On 07/12/15 10:23, Spencer Bliven wrote:
> Nice work! It will be very nice to have python3 compatibility in the future.
>
> It would be nice to organize a section of the pymol-script-repo for
> python3-compatible scripts once this gets merged to SVN.
>
I think, we can make most of the scripts
On 07/12/15 10:42, Justin Lecher wrote:
> On 07/12/15 10:23, Spencer Bliven wrote:
>> Nice work! It will be very nice to have python3 compatibility in the future.
>>
>> It would be nice to organize a section of the pymol-script-repo for
>> python3-compatible scripts o
ot;<pyshell#12>", line 1, in
> import pymol
> ImportError: No module named 'pymol'
>
> I would very appreciate your help.
>
Hi,
simply you can't right now as pymol is not python3 ready yet.
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structur
On 28/05/15 19:26, Thomas Holder wrote:
Hi Brenton,
the logo is currently not available under any license, it's a trademark of
Schrödinger. This means you can't upload it on Wikimedia Commons.
Cheers,
Thomas
Hi Thomas,
That brings up an interesting question about the usage in
On 19/03/15 16:52, Tim Travers wrote:
Hi,
I also had problems compiling this last night. According to the
following (see Compile and install towards the bottom),
you have to callfirst:
export CPPFLAGS=-std=c++0x
before doing the build call.
I used:
export CPPFLAGS=-std=c++11x
so
On 19/03/15 20:45, Thomas Holder wrote:
Hi Justin,
unfortunately, not everyone is on Gentoo... see comment about distutils and
CXXFLAGS here:
https://sourceforge.net/p/pymol/bugs/159/#58a5
Hi Thomas,
absolutely right, scipy is also suffering from this. There is an open
bug at distutils
in the Pymol wiki.
Could this be fixed?
thanks,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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#MODEL
2)
http://wwpdb.org/documentation/format33/sect9.html#ENDMDL
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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On 27/08/14 07:56, James Starlight wrote:
Hi
both of them are present in my ensemble. the problem is not here- if it
possible i could upload the ensemble.pdb to some server if someone could
check it.
James
Hi,
Go for some paste bins or do a gist on github.
Justin
--
Justin Lecher
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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--
Slashdot TV.
Video
On 11/03/14 07:52, Justin Lecher wrote:
On 10/03/14 21:52, Thomas Holder wrote:
Hi Justin,
this is fixed in SVN rev 4070, sorry that it took so long.
Cheers,
Thomas
Hi Thomas,
Thanks a bunch. I will try it out tomorrow on my 3D machine.
Cheers,
Justin
Looks beautiful now
On 10/03/14 21:52, Thomas Holder wrote:
Hi Justin,
this is fixed in SVN rev 4070, sorry that it took so long.
Cheers,
Thomas
Hi Thomas,
Thanks a bunch. I will try it out tomorrow on my 3D machine.
Cheers,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural
On 22/11/13 17:44, Jason Vertrees wrote:
Hi Justin,
We'll fix that, too.
Cheers,
-- Jason
Hi Jason,
did you find time to look into that?
Thanks
justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone
the font rendering during shader activated mode?
thanks
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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Regards,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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On 15/07/13 18:56, Thomas Holder wrote:
Hi Justin,
we fixed this in sourceforge SVN today. Please recompile and check if it
works for you. Thanks.
Cheers,
Thomas
Thanks Thomas,
works perfectly now!
Cheers,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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--
See everything from
*on linux 64.*
I have made this progress
http://pymolwiki.org/index.php/3d_pdf#Linux_install
But when I compile, I get.
Hi,
try this one
http://www2.iaas.msu.ru/tmp/u3d/u3d-1.4.3.tar.gz
it only has problems with gcc-4.7 but I can provide a patch if needed.
Justin
--
Justin Lecher
Institute
Hi Jason,
I found a bug. If you set Display - Quality - Maximum Quality turns
the display around. That means the back is in the front and small, and
the front, larger parts are in the back.
justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre
occurs with sticks
representation. All others are nice and super fast.
justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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On 13.02.2012 20:27, Jason Vertrees wrote:
Greetings,
It is my pleasure to announce the release of open source PyMOL
v1.5.0.1. The source code has been committed to the open-source
repository. It is revision 3976. An svn tag and downloadable bz2
source file were also created. All of this is
to color by atom type after coloring by secondary
structure:
set cartoon_sidechain_helper, on
C Color by ss Helix (red) Sheet (yellow) Loop (green)
C Color by element ...
Cheers,
-- Jason
On Sun, Nov 13, 2011 at 7:11 AM, Justin Lecher j.lec...@fz-juelich.de wrote:
Hi
Hi,
while trying this
http://kpwu.wordpress.com/2011/11/12/pymol-sidechain-helper-in-the-cartoon-view/
I recognised that the color by atom type function doesn't work anymore
if the sidechain helper is on. Bug or feature? Could we enable it?
Thanks justin
--
Justin Lecher
Institute of Complex
@lists.sourceforge.net
mailto:PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural
.
Thanks justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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Hi Jason,
could you please use PYMOL_DATA to determine the location of the shaders
dir? it is actually stored in PYMOL_DATA/shaders and with PYMOL_DATA !=
PYMOL_PATH/data it fails.
Thanks justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
there
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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--
Enable your
?
The fetch command directly fetches the pdb file from the online database.
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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this idea?
Perhaps it is a small fix to get the pyNMR code working with the newer
versions of pymol.
Thanks justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
Hi Hari,
the distutils based build is fine.
justin
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--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
+1 from me
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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, you can find the plugin in the sci overlay as
sci-chemistry/pymol-apbs-plugin.
There is a version for revision 11 as well as a live ebuild available.
Thanks justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich
succesfull. So
please try to provide us the log, in worst case compress it and attach
it to your mail.
What exactly is the output if you start it in a shell?
Justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH
?
pymol HEAD of svn
linux-2.6.30
xorg-server-1.6.3
intel-driver-2.8.0
Thanks justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB3 - structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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I've updated it on the Wiki.
So anyone likes to try git and update the repo?
--
Justin Lecher
Institute for Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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/cy7wj8
If anyone has suggestions feel free to edit the howto. Questions about
unresolved things are also welcome.
Thanks justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
/origin/*
and everything is fine.
Thanks,
justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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everyone to check out the repo and contribute.
http://github.com/jlec/Pymol-script-repo/tree/master
If you have problem with git, just mail me.
Thanks justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425
Hi Warren,
some time ago I asked for the script you used for the image on pymol.org and I
lost it somewhere. Could
you post it again, please?
Thanks, justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institue for structural biochemistry
Research Centre Juelich GmbH
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
--
Justin Lecher
Institute for Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH
=ReplyToListThunderbirdExtension
Justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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figure out where
it comes from.
Thanks for help,
jusitn
--
Justin Lecher
Institute for Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385
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Justin Lecher schrieb:
Hi all,
I am using the latest svn version of Pymol with python 2.5.2. Now I get
following traceback when clicking the set grid button of the apbs plugin:
Traceback (most recent call last):
File /usr/lib/python2.5/site-packages/pmg_tk/__init__.py, line 35,
in run
Hi all,
Just want to know if there are only per user pymolrc files at ~/.pymolrc
or could there be a system wide configuration e.g. /etc/pymolrc. or
somewhere else?
Thanks,
justin
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Yang, Zheng schrieb:
Dear All,
Would you please remind me how to start PyMOL in Linux, without the
GUI, only command lines? Just like Matlab, we using ‘matlab -nojvm’
to disable the graphic interface.
I am running PyMOL to ray-trace a figure. But the protein is too big.
It always
type
@yourpmlfile.pml
Hally Shaffer schrieb:
I installed pymol onto a linux system. I can open the program, open the pdb
file, and open a .pse file, but I cannot open the .pml file which contains the
manipulations that I've already made. Any suggestions?
--
Hally Shaffer
Graduate Student
For all the gentoo guys out there:
I wrote an ebuild for msms. Any Bugs and suggestions should be reported
to me for further improvement.
Robert Campbell schrieb:
Dear Buz,
On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow b...@mac.com
wrote:
Dear all,
I'd like to very accurately
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