Hello PyMOLers,
Happy New Year!
Is there a way to show one of the molecules on image in a foggy state
irrespective of depth-cue? I want to make an illustration showing how one
molecule blocks another for interaction with ligand/receptor.
Thanks in advance.
Vaheh Oganesyan, Ph.D.
Hi Thomas,
Can you also mention appropriate graphics cards that pair well with the Volfoni
hardware?
Thank you.
From: Thomas Holder
Sent: Tuesday, July 7, 2020 10:03 AM
To: David Krause
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Which 3D setup for a new installation? (Since
Thank you Jared.
From: Jared Sampson
Sent: Monday, June 15, 2020 4:47 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber
Hi Vaheh -
I wasn't saying it can't be done, just that pdbset is my preferred way to
handle renumbering when going
Jared,
Are you saying it cannot be done within PyMOL? The ccp4 option is well known.
Thanks.
From: Jared Sampson
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hi Vaheh -
Try `pdbset` from the CCP4 suite.
http
, is there a command that will ignore the
letters in the number field and renumber the amino acids in the order they
appear in the file.
Thank you.
From: Mooers, Blaine H.M. (HSC)
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: RE
Johnson
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hello,
The command shown on this page
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber>
is not one that comes with
Hello PyMOLers,
Wiki uses renumber command to alter residue numbers, but PyMOL doesn't
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?
Regards,
Vaheh
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PyMOL-users mailing list
Archives:
the residue color. I
vaguely remember something like this discussed x number of years ago, but do
not remember why not. Could label become property of the object and not just a
property of a session?
Thank you.
From: Jared Sampson
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh
Thomas and other PyMOL developers,
It looks as if we color the object name similar to the object color it will be
easier to distinguish which structure am I manipulating now. While models can
be colored, the names of the models can't.
Anybody else think it might be helpful?
Thank you.
Regards,
Hello PyMOLers,
In version 2.2.3 under Win upon ray-tracing label color changes. Is there a way
to prevent that from happening?
Thank you.
Regards,
Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics
AstraZeneca
R |
Hi All,
I’m experiencing very annoying behavior of mouse clicks when there are more
than one molecule in ASU. Upon opening the window cartoon mode is showing. If I
click on the part of first listed molecule then all look good. However, if I
click on the part of the second molecule then
Dear all,
In recent past in PyMOL one could move the center of the screen using mouse
middle button (clock-hold-move). Now middle button invokes zooming. Would
anyone know how the center can be moved now?
Thank you.
Regards,
Vaheh Oganesyan, PhD
www.medimmune.com
To the extent this
Found it: set cartoon_tube_radius, number
Regards,
Vaheh Oganesyan
www.medimmune.com
From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, August 22, 2017 11:52 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] tube width
Hello PyMOLers,
When presenting in cartoon
Hello PyMOLers,
When presenting in cartoon tube mode how one can change the tube width?
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its attachments contain
information that is not in the public domain, such information is
Hey PyMOLers,
Would you know how to show smooth ribbon?
I can use cartoon_oval_length command to get almost what I want, however only
for helices. Thanks in advance.
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its
Found:
hide everything
show cartoon
cartoon tube
set cartoon_tube_radius, (number)
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
-Original Message-
From: Oganesyan, Vaheh
Sent: Monday, November 23, 2015 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: smooth-ribbon
Colleagues,
Was wondering if there is a functionality built in PyMOL for coloring of the
molecule based on sequence identity/similarity? This topic was discussed
briefly in 2007 and the answer was from Robert Campbell suggesting using his
scripts. Seems to be a good tool to have for anyone.
Thank you reply, Thomas.
Invoking
alter all, ID = index
didn't help.
Regards,
Vaheh Oganesyan
www.medimmune.com
-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Friday, October 02, 2015 4:05 PM
To: Oganesyan, Vaheh
Cc: pymol-users
Hi PyMOL users,
In measuring wizard I'm consistently facing an annoying property that allows me
to measure only one distance between object1 and symmetry mate invoked through
symexp command. Whenever I click another atom on symmetry mate a completely
different atom from object1 is being
Thank you. Will upgrade.
Regards,
Vaheh Oganesyan
www.medimmune.com
-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Friday, October 02, 2015 4:34 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] measuring wizard
Hi
Hello PyMOLers,
I’m wondering if the figure can have transparent background?
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its attachments contain
information that is not in the public domain, such information is considered
Dear PyMOL developers,
The latest incentive version of PyMOL 1.7.6.0 fails to show residue numbering
in the sequence in the upper part of the screen when the background has been
chosen to be white (i.e., it does not change the color of the font) . Also,
unlike previous versions, after choosing
: Re: [PyMOL] selecting all instead of just one aa
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
I see. Great help, Thank you.
Regards,
Vaheh
8-5851
From: Matthew Baumgartner [mailto:mp...@pitt.edu]
Sent: Thursday, September 25, 2014 3:01 PM
To: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selecting all instead of just one aa
In the bottom right it says
Hi all,
I'm planning migration from CRT monitor to wall mounted screen with projector
that will support stereo. Mid-range emitter like AE125 for small office (4m by
4m) like mine is sufficient. I'm looking for advise on projector and screen. It
looks like ViewSonic PJD7820HD ($699) with
.
Regards,
Vaheh
8-5851
From: Schubert, Carsten [JRDUS] [mailto:cschu...@its.jnj.com]
Sent: Tuesday, April 22, 2014 5:59 PM
To: Oganesyan, Vaheh; pymol-users
Subject: RE: regarding APBS tools in PyMOL
Hi Vaheh,
my recollection is a bit hazy, but I remember having some issues
Colleagues,
The latest PyMOL version 1.7.0.3 looks like having issues with molecule size
when APBS is being used. I’m loading whole molecule consisting of ~500 aa and
APBS plugin after setting up the grid and after starting APBS run few seconds
later opens a window with message: APBS stopped
PyMOLers,
I've installed PyMOL version 1.7.0.1 on my new laptop running Win 7, 64-bit.
Number of issues:
1. Side-by-side stereo shows only one side in cross- or wall-eye mode and both
when ray-traced;
2. Labels can be generated, but I can move in editing mode only the label that
was
Engin,
If you go to Edit_all and change the seq_view_label_color to grey the numbers
will become visible with white bkgr.
Vaheh
-Original Message-
From: Engin Özkan [mailto:eoz...@stanford.edu]
Sent: Wednesday, September 04, 2013 4:40 PM
To: pymol-users@lists.sourceforge.net
I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to
extract the sequence info.
I'm typing save objectname.fasta in old version and get the fasta file. In
1.4.1 it complains
=
Traceback (most recent call last):
File C:\Program
Never mind. After restarting the computer fasta file is being written.
Vaheh
-Original Message-
From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, December 27, 2011 11:16 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] sequence file extraction
I'm
Thank you Warren,
That exactly is what I wanted.
___
Vaheh
From: Warren DeLano [mailto:war...@delsci.com]
Sent: Wednesday, March 04, 2009 8:45 PM
To: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Ca trace
Vaheh
Colleagues,
If the PDB file contains only Ca atoms and PyMOL shows them as
non-bonded atoms what one should do to display them as a ribbon? The
1rh2 entry is one of them.
Thank you.
___
Vaheh
To the extent this electronic communication or any of its attachments contain
Is there a way in pymol to create such two objects that will rotate with
mouse each around its own axis?
I hope I'm clear.
Oganesyan Vaheh
Antibody Discovery
MedImmune, Inc.
___
To the extent this electronic communication or any of its attachments
contain information
-boun...@lists.sourceforge.net]on Behalf Of Robert
Campbell
Sent: Wednesday, May 30, 2007 11:06 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
Hi Vaheh,
* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
I did not get much luck with those recommendations
==
Comments and solutions are appreciated.
VO
-Original Message-
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
I also
I'll appreciate some help with APBS plugin.
In both Win or Lin the same error appears:
ObjectMapLoadDXFile-Error: Unable to open file!
After googling with this error message I've checked all of the
possibilities:
Map file is loaded OK, folders with apbs.exe and psize.py files do not
contain
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