Hi all,
I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting
this error with pymol generated files not being found in the tmp directory:
Could not find
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so
searching for
Hi All,
I am script-plowing through PDB files and extracting unique chain
identifiers only for polymers using PyMOL's polymer selection. Right now
my code is a kind of brute force thing like this:
code
cmd.create (justpolys,polymer)
polymer_chains=[]
for a in cmd.index(justpolys):
examples?
Cheers,
-- Jason
On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris set...@gmail.com wrote:
Hi all,
I feel I should know this one. I have a program looping through
structures
and bringing each small molecule into a single multi-state object so I
can
tab through the states.
I do
scriptwise on a cluster. But you'll be disappointed if you expect it
will keep your scene from crashing Pymol (but then there's the
hash_setting...).
I hope this clarifies things a bit.
Cheers,
Tsjerk
On Sat, Oct 24, 2009 at 8:21 AM, Seth Harris set...@gmail.com wrote:
Tsjerk,
I think you
, 3
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com supp...@delsci.com
--
*From:* Seth Harris [mailto:set...@gmail.com]
*Sent:* Monday, December 01, 2008 2:18 PM
*To:* pymol-users@lists.sourceforge.net
*Subject
I feel like I should already know this one, but is there a command line way
to add an atom at specified coordinates? or at screen center? I thought
there was a new-ish pseudoatom functionality but I can't seem to find or
recall details. Can one specificy atom type as well?
I was looking to
Hi all,
we have a user with a 2 button mouse who would like pymol to start up that
way (i.e. without having to go to the mouse menu and select 2 button viewing
mode every time he starts). I had a look around for a setting we could put
into his pymolrc file, but the only things with promising
Hi Michelle,
In case no one's mentioned it yet, Zac Panepucci has contributed a
grepset.py script which, after being run, allows you to type grepset x
to see all settings (and their values) associated with whatever x is.
It's not directly integrated into the pymol distribution but pretty
This is for the povray gurus out there...
Occasionally I muck around with the time-consuming practice of trying to map
pictures onto molecular surfaces with povray.
I had this working to some extent, but something has changed (I think with
the povray file format produced by pymol make_pov where
Marilyn,
We saw this between unix and PC and one user figured out that
label_font_id's were different. Thus older versions didn't recognize as many
fonts as newer ones. I'm thinking this matches your description if the
binaries on the two machines are in fact different versions.
Try:
set
Paul ( Bob),
Have you tried
set two_sided_lighting, 1
Cheers,
seth
Just to pipe up for the other side, while I would by no means defend the
lack of documentation as a good thing, given limited resources I actually
prefer new features at the expense of documentation. I realize there is a
large range of computer expertise in the pymol user community, and obviously
Hi Sun,
Warren (and others?) has posted some text before about this. A simple
template for it is as follows with the key being that mview interpolate
command at the end. This works, but I haven't been through it recently to
remind myself of the nuances of the animate=0 options and the view=0
Just to throw my 2 cents in following Warren's invitation, I think
Mark Gerstein's programs work well for this (calcsurf.exe or
something...they're on his web site)
ccp4's areaimol does something similar, though I can't recall whether
its output was atom by atom.
In either case, you may have to
Hi all,
Minor thing, but thought I'd ask...
Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom (left-anchored).
Is there a way to choose whether the label is left-anchored, centered, or
right-anchored?
I find that
This is more half an answer than the real deal, but when I had the same
issue I opted for the quick work around of setting the range from -100 to
100 for the blue-white-red palette which effectively made 0-100 correspond
to white to red only since there were no negative B factors/conservation
Hi,
I'm writing a small script to visit alternate conformations, stepping
through each as a frame in a movie with the cursor keys. I'd like to label
them to distinguish the alternates so I can see which I'd like to keep or
not, but:
label alternates, name
only displays the atom name without the
.
label alt a+, A%s-%s % (resn, resi)
label alt b+, B%s-%s % (resn, resi)
hide labels, alt
Cheers,
-bob
On 12/7/05, Seth Harris set...@gmail.com wrote:
Hi,
I'm writing a small script to visit alternate conformations, stepping
through each as a frame in a movie with the cursor keys
Hi Warren et al.,
Thanks very much, Warren, for the rotamer libraries and mutagenesis wizard.
I am very attached to cycling through rotamers using the cursor arrow
keys. However if I have a movie set up, it takes precedence of the
cursor key bindings, and right arrow steps through movie frames
Hi all (again!),
Warren, I know I half brought this up at the user's meeting but I
can't remember if there was a clear answer...so maybe it means not
yet, but didn't recall that either.
Question: is there a way to preserve small molecule bond valence information?
Background: I know pymol has
Hi,
I get these as a digest so sorry if someone's already
spoken to this.
Laurence Pearl wrote some code to interpolate between
scenes as you describe. Kristian Rother wrote a very nice
set of framework commands (and more) to make movies. I
wrote an extension of Laurence's commands so
Yo,
I just wrote a really long email to the list. So long
that my web mail secretly logged me out during the time
that I was writing it. The upshot of this is that 1) I am
angry and 2) you are all spared the rambling version and
hopefully get the more succinct version summarized here:
I
I was curious if anyone has successfully done stereo over
a projector with PyMOL. That is to say not the cross-eyed
stuff but the shutter-glasses type stereo. I was recently
trying to do this for a company presentation from an SGI.
On the same machine Insight can do stereo (although they
Hello PyMOLers,
I am displaying hydrogen bonds using:
distance hbond, protein, ligand, mode=2
which makes some nice dashed lines for hydrogen bonds but
doesn't always display all the hbonds one might expect.
For instance, in some cases there are is an N on the
ligand molecule and a backbone
hugging
along one edge of a helix.
upgraded script version available shortly as I now have it working
from the command line rather than just from scripts.
Thanks for any ideas,
seth
--
Seth Harris, Ph.D.
Agard Laboratory Suite S416
Box 2240
UCSF/HHMI
600 16th Street
San Francisco, CA 94143-2240
try to post the script somewhere for download later today for
those who have/had trouble with the binhex.
Thanks for the interest and apologies for the mistakes!! All my
attempts at code should come with a blanket warning concerning the
perils with which they are fraught.
Ciao,
Seth
--
Seth
, I have
sample scripts for those who are just getting started and can share
them if needed but this tome seemed enough for now!
--
Seth Harris, Ph.D.
Agard Laboratory Suite S416
Box 2240
UCSF/HHMI
600 16th Street
San Francisco, CA 94143-2240
(Shipping Zip 94158)
415.502.2930
MasterMovie.py
Hello all,
I am trying to write a script that will go through each residue in a
dimer interface and determine for each one how close it is to the
partner monomer.
I can interactively plot all the distances within a certain cutoff
using the handy:
distance chosen,
Hi,
I wrote a rudimentary Python script to be run from PyMOL that makes
png snapshots of identical views of your NCS-related molecules. I
find it helpful for comparing map features and different
conformations between NCS copies, particularly since I have 8 NCS
copies in my current project's
Quick question, I hope:
It seems that ray always renders the image in the orthoscopic view
regardless of whether I set orthoscopic, 0 or set orthoscopic, 1
although these settings do influence the non-ray traced standard
view. Is this true or am I missing something? I'm trying to ray
trace
) by Seth Harris.
### shar...@msg.ucsf.edu for any suggestions/feedback/gratitude
### Thanks to Warren DeLano for PyMOL!
from pymol import cmd
from Numeric import *
from LinearAlgebra import *
import re
### define function to put out set_view command for a given molecule
def outview (mol, n
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