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
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 wrote:
> I'm no expert but I guess my favorite would be EP
I've reported this last week.
http://sourceforge.net/tracker/?func=detail&aid=3523770&group_id=4546&atid=104546
For the moment is not assigned.
Marius
On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets wrote:
> I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch
> to the latest
ource 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
> wrote:
>> Maybe I'm doing something wrong
MOL.app/pymol/ext/lib/python2.7/site-packages/PIL',
'/Applications/MacPyMOL.app/pymol/freemol/libpy']
On Sat, May 5, 2012 at 7:00 PM, Jason Vertrees
wrote:
> Hi Marius,
>
> The new plugin code was built and tested on Mac OS X before release.
> It worked just as well as
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 wrote:
> Hi,
>
> On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote:
>> Thanks for this feedback. Since the ince
Hi Troels,
Take a look at the layer3/Selector.c. I think you'll have search in
the code in order to see how these selection rules are defined.
Marius
2011/12/4 Troels Emtekær Linnet :
> Hi.
>
> I sometimes see, that you can do
> select polymer
> select organic
>
> Is there a list somewhere with
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 :
> Try Following this script.
>
> http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_wit
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 wrote:
> Referring the following, I'm trying to install
pplied.
> [swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2
> FATAL: Cannot initialize video driver.
> Movie-Aspect is undefined - no prescaling applied.
> FATAL: Cannot initialize video driver.
> Exiting...
>
>
> 2011/11/9 Marius Retegan
>>
>&
On a Linux system you can use the following commands to stick them all together
mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts
bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25
-ofps 25 -nosound -noskip -of raw
Could you please write the _exact_ steps you are doing? Also please
attach a the compressed cube file?
Best regards,
Marius
--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7H
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 regards
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
>> Marius
>>
>> GnuPG http://db.tt/rr7Hd0Y
>>
>>
>>
>> On Tue, Aug 23, 2011 at 2:53 PM, Tatyana Sysoeva
>> wrote:
>> > true, my bad, but it does not work with 0,1,2 etc, as well as set
>> > security,
>> > off or set s
or set security = 0
>
> I am sorry for the wrong file I sent.
>
> On Tue, Aug 23, 2011 at 8:51 AM, Marius Retegan
> wrote:
>>
>> That variable (ray_trace_mode) dows not accept logical values.
>> http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes
>>
>>
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
wrote:
>
> Hi Tsjerk,
>
> I am attaching the file and the terminal text.
>
> ++
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 wrote:
> Hi all,
>
> Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
> know it's simple to convert them to pdb using edi
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 wrote:
> Hey Ram,
>
> It's scriptable, but not very doable on this Android :p
> The best soluti
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 wrote:
> Dear Hong
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,
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 i
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 loading
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 wrote:
> I have two points corresponding to center of masses of 2 proteins. I have
> to draw a line between both. Is there a feature that can do this?
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 t
Hello Maia,
Does this work?
color black, hb*
Marius
On Tue, Mar 15, 2011 at 5:40 PM, Maia Cherney 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 color
set label_digits, 3
On Wed, Nov 10, 2010 at 3:50 PM, Martin Hediger wrote:
> Dear all
> Is it possible to increase the number of digits displayed when measuring
> the distance between two atoms?
>
> Thanks
> Martin
>
>
>
>
>
> -
Are you using cyrillic characters for your file names?
If yes try changing that and see what happens.
On Tue, Jul 20, 2010 at 4:35 PM, Павел Кудрявцев wrote:
> Hi,
> I'm installed Pymol version 1.2 from repository on Mandriva Linux and
> I'm constantly getting following errors when trying to op
rk/Versions/2.6/lib/python2.6/lib-tk/Tkinter.py",
> line 1643, in __init__
> self.tk = _tkinter.create(screenName, baseName, className,
> interactive, wantobjects, useTk, sync, use)
> TclError: Can't find a usable tk.tcl in the following directories:
>
>
>
> On Fri, Ju
Did you try the macports (http://www.macports.org/) version?
Marius
On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) wrote:
> 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 the
> attachme
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 wrote
Hello,
Take the following scenario. I have two cube files, the first one holds some
values of a function (electron localization function),
while in the second cube for each value in the first cube file i can have
either one of the numbers from 0 to 6.
After loading the first cube file in Pymol, I c
us, 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 > wrote:
>
>> Just a wild guess
Just a wild guess
fetch 1htr, async=0
Marius
On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann wrote:
> 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
> are executed an
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 wrote:
> 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 as a
> python ta
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 Gla
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
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 wrote:
> Hi folks,
>
>
>
> Sorry for th
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 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
> exceed "z" and st
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 wrote:
> Hi!
>
> I need to make some pictures of ve
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
Hi Tom,
On Wed, Mar 18, 2009 at 12:03 AM, Thomas Evangelidis 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 matter of fact
Hi,
This line is self explanatory "error: GL/glut.h: No such file or
directory". You need to install glut development libraries
On Ubuntu you can use apt to install pymol.
sudo apt-get install pymol or something similar
Marius
On Thu, Feb 12, 2009 at 12:52 PM, Abhik Mukhopadhyay
wrote:
> Dear A
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
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 her
\n")
> > iterate selection, ndx.write("%d\n" % ID)
> > ndx.close()
> >
> > I did make the assumption that you wanted the atom id's rather than
> > the residue id's, since the latter are of no use to Gromacs.
> >
> > Hope it helps,
> &
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?
Thank
You need to install libGLU. My bet is that after you going to install
it pymol is going to ask you for another library (I don't recall the
name wright now).
Just go on Google and search the name of the missing library, get the
rpm and install it.
On 7/10/07, Kailee wrote:
Dear all,
I have down
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