[PyMOL] foggy state just for one of the molecules

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. [cid:image001

Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

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 3D

Re: [PyMOL] Renumber

Hi Annemarie, Thank you for the offer. I was specifically interested in doing it PyMOL. It was my longtime firmly held belief and I still do think that most of the PyMOL users are the biochemists that do not solve x-ray or EM structures. Hence the need to manipulate molecules, domains, numberi

Re: [PyMOL] renumber

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 go

Re: [PyMOL] renumber

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

Re: [PyMOL] renumber

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

Re: [PyMOL] renumber

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 Py

[PyMOL] renumber

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 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users

Re: [PyMOL] feature request

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

[PyMOL] feature request

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,

[PyMOL] label color

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&D | Ant

[PyMOL] aberrant behavior of mouse clicks in PyMOL

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 another

[PyMOL] PyMOL 2.0.4 mouse middle button

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 elect

Re: [PyMOL] tube width

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

[PyMOL] tube width

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 c

Re: [PyMOL] smooth-ribbon

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

[PyMOL] smooth-ribbon

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 attachmen

[PyMOL] coloring based on alignment

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.

Re: [PyMOL] measuring wizard

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

Re: [PyMOL] measuring wizard

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-

[PyMOL] measuring wizard

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 chosen.

[PyMOL] transparent figure

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 by

[PyMOL] white background

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

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

Re: [PyMOL] selecting all instead of just one aa

ubject: 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 ami

[PyMOL] selecting all instead of just one aa

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 elaborate scene to start it over. Thank you for help. Regards, Vaheh Oganesyan MedImmune, ADPE www.medimmune.com To the exten

[PyMOL] migration from monitor to wall mounted screen and projector

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 native

Re: [PyMOL] regarding APBS tools in PyMOL

. 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 with the

[PyMOL] regarding APBS tools in PyMOL

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 wo

[PyMOL] labels in version 1.7.0.1

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 generate

[PyMOL] saving

Dear PyMOL users, After upgrading my notebook to Win7 from XP 'save' function started to function differently. Before PyMOL would save everything in the directory where I'd launch it from. Now, by default, it goes to Win32. In some cases I can use 'save as' option and after few clicks get to th

Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

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 Sub

[PyMOL] color change upon ray-tracing

PyMOLers, Upon ray-tracing PyMOL v1.6.0.0 (Linux 64 bit) changes the color and the mesh line width of the electron density maps. How can I disable this metamorphosis? Thank you. Vaheh To the extent this electronic communication or any of its attachments contain information that is no

[PyMOL] APBS in v1.6.0.0

Hi PyMOLers, It looks like v1.6.0.0 treats APBS plugin differently, at least on my 64 bit Windows laptop. After setting grid and few seconds after clicking "Run APBS" button message appears in new window stating that program stopped working and needs to close the window. Also, it looks like I

Re: [PyMOL] sequence file extraction

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&#

[PyMOL] sequence file extraction

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 Files\PyMOL\PyMOL/mo

Re: [PyMOL] Ca trace

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

[PyMOL] Ca trace

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 inform

[PyMOL] two objects with synchronous rotation about their axes

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 that is n

Re: [PyMOL] APBS

-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 [2007-05-30 09:45] wrote: > I did not get much luck with those recommendations either. I was doing exac

Re: [PyMOL] APBS

s.py", line 975, in _execute_child raise child_exception OSError: [Errno 8] Exec format error == 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: Ogan

[PyMOL] APBS

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 b