Hi,
You run the command 'run colorbyrmsd.py' in the Pymol command line. That
initializes the function in pymol. If everything goes well, you
shouldn't see anything (no errors). Then to use the command, type just
'colorbyrmsd [args...]' into the command line.
You can see the usage
Hi Amali,
For adding hydrogens, I have found that PyMOL does an OK job normally,
but if you need more accurate placement of hydrogens, I can recommend
using Reduce.
http://kinemage.biochem.duke.edu/software/reduce.php
HTH,
Matthew Baumgartner
On 11/11/2015 02:06 AM, Osvaldo Martin wrote
Hi,
I googled for the pymol wiki to check it out and I saw a message in the
search results that says: "This site may be hacked." Do you know why
that is?
On 09/09/2015 07:40 AM, Osvaldo Martin wrote:
Hi Jason,
Thanks very much for the effort! Now the Wiki is far more useful than
before!
Hi,
I'm using pymol 1.7.4 from the SVN. When I use the File Log... feature
to log the commands that I use to a file the output commands are not
recognized when I do File Run... in a new session.
To reproduce:
Open a new pymol session.
File Log... log.pml
Change the background to white.
Hi,
I had problems with the retain order setting as well. The autodock vina
pulgin turns it on. Unload the plugin to fix it, or manually set it
after plugins are loaded.
Matt
On 4/22/15 8:56 PM, Thomas Holder wrote:
Hi Spencer,
please check your retain_order setting, it should be off
past 1.7.4.
On 4/8/15 2:38 PM, Thomas Holder wrote:
Hi Matt,
PyMOL session files are in general not forward compatible.
See for example:
https://sourceforge.net/p/pymol/mailman/message/31070268/
Cheers,
Thomas
On 08 Apr 2015, at 14:19, Matthew Baumgartner mp...@pitt.edu wrote:
Hi
Hi,
I'm running pymol 1.7.5.0 (r4114) from the SVN and I can't load pse
files created in 1.7.5.0 in any older version of Pymol.
When I create a pymol session file where I fetch a PDB, show as
cartoons, and save the session (see
https://dl.dropboxusercontent.com/u/22529812/test.pse) and open
Hi,
I'm getting compile errors on the latest SVN build (4111).
Any help would be appreciated.
Thanks,
Matt Baumgartner
$ sudo python setup.py build -j 1
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Hi,
I'm using pymol 1.7.4.0.
The A assign sec. struct. command doesn't seem to work when you call it
on a group. It works fine on the objects in the group individually, but
it doesn't apply the command to the objects when called from a group.
Thanks,
Matt Baumgartner
Hi Adam,
You can retrieve them using the iterate method.
See: http://pymolwiki.org/index.php/Color#Getting_Atom_Colors
HTH,
Matt Baumgartner
On 2/27/2015 4:28 PM, H. Adam Steinberg wrote:
I am creating a new PyMOL session and I have to match the colors that
someone else used in a different
Yes, I've been having this problem for a while.
I contacted Jason Vertrees about it a while ago, but never heard back
from him.
However, when I search color (an exact article title) I actually do go
to the page.
In addition, if you search for a something that doesn't have a page in
the
Hi,
I've discovered a (relatively minor) bug in the Save Molecule... dialog
box. This happened because I always have tons of windows up on multiple
monitors and it got lost.
To reproduce:
Go to File Save Molecule...
Don't close the window, and do it again
Go to File Save Molecule...
Now you
]
cmd.load_cgo(sph2, sph2, 1)
Cheers,
Osvaldo.
On Tue, Jan 20, 2015 at 7:19 PM, Matthew Baumgartner mp...@pitt.edu
mailto:mp...@pitt.edu wrote:
Hi,
I'm having some trouble using CGO spheres. When I create one, it
is not visible in the viewer, although there is an (apparently
Hi,
I'm having some trouble using CGO spheres. When I create one, it is not
visible in the viewer, although there is an (apparently empty) object in
the object pane. It is somewhat confusing because with some parameters
the spheres ARE visible when ray tracing, although they are still not
Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image{}.png.format(str(i).zfill(4)).png! Please check
directory...
Thanks for your time,
Brenton
On 7/01/2015 12:33 AM, Matthew Baumgartner wrote:
The problem that you have is not a PyMOL problem, but a bug in your
code. You didn't change the file
Hi,
When you ray trace you can specify the dimensions of the resulting image
in pixels, eg:
ray 600,800
You can also set the resolution when saving the png file:
png image.png, dpi=300
HTH,
Matt Baumgartner
On 01/06/2015 12:39 AM, Brenton Horne wrote:
Hi,
I'd like to know how to create a
(str(i).zfill(4)), dpi=300,
ray=1)
On 7/01/2015 1:33 AM, Matthew Baumgartner wrote:
Is it in your for loop?
for i in range(2,61):
rotate y, 6
cmd.png(C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image{}.png.format(str(i).zfill(4)), dpi=300,
ray=1
in the correct location without that directory error.
On 7/01/2015 2:11 AM, Matthew Baumgartner wrote:
I think that is because that the directory there doesn't exist. I
think I made a copy paste error of your directory structure.
Please double check, but from your earlier email, it was
C:\Users
Hi,
Just to chime in, you might need to call 'sort' and/or 'rebuild' after
using the alter command to see the changes.
Matt Baumgartner
On 11/20/2014 08:20 AM, Osvaldo Martin wrote:
Hi Erica,
I think something like:
alter name ca, vdw=10
should help. Change 10 for the value you want.
Hi,
Can you check to see if the python bindings are compiled openbabel?
On the bash command line, run the command 'python' to get an interactive
shell and then run 'import openbabel'.
Matt
On 11/12/2014 07:14 AM, Douglas Houston wrote:
Hi all,
I installed Optimize.py, now when I start Pymol
Hi Cedric,
Check out the Launching PyMOL from Python programs section from here:
http://www.pymolwiki.org/index.php/Python_Integration
HTH,
Matt
On 10/24/2014 02:02 PM, Cedric wrote:
Hi,
I know how to write small scripts in pymol and then call them within pymol.
But I am not sure how to
,
Thomas
On 20 Oct 2014, at 19:10, Matthew Baumgartner mp...@pitt.edu wrote:
Hi,
I updated pymol to r4098 and now it crashes on launch. I'm assuming that
it was something I did, but I can't figure out what.
Thanks for your help,
Matt
$ pymol
Traceback (most recent call last):
File
Hi,
I updated pymol to r4098 and now it crashes on launch. I'm assuming that
it was something I did, but I can't figure out what.
Thanks for your help,
Matt
$ pymol
Traceback (most recent call last):
File /usr/local/lib/python2.7/dist-packages/pymol/__init__.py, line
71, in module
Hi,
Go to the Mouse Menu Selection Mode Residues
Matt Baumgartner
On 09/25/2014 01:48 PM, Oganesyan, Vaheh wrote:
All,
During my PyMOL session I’ve “accidentally” entered into a mode when
by clicking one amino acid whole chain becomes selected. How can I
turn it off? It is a quite
? Just
curious.
/Regards,/
//
/Vaheh/
/8-5851/
*From:*Matthew Baumgartner [mailto:mp...@pitt.edu]
*Sent:* Thursday, September 25, 2014 2:19 PM
*To:* pymol-users@lists.sourceforge.net
*Subject:* Re: [PyMOL] selecting all instead of just one aa
Hi,
Go to the Mouse Menu Selection Mode Residues
Hi,
you can just use the 'angle' command.
cmd.angle('angle1', 'start_point', 'end_point', a)
To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')
HTH,
Matt Baumgartner
On 09/24/2014 06:35 PM, rainfieldcn wrote:
Hi
Use the -h flag with grep to suppress the filename.
Also, you don't need to pipe to cat, you can write directly to the file.
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
On 09/04/2014 10:38 AM, James Starlight wrote:
..and one question about grep (really didn't find
it
produce pdb with both merged layers (and its backbone trace only) as
the result if -o flagg is provided)
Kind regards,
Gleb
2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu
mailto:mp...@pitt.edu:
You can use sed
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed
Hi,
When you call cmd.extend(), it does not add the function to pymol.cmd.
Just call it directly:
Change
pymol.cmd.align_all_to_all()
to
align_all_to_all()
You may need to import it if you haven't already (and make sure it is in
the PYTHONPATH).
HTH,
Matt Baumgartner
On 09/02/2014 10:38
Hi,
I ran into a bug with the find polar contacts function (distance with
mode=2) today. The problem arises when I was trying to find the hydrogen
bonds between a ligand and a receptor that had been processed with
reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A
bug/feature of
,
this was a bug with the dynamic_measures setting. It was fixed in PyMOL
1.7.0. So please upgrade PyMOL or read this old post for workarounds:
http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501949e8.2080...@users.sourceforge.net/
Cheers,
Thomas
On 27 Aug 2014, at 10:30, Matthew
as possible.
Cheers,
Thomas
On 23 Jul 2014, at 13:06, Matthew Baumgartner mp...@pitt.edu wrote:
Hi, I am using pymol from the SVN, and I have run into a problem when
using revision 4083.
When loading an sdf file of small molecules, pymol segfaults with the
following error:
/usr/local/bin
Hi, I am using pymol from the SVN, and I have run into a problem when
using revision 4083.
When loading an sdf file of small molecules, pymol segfaults with the
following error:
/usr/local/bin/pymol: line 3: 29872 Segmentation fault (core
dumped) /usr/bin/python
Hi,
If you don't need the GUI you can access your command using the extend
command.
In your script, put something like:
from pymol import cmd
def foo(bar):
print bar
cmd.extend('foo', foo)
Then in pymol first use the 'run' command to have pymol read your
script, and then call the
Hi,
Adding to thread.
I'm using pymol 1.6 (built from svn yesterday) on Ubuntu 13.04.
I've noticed that the selection indicators are not working properly.
Steps to reproduce:
#launch ignoring the config file
pymol -k
#in pymol
fetch 1YCR
Then open sequence viewer and select a range of
Hi,
I may have found a bug in the way pymol interprets connectivity of
atoms. I noticed this in one pdb structure that I am working with 1RV1.
Steps to reproduce:
fetch 1RV1
#extract one of the ligands to it's own object
extract 'lig', /1RV1//A/110
#add hydrogens
h_add lig
Now look at atom C2
Hi,
When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr'
the hydrogens are added to the structure as expected, but they are put
in the sequence viewer as their own residue with the same chain.
This is problematic for several reasons, one is that it breaks
selections, when I
Hi Tim,
You can use two dashes on the command line, like:
pymol -r get_neighbors.py -- ALA
And then access them using sys.argv in your script.
For example: save the following as tmp_pymol.py and run: 'pymol -r
tmp_pymol.py -- ALA' ( without quotes)
from pymol import cmd
import sys
def
this. Can you please send us some
screenshots of what you'd like to see implemented?
Cheers,
-- Jason
On Tue, Oct 23, 2012 at 4:16 PM, Matthew Baumgartner mp...@pitt.edu wrote:
Hi,
Is it now possible to have wire mesh cgo object spheres in pymol?
I found this thread from a while ago (2004
, Matthew Baumgartner mp...@pitt.edu wrote:
Hi,
Is it now possible to have wire mesh cgo object spheres in pymol?
I found this thread from a while ago (2004) but googleing, I didn't
find anything more recent.
The one sort of work around that I though of was to create pseudo-atoms
and somehow
Hi,
Is it now possible to have wire mesh cgo object spheres in pymol?
I found this thread from a while ago (2004) but googleing, I didn't
find anything more recent.
The one sort of work around that I though of was to create pseudo-atoms
and somehow modify their radius and then show them as
Hi,
I wrote a short script that I am going to use in pymol. I need to parse
a json file and then display the contents in some manner. It works just
fine in Ubuntu 12.04, but when I try it on OSX, it doesn't work. The
problem that I am having is that when I try `import simplejson` or
`import
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