reply. ma
Hi all,
In doing my usual sweep of the PyMOLWiki for spam, I noticed Thomas
Holder's new script that calculates and annotates with CGO arrows, the
orientation of a single helix and the angle between two helices.
Thomas didn't mention the script here, so I thought I would, as it
will be useful for
These are all great ideas--I'm glad I asked.
I updated the wiki page (http://www.pymolwiki.org/index.php/Aa_codes)
to reflect this discussion.
Cheers,
-- Jason
On Mon, Sep 13, 2010 at 4:17 AM, Tsjerk Wassenaar wrote:
> Hi Jason e.a.,
>
> I usually do the hashing like:
>
> aa1 = list("ACDEFGHIK
Hi Renuka,
Are you sure that's what you want? It will read something like:
for i in __import__("glob").glob("cluster_*.sdf"): cmd.load(i)
But I think it's more elegant to use two commands for this... :-P
import glob
for i in glob.glob("cluster_*.sdf"): cmd.load(i)
May seem like a small differe
Hi,
I wrote a script to calculate angles between helices and put it on the
pymol wiki. I played around with how to fit the helix direction best
and finally implemented 4 different methods to do it.
http://www.pymolwiki.org/index.php/AngleBetweenHelices
Cheers,
Thomas
--
Thomas Holder
Group o
p { margin-bottom: 0.08in; }
Dear Pymol users
I have set of ligand files in *.sdf
format as follows:
cluster_1.sdf
cluster_2.sdf
cluster_3.sdf
cluster_4.sdf
Could you please tell me how to load
these multiple *.sdf files in one command?
Regards
Renuka
Hi Jason e.a.,
I usually do the hashing like:
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS MET ASN PRO GLN ARG SER THR
VAL TRP TYR".split()
aa123 = dict(zip(aa1,aa3))
aa321 = dict(zip(aa3,aa1))
The real convenience in there is that you can easily construct any
ki
On Mon, Sep 13, 2010 at 12:30 AM, Jason Vertrees
wrote:
> # get it's one-letter residue id
> print string.split(cmd.get_fastastr("mySelection"),'\n')[1]
> # get it's three-letter residue id
> print three_letter[string.split(cmd.get_fastastr("mySelection"),'\n')[1]]
>
> I just posted this on http:/
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