Hi All,
I'm using pymol to select (by residue) all the atoms around 10 angstroms
from a certain atom. Now I would like to write the residue id's of my
selection to an external file, so that I can integrated in the ndx file from
Gromacs. Do you have any idea how I could do that?
Thanks,
Marius
rather than
the residue id's, since the latter are of no use to Gromacs.
Hope it helps,
Tsjerk
On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
marius.s.rete...@gmail.com wrote:
Hi All,
I'm using pymol to select (by residue) all the atoms around 10 angstroms
from a certain atom
Hello Leo,
You could use Unicode to get the special characters you were taking about.
angstrom = u\u00C5
angstrom_utf8 = angstrom.encode ('utf-8')
label (residue 200 and name ca), Distance: 8+angstrom_utf8
To see the label bigger use set label_size, 20
You can get the unicode charts from here
Hello,
While I am in editing mode, there is a keyboard shortcut to display the
distance between to selected atoms, but I cant remember it. I would
appreciate if someone could refresh my memory. Another related question
would be where I can find a list of shortcuts currently available in Pymol?
And
Hi Tom,
On Wed, Mar 18, 2009 at 12:03 AM, Thomas Evangelidis te8...@mbg.duth.gr wrote:
Dear Pymol users,
does anyone know where I can find a 64 bit version for my Fedora 10.
The package from the repositories works fine but when it comes to
install new plugins it yields error messages. As a
did that now, run again
pymol setup.py build install
pymol setup2.py install
but still the same error ...
Hugo
Marius Retegan wrote:
Did you uncomment in setup.py the lines related to VMD support?
On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran hugo.te...@usc.es
wrote:
Hi,
I
I don't know if this is version dependent, but in my case (version
1.2r2) you have to enter in editing mode (Mouse - 3 Buttons Editing)
and Ctrl+left click the label and drag.
Hope this helps
Marius
On Wed, Oct 14, 2009 at 11:55 AM, Per Larsson per.lars...@sbc.su.se wrote:
Hi!
I need to make
Try this one
select allothers, chain 0:4 or chain C:J or chain L:Z
Marius
On Thu, Oct 15, 2009 at 3:34 PM, Sean Moore semo...@mail.ucf.edu wrote:
Hello,
I am trying to find an easier way to select multiple chains at once in
a large file with many chains (PDB 2i2t). The chain assignments
In my opinion CentOS is not made for a desktop environment.
If you are confortable with the rpm system package, try switching to Fedora
and install the rpmforge repository (https://rpmrepo.org/RPMforge).
Marius
On Tue, Dec 15, 2009 at 4:33 AM, Joel Tyndall joel.tynd...@otago.ac.nzwrote:
Hi
Thank you for the nice tutorial.
On Tue, Dec 22, 2009 at 8:17 PM, Shiven Shandilya
shiven.shandi...@gmail.com wrote:
Hello List,
An initial attempt at a PyMOL + Blender tutorial is now on the pymolwiki:
http://pymolwiki.org/index.php/Blender
Hope some of you will find it useful.
On Wed, Jan 20, 2010 at 9:35 AM, Jesper Lykkegaard Karlsen
je...@bioxray.au.dk wrote:
Hi Deepangi,
1. OS: Windows 7
2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD
3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI
4. Glasses: NVIDIA 3D Vision Glasses
Wrong
Try the expand command on linux or google for sed tab to space
replacement.
Marius
On Tue, Jan 26, 2010 at 5:48 PM, Michael Zimmermann micha...@iastate.eduwrote:
If you have a lot of files to do this to, I would suggest learning at
least a little bit of perl. It might not be as nice an option
Just a wild guess
fetch 1htr, async=0
Marius
On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann micha...@iastate.eduwrote:
Dear PyMOL users,
I was just making a script to selectively download sections of PDB files
using fetch. When I run the pml from the GUI I see that all of the commands
:
Thank you Marius, that does appear to do the job. I guess this tip is
sortof present on the wiki page for fetch, but I didn't understand it as
written.
Sincerely,
Mike
On Tue, May 4, 2010 at 4:13 PM, Marius Retegan marius.s.rete...@gmail.com
wrote:
Just a wild guess
fetch 1htr, async=0
Hello
With help from Jason I've managed to solve my problem. As a result I've
updated the wiki page for the ramp_new command to include my particular case
(see bottom of the page)
http://pymolwiki.org/index.php/Ramp_New
Marius
On Mon, Jun 28, 2010 at 10:32 PM, Marius Retegan marius.s.rete
Did you try the macports (http://www.macports.org/) version?
Marius
On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) paul.ri...@uci.eduwrote:
Hi gang,
Actually, I spoke too soon! I attempted this compilation to address another
user's problems with an external script. But as you can see from
,
interactive, wantobjects, useTk, sync, use)
TclError: Can't find a usable tk.tcl in the following directories:
On Fri, Jul 9, 2010 at 2:03 PM, Marius Retegan marius.s.rete...@gmail.com
wrote:
Did you try the macports (http://www.macports.org/) version?
Marius
On Fri, Jul 9, 2010 at 10
Hello Maia,
Does this work?
color black, hb*
Marius
On Tue, Mar 15, 2011 at 5:40 PM, Maia Cherney ch...@ualberta.ca wrote:
Hi,
Can anybody advise me what is the right command for selecting or
coloring many hbs?
Instead of
color black, hb1
color black, hb2
etc
I want something like
Dear Edith,
You have overwritten the python that comes with the system with that from a
mgltools install. That particular install is 32 bit, your system is 64 bit.
Look in your shell configuration file (.bashrc most probably) for something
like export PYTHON_PATH and comment it temporally.
Rerun
Enter editing mode, select the 2 points, press Ctrl + t or type bond on the
cli.
Cheers,
Marius
On Thu, Mar 31, 2011 at 11:36 AM, kanika sharma ksharma...@gmail.comwrote:
I have two points corresponding to center of masses of 2 proteins. I have
to draw a line between both. Is there a feature
Hello,
There's been quite a while since I wanted to ask this on the list, but would
it be possible to have in Pymol some kind of technique to emulate realistic
lighting (global illumination) in a rendered scene?
The next point is related to the new volume representation. For example
after
Hello,
On Fri, Apr 8, 2011 at 6:49 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Marius,
There's been quite a while since I wanted to ask this on the list, but
would
it be possible to have in Pymol some kind of technique to emulate
realistic
lighting (global
This depends on how you touch pad is configured and what mode you
selected froum the Mouse menu.
I would suggest a trial and error approach to your problem. Try doing
something and see what it does.
Also Google is your friend. http://www.google.fr/search?q=pymol+mouse
Marius
On Thu, Jun 23, 2011
Hello
Have you tried
load A.pdb
load B.pdb
If this does not work for you, could you please define the what
simultaneous means to you, i.e what exactly are you trying to do
that requires simultaneous loading of two files?
Marius
On Wed, Jun 29, 2011 at 3:36 PM, leila karami
You could try something like this in a terminal
for i in $(seq 1 1 100); do pymol $i.pdb; done
if your file name are 1.pdb, 2.pdb ... 100.pdb
Marius
On Fri, Jul 15, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey Ram,
It's scriptable, but not very doable on this Android :p
Maybe this can help you
http://sourceforge.net/mailarchive/message.php?msg_id=19472192
Cheers,
Marius
On Tue, Aug 16, 2011 at 2:19 AM, Michael Daily mdaily.w...@gmail.com wrote:
Hi all,
Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
know it's simple to convert
That variable (ray_trace_mode) dows not accept logical values.
http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes
GnuPG http://db.tt/rr7Hd0Y
On Tue, Aug 23, 2011 at 2:44 PM, Tatyana Sysoeva
tatyanasyso...@gmail.com wrote:
Hi Tsjerk,
I am attaching the file and the terminal text.
security,
off or set security = 0
I am sorry for the wrong file I sent.
On Tue, Aug 23, 2011 at 8:51 AM, Marius Retegan marius.s.rete...@gmail.com
wrote:
That variable (ray_trace_mode) dows not accept logical values.
http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes
GnuPG http://db.tt
, but it does not work with 0,1,2 etc, as well as set
security,
off or set security = 0
I am sorry for the wrong file I sent.
On Tue, Aug 23, 2011 at 8:51 AM, Marius Retegan
marius.s.rete...@gmail.com
wrote:
That variable (ray_trace_mode) dows not accept logical values.
http
Google search lead me to this
http://www.pymolwiki.org/index.php/Atom_name_wildcard
I think this should to the job in you case
alter all, name=string.replace(name,H0,H)
Best regards,
Marius
--
Dr. Marius Retegan
Postdoctoral Fellow
Dear Lina,
I don't want to be rude, but you should read this part of a document
on how to ask questions on a mailing list
http://catb.org/~esr/faqs/smart-questions.html#before.
Some of the question that you posted on this mailing list could have
been solved by a simple Google search.
Best
initialize video driver.
Movie-Aspect is undefined - no prescaling applied.
FATAL: Cannot initialize video driver.
Exiting...
2011/11/9 Marius Retegan marius.s.rete...@gmail.com
On a Linux system you can use the following commands to stick them all
together
mencoder mf://*.png -mf fps=25
Hello,
The latest revision 3971 compiles without problems with gcc 4.5.1 on Fedora 14.
I usually install all the dependencies with yum.
My suggestion would be to try compiling with gcc4.5.
Marius
On Fri, Dec 2, 2011 at 8:19 AM, grantaka36 grantak...@gmail.com wrote:
Referring the following,
Could you please specified what exactly did the gcc 4.5 broke in Pymol?
Maybe this is not the case for every linux distribution.
Cheers,
Marius
2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
Try Following this script.
Hello,
Was the plugin manager tested with the incentive builds on mac osx? Is
the setup procedure similar?
Thank you
Marius
On Wed, May 2, 2012 at 3:43 PM, Michael Banck mba...@debian.org wrote:
Hi,
On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote:
Thanks for this feedback.
open-source code in PyMOL. The plugin system is now
built-in. If you try to integrate the plugin code yourself, it might
take a little work.
Cheers,
-- Jason
On Sat, May 5, 2012 at 4:24 PM, Marius Retegan
marius.s.rete...@gmail.com wrote:
Maybe I'm doing something wrong...
I started
I've reported this last week.
http://sourceforge.net/tracker/?func=detailaid=3523770group_id=4546atid=104546
For the moment is not assigned.
Marius
On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets kheyfbo...@gmail.com wrote:
I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch
Hello,
+1 for svg. It would be easier to add/remove stuff from them with a
vector drawing program like Inkscape.
Also .svg is also an open format. Not sure about .eps.
All the best,
Marius
On Tue, Jan 15, 2013 at 1:32 PM, Martin Hediger ma@bluewin.ch wrote:
I'm no expert but I guess my
Dear PyMol users,
The mutagenesis wizard does not seem to work if ignore_case is set to
0. I can reproduce this on an older incentive build and on the OS X
compiled version from svn revision 4007.
Thanks,
Marius
--
This
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