Hi,
Does anybody have suggestions for the simplest way to script loading an
apbs grid and displaying the molecular surface colored by charge
(possibly changing the low/high values as well)?
I can do this interactively, but have come up blank trying to script this.
Thanks,
Pete
with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or
31 MB after reducing objects I do not need for the figure production).
If lack of memory is the problem, try loading your scene manually or
through a script instead of using a session file. For reasons I don't
recall at
I am trying to fire up a script with pymol -r doit.pml
pymol doit.pml should be sufficient (no need for -r).
File doit.pml, line 2
select resname SOL
Unless the syntax has changed, try 'select resname, SOL'. Does this
script work when run from an already started pymol?
Pete
Hi,
I have experimental phases/map_coeff's in a .phs file. Can anyone tell me
how to most easily get them read read into PyMol to display electron
density? I assume I need to convert the file somehow first, I usually use
mapman for this utility but don't see an option for .phs files.
how would I go about adding a package to the
$PYMOL_PATH/ext/.../site-packages w/o screwing up the install?
For most packages the mechanism is python setup.py install. Would this work
to run this from within pymol?
With my usual way of installing pymol is to build most of the
dependencies
I wouldn't claim it's necessarily the best way, but if I've had decent
luck with scripting the transitions (either pymol or python) to generate
a set of images. From there, it's fairly easy to encode a movie with
ffmpeg or mencoder.
But it probably depends on the type of movie you're trying to
Is it possible to load a map to only cover the molecule and not the
complete asymmetric unit? Or is this only possible at the time of
creating the map?
Yes and no. For displaying a map, if you give a carve option to isomesh
or isosurface, it'll only display around a molecule (or other
The way I use (which I'm sure could be improved), is to get the color
index with iterate sele, print color, followed by print
cmd.get_color_index( idx ). This gives you the rgb tuple for the color
on 0-1 scale.
I'd be curious to know if there's a way to avoid the iterate step, or
get the color
Looks like you need to install the appropriate python-dev package (or
otherwise point setup.py to the appropriate include directory if you
build python from source).
Vivek Ranjan wrote:
I downloaded the latest pymol by using the following command:
svn co
Hi Sean,
I ended up using light, [1,5,-100]. I know these are X,Y,Z
coordinates, but relative to what origin and in what units? After
wasting way too much time, I concluded that the values might be
Angstroms relative to the eyes of the current view. In examples I
found online, the
Does anyone have any thoughts?
Two things to try that may or may not help:
1. Check if the problem persists when running pymol in single-threaded
mode (cmd.set('max_threads',1)). libpthread in the trace might
indicate that one of the libraries is having issues with multiple threads.
2. On
Hi,
From a security perspective, it seems like the ideas on the wiki page
are all related to securing the remote source. It might be worth
considering what could be done to minimize how much pymol has to trust
the remote source or the network.
A few ideas:
- Sandboxing would be ideal,
I don't know if there's a way to do this from within pymol, but it's
fairly straightforward to do using mapman (from ccp4) - or your favorite
map utility.
Pete
Tatyana Sysoeva wrote:
Dear Pymol experts!
I am going to make a presentation with running Pymol during it. I would like
to show
Another approach would be appending to sys.path, and loading the scripts
with import instead of run.
Arne Dieckmann wrote:
That is a hot tip. However, can I also specify some path that would tell
pymol the location of my scripts? I have a number of scripts that I need to
call while already
isomesh [mesh name], [map name], 6.0
Manas Sule wrote:
Is there some way to show electron density at 6 sigma and above in pymol
especially for metal ions like in Coot?
Manas
--
All the data continuously
Hi John,
I don't think you need a re-install. My take on the problem is that
using the repositories installs the pymol libraries to the system python
(not sure offhand which that is for ubuntu 11.10). But pymol is
apparently trying to start up with /usr/bin/env python, which is
picking up
I've run into similar situations in the past, although in my case
usually due to large maps (a 3.5 MB pdb file, or even a set of them,
typically requires less memory than a ~50MB electron density map). In
my experience, it's much better to load things from scripts (pml) rather
than storing
Anyone thinking about upgrading to 1.5 should be aware that there's a
bug in loading session (pse) files containing map objects. Loading pse
files (I checked ones created with 1.2 or 1.4) deletes these objects and
reports an error: ExectiveSetSession-Error: after
Hi Gudrun,
But the mesh is black afterwards and not anymore blue.
You may want to check your light position, or try a slighter blue.
Is there a chance to keep the color and have less dominant lines for the mesh?
I'm not artistically skilled enough to know about less dominant lines,
but the
It may be worth trying pymol 1.4 (instead of 1.5) - although this
shouldn't make a difference, it might provide some more information (you
also mentioned that you've got a large scene - depending on composition
1.4 may use less memory than 1.5).
You may also want to try using a pml script vs
Hi Vasan,
Changing the sampling of the map would require re-calculating it on a
different (coarser or finer) grid. This would have only incidental
effects on normalizing the map values.
Hope this helps,
Pete
Srinivasan Rengachari wrote:
Dear Pymol Users,
I am a basic
The handling of density maps changed with (I believe) version 1.5 -
earlier versions would just load the map as given, later ones appear to
try to do symmetry expansion (even if the map isn't covering the ASU).
I've seen this result in a similar error message when loading session
files (with
Unless the values have changed since I last checked the documentations,
by default pymol contours maps at 1.0 sigma and coot defaults to 1.5
sigma (for non-difference maps).
Pete
Yarrow Madrona wrote:
Hi,
When I display ccp4 maps in pymol they look a bit larger than I am used to
seeing in
I suspect this depends on the browser you're using. If you're serving
the PDB files with an appropriate MIME-type, and the browser is
configured to open files of those types with pymol, then things should work.
That said, going through pymol through a web interface seems like it
might be more
Hi James,
Assuming your going from the pymol wiki loadDir script; you'd need to
change glob(c) loop (sort the list in your preferred order before the
loop, rather than using the result list unmodified).
If I'm understanding your problem correctly (numbered pdb files being
loaded as 1.pdb,
Hi Blake,
I haven't used the autodoc plugin, but from your stack trace (and a
quick check of the numpy install on my system) you may be able to
resolve this by changing the import multiarray statement to from
numpy.core import multiarray.
Hope this helps,
Pete
Blake Mertz wrote:
Hello,
I
On Tue, Jan 28, 2014 at 4:02 PM, Pete Meyer pame...@mcw.edu wrote:
Hi Blake,
I haven't used the autodoc plugin, but from your stack trace (and a quick
check of the numpy install on my system) you may be able to resolve this by
changing the import multiarray statement to from numpy.core import
For what it's worth, for teaching/training (and general research use), I've
always recommended using pml scripts instead of pse sessions. Turning on
logging can help with tracking what should end up going into the pml.
It's a little more work, and requires a little more forethought - but it's
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