On Sun, May 23, 2010 at 3:55 PM, Maia Cherney ch...@ualberta.ca wrote:
I would like to show coordination bonds between Mg ion and its ligands
(oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A.
dist elem mg, (all within 2.2 of elem mg)
Might need to try a slightly
On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon vicken...@gmail.com wrote:
i am an academic using pymol and the new build places a for
evaluation only graphic on top of the rendered structure. not very
helpful for presentations, publications and the like. how do i
circumvent this without using
On Fri, Mar 26, 2010 at 5:14 PM, Werner Schroedinger
werner.schroedin...@googlemail.com wrote:
For making this procedure faster and more automaticm I wonder if somehow
can I tell pymol to pay atention to some external file, or for the
ligand being visualized now, to its copy on the hard disk,
Is there a way to do this in such a way that the rest of the view matrix
changes appropriately, including clipping planes, etc.? There is a handy
pair of functions in Coot that do this:
set_rotation_centre(x, y, z)
set_zoom(30)
which has the advantage of adjusting the perspective and
On Tue, Mar 23, 2010 at 12:48 PM, hari jayaram hari...@gmail.com wrote:
Hi
I want to write a python/pymol script that will give me residue -residue
distances within a pdb file programmatically
I know that within pymol I can get a distance object using
select r55 , chain A and resi 55
On Sun, Feb 14, 2010 at 4:39 PM, David Hall li...@cowsandmilk.net wrote:
I don't think DynoPlot can't do this. Are there even callbacks to
watch for things like changing state in the Pymol GUI? Maybe that
should be a feature request as it would allow for a lot more powerful
plugins.
On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cu wrote:
How can I use the color by element (HNOS) function present in the GUI,
in a script?
I don't think there's a single command that does this; I've always done
something like this:
color grey80, elem c
color white, elem h
On Thu, Jan 21, 2010 at 6:10 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
4) A better density wizard, let's just copy coot and be done with it.
Ability to dynamically bind density levels or some other properties to
the scroll-wheel for that matter.
+1
6) Integration/bundling
On Tue, Jan 12, 2010 at 11:13 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
I am trying to make a movie form a set of morphed pdb files. Currently
the individual files are loaded into the same object with increasing states,
all pdb files contain the SHEET and HELIX record created
On Thu, Dec 17, 2009 at 10:54 AM, Jason C Porta jpo...@unmc.edu wrote:
I have been trying to modify the grid spacing on 2Fo-Fc map that was loaded
into PyMol directly from phenix.refine. The mesh object is generated from
the isomesh command. Basically, I would like there to be fewer grid
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney ch...@ualberta.ca wrote:
Is it posible in pymol to select all residues of a certain type
automatically, like all arginines or all lysines + arginines in a chain?
select resnam arg
select chain A and (resnam lys or resnam arg)
On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow b...@mac.com wrote:
I have a very large library (almost 1000) of similar genetic
sequences, for which I would like to generate homology models. Does
anyone know of a way to automate requests to a homology modeling
server, such as SWISS-Model
On Fri, May 1, 2009 at 3:57 AM, Luke Goodsell luke.goods...@gmail.comwrote:
I'm trying to set up my machine to be able to run python scripts using
the PyMol API, but whenever I try to import the pymol module, I get the
following output:
. . .
I am running Mac OS X 10.5.6. I downloaded
Hi--
Can the roving mesh be used without changing the model appearance?
I'd prefer to just show the entire structure as lines only, but it
looks like the roving_detail setting controls both model and mesh.
thanks,
Nat
On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D.
l...@aecom.yu.eduwrote:
Every once in a while, I try to show a metal ion as a tranparent
sphere and inevetiably get stuck trying to make the tiny cartesian
coordinate system that appears at the center of the sphere disappear so it
Tim Fenn wrote something to do this a few years ago, but I don't think you
can ray-trace them:
http://www.stanford.edu/~fenn/pdb_aniso.py
On Mon, Sep 22, 2008 at 2:48 PM, Javier M. González
gonza...@ibr.gov.arwrote:
Hi all, could someone advise me on the simplest way to display anisotropy
Just use the (PyMOL) command line: save complex.pdb will save all objects.
You'll need to figure out what directory you're in first - by default, this
is probably /Applications, but cd ~ will get you home. (Hey Warren, could
this be changed so cd alone works, like in a Unix shell?)
(Or if you
I don't understand how these work at all. Is there any straightforward
way, given a structure's position and dimensions and the desired camera
position, to calculate the ideal position for the plane? How does
PyMOL decide where to put the planes? Right now I'm missing by a small
amount and
Yes, please. There are some structures that have to be generated by using
symmetry operations defined in the REMARK 350 lines in the pdb file
(example:
1jjy.pdb). The only way (I know of, if you know a better one, please tell me)
to
do this is going to http://pqs.ebi.ac.uk where the
Ideally util.ss could become a shell that would know (from the environment?)
if dssp or similar was installed, then either run dssp and parse the output
to assign the ss, or else run the ss asignment code in the current util.ss if
no other options were available.
I've basically done this,
programs. So I am in search of a solution. Can one manually create a
secondary structure assignment matrix to insert into the PDB file? I must
admit that as a novice I do not understand the formatting of the secondary
structure matrices that I have seen embedded in some PDB files. Is
Is there a way to keep my program 'quiet',
or I can customize the output message myself?
Depending on your OS and shell, something like this may work:
denethor:~ /usr/local/pymol/pymol.com /dev/null 2/dev/null
This works under Bash in any modern Linux distribution, from what I've
seen. I
quick question: I'm trying to do batch jobs on a server. Obviously,
there's no X or OpenGL installed. Is there any way to build PyMOL without
any graphical frontend, and just use it as a raytracer? I don't want to
go through the trouble of adding in these libraries...
thanks,
Nat
pymol.com -c scriptname
But you have to get your view first somehow.
I can't do this until I compile it; if I try running a pre-existing build
I get errors because one of the GL libraries isn't found. I've ended up
just installing GL on my system, but the crack technical wizards at SuSE
have
Hi--
I'm trying to render a large number of images of a trajectory
automatically. I have two problems:
1. There doesn't seem to be any way to manually speciify the view area.
Thus, if I want all images to be in the same frame of reference, I need to
load them all as different states of the same
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