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For some reason, the people doing brew have decided to stop supporting
compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain
pymol cannot use tcl-tk with aqua.
If you already had pymol installed, this seems to eliminate the external
gui. If you didn't, new installations of
Hi,
pymol external gui menus missing, I have compiled pymol in mac os by using
brew.
Anyone can provide some suggestions?
Jacky
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Associate Professor
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National Engineering Research Center for Antibody
This worked! Thank you Leandro and Jed!
From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone
Sent: Tuesday, April 4, 2017 11:35
To: Vivien Schoonenberg <vivienschoonenb...@gmail.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] (no subject)
Try
Try using
remove not alt +A
to remove alternative conformations.
Jed
On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:
> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
>
Hi,
You probably have a pdb file which has multiple possible conformations
for some residues. You can check this by visual inspection of such
residues. They have two side chains coming from the same CA. In the text
file you can see the conformations marked as A and B in the residue name
Hi there,
I'm saving the sequences from each chain of the PDB via pymol with
>>save something.fasta, chain A
This is the same sequence that is shown in pymol and seems to correspond to
the structure I am looking at.
However, when I loaded new B-factors in my structure, I noticed
Dear all:
It appears that pymol only interpolates motions that include rotations by
moving the object along an arc. I would like to make a movie that does not
do this, but rather, moves the object along a straight line while rotating
the object. Unfortunately, I'm absolutely at a loss about how I
Hi!
What is the command for superimposing a .gro file and a .pdb file in PyMOL?
I tried opening the .gro file and then loading the .pdb file. Consequently,
I could only see the latter and not the former.
Thank you in advance!
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On 04/19/2015 02:08 AM, leila karami wrote:
Dear Marcelo
Thanks for your quick answer.
Unfortunately, I can't open the link (https://www.pymol.org/citing) you
suggested me.
perhaps your firewall or browser is blocking the https: connection or rejecting
the certificate?
Try http:
Hi Leila,
No problem, here is the content of the site. If you need the reference manager
files (BibTex or EndNote files), I am happy to email them to you as well.
Cheers,
Marcelo
Citation Format
Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the
version number in
Dear Marcelo
Thanks for your quick answer.
Unfortunately, I can't open the link (https://www.pymol.org/citing) you
suggested me.
Thanks in advance.
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PyMOL
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JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
AxPyMOL
The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4
Schrödinger, LLC.
On Apr 18, 2015, at 11:08 PM, leila karami
Hi Leila,
Take a look at the link below:
https://www.pymol.org/citing https://www.pymol.org/citing
Cheers,
Marcelo
On Apr 18, 2015, at 11:55 PM, leila karami karami.lei...@gmail.com wrote:
Dear all
How to cite pymol in my paper?
Thanks.
Dear all
How to cite pymol in my paper?
Thanks.
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Hi all,
I wonder if it's possible to fill the space (like in the case of
nucleotide's ring) between three arbitrary/selected atoms.
I'm trying to render an object which is not a biomolecule so
cartoon_ring_mode is no use for me.
Cheers,
pawel
Hi Aliya,
yes, likely there is a clash. But that's hard to tell without seeing your data.
Cheers,
Thomas
On 01 Jul 2014, at 11:34, Aliya Holland holland_al...@wheatoncollege.edu
wrote:
Hello,
I just created an animation of a conformational change of a specific domain
on a molecule.
Hello,
I just created an animation of a conformational change of a specific domain
on a molecule. During the animation the domain rotates just as it should,
however other parts of the molecule moves with the conformation change. I
was wondering if that was part of the PyMOL programming or if
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Hi Nina Marie,
I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
runs fine on Windows 8.
Cheers,
Thomas
Wolf, Nina Marie wrote, On 03/19/13 21:11:
Hi,
I recently upgraded my computer to windows 8. Since then, pymol will not
open. Is the latest version of pymol
Hi,
I recently upgraded my computer to windows 8. Since then, pymol will not
open. Is the latest version of pymol incompatible with windows 8? Or is
there something I can do to get it working on my computer?
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receiving emails.
Thank you.
M. Hall
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Hi Mary,
Just a hint for any future lists you might be on: most modern email
lists, including pymol-users, have footers with links to subscription
options. You simply click that to get to a subscription page where you
can unsubscribe.
In this case, I removed you from the list to save you the
I have downloaded the pymol linux version in my kubuntu 12.4 , but while
installing, it is asking for -Kubuntu 11.04 _Natty Narwhal_ - Release i386
(20110427.1). Please suggest me what shoul i do???
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Deal list,
I would like to calculate partial charges of my pdb. Is it possible to do it by
Pymol? If not, Is anyone know any server
or software to do it?
I have another question too, when aligning two structure in Pymol, there is a
RMSD for the total structure, is there any command to
Hi Noloofar and Lina,
I would like to calculate partial charges of my pdb. Is it possible to do it
In pymol:
Action- compute - partial charge sum
this doesn't calculate partial charges, sorry.
This does:
Action - generate - vacuum electrostatics
But better would be to use pdb2pqr:
Please stop sending me daily emails its very annoying, i would
appreciate if you erase me from the list
Thank you!
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If you don't want them anymore you need to unsubscribe.
Click on Show details at the top of this email. Click then on:
unsubscribe Unsubscribe from this mailing-list
That will do the magic.
On Fri,
On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann juettem...@gmail.comwrote:
Hi Chris,
the emails are only sent to you because you subscribed to the pymol-users
list.
If you don't want them anymore you need to unsubscribe.
Click on Show details at the top of this email. Click then on:
PS is it possible to run two versions at once on a PC (a quick test failed)
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
Hi,
I think that it probably is possible to do this from within pymol, and
probably quite convenient for single molecules.
However, there are two other possible approaches, which would be
helpful for multiple molecules.
Firstly, there is a program called 'dang' made by the Richardson group:
@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hi,
I'm looking for a way to calculate set of torsion angels from selected residues
(for example Chi1 dihedral of all His residues). Is it possible to write PyMOL
script for such task ? Any hints to write such script will be appreciated!
Thank
Hello all especially Warren,
What does
Sorry, time-sequential stereo 3D not available
mean. It is printed out when I start pymol. I am using current HEAD.
Thanks justin
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Research centre Juelich GmbH,
5:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hello all especially Warren,
What does
Sorry, time-sequential stereo 3D not available
mean. It is printed out when I start pymol. I am using current HEAD.
Thanks justin
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Institute
hasg...@yahoo.com
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Hello,
I would like to ask about building phosphate group at Tyr residue. Is there
any posibility to do it at PyMOL programe?
Thank you for answer
Martin Sztacho
Dear Users,
I would like with a simple script to export
some data regarding distances.
Do any of you know how to write an output with
all distances that I set up?
Thanks in advance
Giacomo
Giacomo Bastianelli
EIMID Ph.D Fellow (www.eimid.org http://www.eimid.org/ )
Marie Curie EST
hello all
pymol draw lines between near atom with no real connection between them!
I wanted to know if there is a way to prevent pymol of making the
bonds (lines)
between atom and that pymol will connect atom only by a specific request
(like a connect line in the pdb file)
CONECT 416 778
@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hi Dear Pymol-users,
Sorry about this long message. I am struggling to configure X Windwo to
enable stereo.
Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One
monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb
Hi Dear Pymol-users,
Sorry about this long message. I am struggling to configure X Windwo to
enable stereo.
Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One
monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try to
configure X widnow to enable stereo with
Hello all,
I am a new PyMOL user trying to prepare figures for publication. I'm confused
about the difference between the isomesh level of the 'mesh' in PyMOL and the
contour level of the electron density map that I read in from CCP4. For
example, for one of my figures I created a 3sigma
dear sir iam a pymol user, do we can find area volume of active site in pymol if we can, just tell me how to do it thanking you srilathaThanksRegardssrilathapotlapellyMScBiotechnology
Hi,
for this purpose I have used caver program. You can download it free
of charge from here http://loschmidt.chemi.muni.cz/caver/download.php
I hope this help
Regards
andrea
2006/3/27, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com:
dear sir
iam a pymol user, do we
Hi,
I found out how to do ... something ... like this the other day.
Hi pymol community
I would like to recapitulate the crystal packing arrangement of a
protein structure to look for neighbor interactions. Is it possible
to do this in pymol? If so, please provide me some insight.
Thanks,
Blanton Tolbert
Graduate Student
University of Rochester
Tolbert
Sent: Sat 2006-03-04 15:01
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hi pymol community
I would like to recapitulate the crystal packing arrangement of a
protein structure to look for neighbor interactions. Is it possible
to do this in pymol? If so, please
dear all can we superimpose structures in pymolThanksRegardssrilathapotlapellyMScBiotechnologyDrugdiscovery,#450,4thDMain,12thcross,Mahalakshmipuram-560086BangaloreOffice:+9180-23495461-64Extn.-1029
Hi
try align or fit
regards
andrea
2006/3/3, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com:
dear all
can we superimpose structures in pymol
Thanks Regards
srilatha potlapelly
MSc Biotechnology
Drug discovery,
#450,4th D Main, 12th cross,
Mahalakshmipuram - 560086
To all:
I am new to PyMol, and to structure programs in general. I am trying to
build a beta sheet from a peptide molecule in the pdb. I can't seem to
load more than one molecule at a time, and I do not see any
instructions related to it in the manual. I am running version 0.98
beta 32 on a
There is a very useful functionality in Sybyl, whereby
the user can merge a residue from one molecular
area, into another molecular area. The residue then
becomes a part of the latter moleculear area, without
deleting it. I wonder whether there is such a
functionality in PyMol.
As an example,
] On Behalf Of
Joseph Fernandez
Sent: Sunday, September 25, 2005 11:19 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
There is a very useful functionality in Sybyl, whereby the
user can merge a residue from one molecular area, into
another molecular area. The residue
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang
Sent: Sunday, July 24, 2005 8:43 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hi, everyone,
I used symexp
On Sunday 24 July 2005 05:42, yi zhang wrote:
cmd.symexp('sym', 'obj', 'obj',10 )
of course, I can manually save each symmetry-related
molecule to *.pdb file by clicking save molecule
button, but how can I write a script to save all of
them or part of them? the symmetry-related objects
are
Hi, everyone,
I used symexp command in pymol to generate
symmetry-related molecule, something like:
cmd.symexp('sym', 'obj', 'obj',10 )
of course, I can manually save each symmetry-related
molecule to *.pdb file by clicking save molecule
button, but how can I write a script to save all of
them
Hi,
I've just started using PyMol for making some figures. I'm very happy
that it is so easy to use. However the resolution of my pictures is
very bad even after rendering them. When I print them they are very
pixellated. I'm sure there is something I'm not doing right. Any help,
suggestions
Check out the post on High end graphics. This will solve the problem.
Basically you can ray-trace your molecule at a resolution bigger tahn
teh screen size and then cut it down afterwards effectively generating a
high resolution graphic from a 72 dpi starting point
Cheers
J
Kolli, Madhavi
Hello!
I have 2 questions:
1) What is the correct/common email address to send your questions on PyMOL?
2) I have downloaded PyMOL on a PC(microsoft windows XP)using the instructions
posted on the PyMOL site. But I am not able to get input files form the
Internet--I simply wanted to go to the
hi ppl,
is there a way to sort the list of objects/selections in the panel on the
right side other than loading/selecting stuff in a specific order?
simple example: I compare several ligands in a specific site, and save the
data as pymol sessions; after adding new ligands//site conformations I'd
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
hi ppl,
is there a way to sort the list of objects/selections in the
panel on the right side other than loading/selecting stuff in
a specific order?
simple example: I compare several ligands in a specific site
Hi,everybody:
Is there someway so that I can generate several asymmetry molecules from
one asymmetry unit in pymol?
Thank you.
Xiaofeng
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safe.
Hi Blanton,
Are you running the unstable tree, or have you just copied the
pymol-0.90-2 package to stable, you either have to enable the unstable
tree, or copy the numeric-py22 package from the unstable to stable, it
can be found at '/sw/fink/dists/unstable/main/finkinfo/sci'
see here;
I was attempting to install pymol 0.9 using fink and got the following error
message,
Failed: Can't resolve dependency numeric-py22 for package pymol-0.90-2
(no matching packages/versions found)
Can anyone advise me on what to do to get around this? Thanks in advance.
Blanton
Dear All,
How do I show the unit cell using pymol?
Martin
Martin Kienetz
429 MSB
Department of Biochemistry
University of Alberta
Edmonton AB
T6G 2H7
(780) 492-2422
Hi Martin,
Visit Robert Campbell's repository of PyMOL scripts
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find
Python scripts to import into PyMOL for drawing unit cell edges
(draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff...
Cameron
HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?
Have a nice day!
Fei
Fei Xu wrote:
HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?
Dear Fei Xu:
1. You select an atom
2. You display it as a ball
3. You type:
set sphere_scale = 2.0
Here, the number is the size proportional to an
Hi!
Just wondering if there is a way to save a pymol session like in Insight
and setor if I want to get back to it.
Thanks.
sona
Sona Vasudevan
National Center for Biotechnology Information
National Library of Medicine
National
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