On Sun, May 23, 2010 at 6:33 PM, Maia Cherney wrote:
> Thank you for your help. However, I have 4 Mg ions in the au, so all Mg
> ions (and all coordinated ligands) got connected. I need only coordination
> for one Mg.
>
Then you need to qualify the selection with the residue number, and repeat
On Sun, May 23, 2010 at 3:55 PM, Maia Cherney 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 longer length to ca
On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon 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 chimera to ge
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 d
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 foc
On Tue, Mar 23, 2010 at 12:48 PM, hari jayaram 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
> select r 22 ,
On Sun, Feb 14, 2010 at 4:39 PM, David Hall 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. Callbacks that we can bi
On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera 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
color red, elem o
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/bu
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 cre
On Thu, Dec 17, 2009 at 10:54 AM, Jason C Porta 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 points
> so that t
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney 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, Jul 21, 2009 at 12:23 PM, Paola Beassoni wrote:
> Dear Pymol Users,
> i am working with some pdb files with no secondary structures assignments
> embedded on it. Then when i try to see my molecules on cartoon diagrams, i
> see the secondary structure different to another programs, VMD for
On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow 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 through pymol,
On Fri, May 1, 2009 at 3:57 AM, Luke Goodsell wrote:
> 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 MacPyMol 1.1r1 from
> ht
On Wed, Apr 22, 2009 at 6:37 PM, Craig Smith wrote:
> I was looking at the demos in pymol (wizard --> demo) and saw
> interesting features called roving detail and roving density. I
> looked in the manual on how to do this feature but couldn't find it.
> Could anyone point me in the right direct
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 Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow wrote:
> I'm making a gallery of protein molecules for my PhD thesis. I'd like
> to find an automatic way to ensure that all of the ray traced images
> have the same scale. Is there an easy way to do this?
>
Translate every model so that the center i
On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D.
wrote:
> 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
> doesn't "show
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"
wrote:
> Hi all, could someone advise me on the simplest way to display anisotropy
> ellipsoids in PyMOL
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 y
> I have downloaded the version (0.79.dmg.gz) of the PyMol package
> suggested by Luca Jovine, but don't know how to get a working version of
> Python installed. The only links I can find are to Python .exe files
> for versions 2.1 and 1.5.2, and I have no idea which of the other
> downloads
> The best way to avoid "derivative work" concern is to code in a "clean room"
> fashion, without reference to someone else's code. In principle, this could
> be done working from the original paper(s) that describe an algorithm.
I assume this is what authors of other packages have done in the pa
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 at
> 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 thi
> 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
> 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 t
> 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.
> 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
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
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 o
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