a lot
changes, sorry ;-)) and now can read any of mac/unix/dos text files
using MacPyMol.
Cheers,
Thomas
--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Copyright (c) 2003 Robert L. Campbell
Copyright (c) 2010
,
nick
'''
(c) 2010 Thomas Holder
PyMOL python script (load with `run supercell.py`)
Usage: See help supercell
'''
from pymol import cmd, cgo
from math import cos, sin, radians, sqrt
import numpy
def cellbasis(angles, edges):
'''
For the unit cell with given angles and edge lengths calculate
Hi Nick,
I noticed a few things:
- when I run supercell 2, 1, 1 I get another cell outline along the
a axis, but no atoms are shown in the second cell. Do I have to run
another command for them to show up?
the script does not create symmetry mates. The symexp command can
create symmetry
On Thu, 2010-04-15 at 15:46 -0600, Nicolas Bock wrote:
the script does not create symmetry mates. The symexp
command can create symmetry mates within a given radius (it
will not just fill up the cell).
Maybe I just don't understand the symexp command, but
Hi Jason,
the result of symexp is not supposed to be the biological unit, right?
It produces any symmetry mate, whereas your ManualSymExp reads the
REMARK 350 which is the annotated biological unit. It is a very useful
script, but has a bug: If there is more then one biomolecule annotated,
for
- when I run supercell 2, 1, 1 I get another cell outline along the
a axis, but no atoms are shown in the second cell. Do I have to run
another command for them to show up?
the script does not create symmetry mates. The symexp command can
create symmetry mates within a given radius
. To more effectively support and develop PyMOL, I
packed up moved to NYC to be in the Schrodinger main office. This
gives me better access to bright minds and resources that should lead
to quicker improvements for PyMOL.
Cheers,
-- Jason
--
Thomas Holder
Group of Steffen Schmidt
Department
Hi pymol users,
there is a new script on the wiki that does arbitrary gradient
coloring, it's called spectrumany.
http://pymolwiki.org/index.php/Spectrumany
Cheers,
Thomas
--
This SF.net email is sponsored by Sprint
use the `alter` command to set `formal_charge`:
alter sele, formal_charge=0
alter sele, formal_charge=1
alter sele, formal_charge=-1
Cheers,
Thomas
On Mon, Jul 26, 2010 at 7:34 PM, Davide Cruz davide.r.c...@gmail.com wrote:
Hello there,
Is there a command to change the charge of a
On Mon, Sep 13, 2010 at 12:30 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
# get it's one-letter residue id
print string.split(cmd.get_fastastr(mySelection),'\n')[1]
# get it's three-letter residue id
print three_letter[string.split(cmd.get_fastastr(mySelection),'\n')[1]]
I just
, which is another nucleic acid
with a calcium ion I just pulled out.
In pymol 1.2, it also behaved incorrectly:
~ pymol -qrkc script2.py
PyMOLrun script2.py,main
1acb_2
0.0
426d
nan
1acb_2_again
nan
-David
--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI
,
Ramiro Tellez Sanz
Dept. Physical Chemistry
University of Almeria
Spain
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
--
Thomas Holder
Group
Hi Ramiro,
* How do I adjust the code with my selected rings? Do I need to include
both residues in the same selection in pymol, then rename the selection,
and then include the chosen selection name in the code where you write
selection?
you need two selections of two residues, in my example
On Thu, 2010-09-23 at 09:54 -0400, Jason Vertrees wrote:
Hi Ramiro,
Another option is to fit (in a least-squares sense) a plane to each of
your rings and then calculate the angle between the fitted planes'
normals.
that's what the recently posted ring_angle.py script does.
Cheers,
Thomas
What does this .pml script do? I once had artefacts on the interface
after loading an incomplete CGO object.
Cheers,
Thomas
Bradley Hintze wrote, On 12/10/10 18:26:
Hi Jason,
I'm using Snow Leopard. It only happens when i run my .pml script. If I
put 'load .pdb' at the end of the
Hi Sean,
since the PyMOL GUI is written in python, it's quite easy to manipulate
menus. See attached script to get the ID into the right click menu title.
Cheers,
Thomas
Sean Law wrote, On 12/14/10 18:20:
Hi PyMOLers,
Is there a way to display PDB atom numbers when you right click on an
Hi Jared,
this is a numerical problem. Look in transformations.py for the lines
where values get compared to 1e-8 and change this number to something
like 1e-7.
And in your script the angle calculation missed the arccos:
elbow = 180 -
Hi Seth,
I think this one-liner will do the job for you:
print cmd.get_chains('polymer')
Cheers,
Thomas
Seth Harris wrote, On 01/23/11 10:04:
Hi All,
I am script-plowing through PDB files and extracting unique chain
identifiers only for polymers using PyMOL's polymer selection. Right
, I'd like to state explicitly how many
degrees domain B closes by. I'd also like to draw a CGO arrow showing
the angle of rotation.
Thanks,
Mark
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
domainangle.py
Description: Binary data
Hi Roberto,
you can make a movie for subsequent zooms, like this:
zoom all
mset 1x100
frame 50
zoom chain A
mview store
frame 100
zoom chain B
mview store
mplay
There might be other ways to achieve this, though.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
Hi Angelo,
instead of calculating RMSD you could monitor pairwise helix angles
over states. See attached script, it depends on the
http://www.pymolwiki.org/index.php/AngleBetweenHelices script.
Cheers,
Thomas
On Thu, Mar 10, 2011 at 12:05 AM, Angelo Rossi
angelo.raymond.ro...@gmail.com wrote:
PDB mirror.
http://www.pymolwiki.org/index.php/BiologicalUnit/Quat
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Colocation vs. Managed Hosting
A question and answer
interaction surface between 2
subunits of my protein?
I found this website http://crick.mbu.iisc.ernet.in/~PIC/index.html,
but I would rather use pymol if possible.
Thanks a lot, Tomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
, but how can I visualise the output
from pisa in pymol? I am not able to download residue list which are
in interface, I can see just table where are interface residues
marked.
Tomas
Dne 14. března 2011 14:56 Thomas Holder
spel...@users.sourceforge.net napsal(a):
Hi Tomas,
have you checked
It seems REMARK 290 that contains crystallographic symmetry
transformations is used for computing the positions of neighboring ASUs.
the CRYST1 record is sufficient for generating symmetry mates, so
pymol most likely does not read REMARK 290.
Cheers,
Thomas
--
Thomas Holder
MPI
0.866025 0.50 0.00 0.0
REMARK 350 BIOMT3 2 0.00 0.00 -1.00 0.0
Regards,
kanika
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
for the sculpting
functions. Pressing the Sculpt button in the PyMOLX11Hybrid does not
lead to a command I can see in the log file.
What would be the Python code to start the sculpt process?
Any hints are welcome.
Thanks a lot.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D
there was a bug in the script, sorry. Corrected script attached.
Cheers,
Thomas
On Thu, Mar 24, 2011 at 8:40 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Martin,
I have a script that does almost exactly what you want (I guess). See
attachment.
Cheers,
Thomas
--
Thomas
A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076
)**2 for i in zip(*xm))
# Radius of gyration
rg=math.sqrt(rr/tmass-mm)
# Print it...
print Radius of gyration:, rg
return rg
cmd.extend(rgyrate,rgyrate)
Hope it helps,
Tsjerk
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
in the wiki so it should work with older python now. Can you
download again and try?
Cheers,
Thomas
On Tue, Apr 5, 2011 at 8:49 PM, Anastassis Perrakis a.perra...@nki.nl wrote:
Hi -
I am trying to use the script by Thomas Holder, Spectrumany
http://www.pymolwiki.org/index.php/Spectrumany
Jason Vertrees wrote, On 04/08/11 20:09:
Hi Matthias,
There is no script that I'm aware of, but writing one should be rather
straightforward because of how the API is organized:
commandName arg1, arg2, arg3
becomes
cmd.commandName(arg1, arg2, arg3)
I would use the cmd.keyword
, have fun!
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
http://sourceforge.net/mailarchive/message.php?msg_id=27331786
Subject: [PyMOL] Convert pml script to Pymol Python script
Date: Fri, 8 Apr 2011 18:01:32 +0100
'''
import sys
from pymol
it's on the wiki now:
http://pymolwiki.org/index.php/Pml2py
Cheers,
Thomas
Thomas Holder wrote, On 04/09/11 11:17:
Michael Lerner wrote, On 04/08/11 20:16:
It's not elegant at all, but it's worth knowing that you can use
cmd.do(...) as a quick fix for lines that aren't immediately easy
the output using BioPython. It then makes several
selections, each for a kind of secondary structure elements (SSE) if
there is at least one residue in the input selection is assigned with
the SSE.
regards,
hongbo
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076
)--
how to fix it?
I want to know how label dna residues by command line?
please guide me.
best wishes
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
Thomas Holder
MPI for Developmental Biology
Spemannstr
Hi Leila,
I want to know how to change color of dashed line. (color of dashed line
is yellow by default).
it's the dash_color setting, so to make them blue for example type:
set dash_color, blue
http://www.pymolwiki.org/index.php/Dash_color
Cheers,
Thomas
--
Thomas Holder
MPI
://pymolwiki.org/index.php/Python_Integration
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost
how to do this.
As an example, when downloading the PDB file of 1AVD, I get a file
with two chains. The biological assembly would be a tetramer, so I
wonder what URL I would require to write into a script that does the
downloading.
Thanks for help on this.
Martin
--
Thomas Holder
MPI
python knowledge
is very basic.
Thanks
Sena
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
WhatsUp Gold - Download Free Network Management Software
The most intuitive
letter residue names.
Any clue ?
I tried the following :
*pdb_truncate_residue_name* (boolean, default: off) controls whether or
not PDB residue names are truncated to three letters only.
with no effect
Thanks for help
Pascal
--
Thomas Holder
MPI for Developmental Biology
.
see attached patch (untested, since my build seems to be broken at the
moment).
This an
important bug (at least for me). I and many others on the list don't
master C languages (oups ... Am i the only one ?)
for sure you're not the only one ;-)
Cheers,
Thomas
--
Thomas Holder
MPI
=4546atid=104546
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help
Generale
Universita' di Pavia
Via Ferrata, 1
27100 Pavia
Italia
Tel. 0039 0382 986335/8/1
Facs 0039 0382 303673
--
Thomas Holder
MPI for Developmental Biology
show_bumps.py
Description: application/chimera
--
Simplify
://qmviews.blogspot.com/. If I cant
come up with a PyMOL solution, then I guess I'll just try to find a
Python solution.
Thanks for any hints on this.
--
Thomas Holder
MPI for Developmental Biology
--
EditLive Enterprise is the world's
guess).
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing
(exp_interest, exp_interest, cutoff=3.6, \
name=interest_polar_conts)
You can drop the 'name' argument if you don't need the object for visual
inspection but only the pair list.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
pairs.py
Description: application/chimera
,
Thomas
jp d wrote, On 06/24/11 22:57:
hi,
is there a way in pymol/python scripts to
determine what the next or previous resi would be?
it needs to handle insertions and deletions
thanks
jpd
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Hi pymolers,
I wrote a script to use a personal plugin directory.
http://pymolwiki.org/index.php/PluginDirectory
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
All of the data generated in your
wrote, On 07/09/11 22:32:
Hi,
I made a nice movie and it's fine and I would just like to delete a
part of it or to insert some frames. How is that possible? Mset resets
the whole movie and mview does not seem to do what I would like it to
do...
Best,
Matthias
--
Thomas Holder
MPI
,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats
.]
cmd.transform_selection('(all)', M, transpose=1)
cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
cmd.extend('transform_by_camera_rotation', transform_by_camera_rotation)
Example:
fetch 2xwu
orient
transform_by_camera_rotation
save /tmp/withneworientation.pdb
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental
that, PyMOL knows the transform_by_camera_rotation command.
For more details see:
http://pymolwiki.org/index.php/Run
http://pymolwiki.org/index.php/Running_Scripts
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
, matrix
R = identity(4)
T = identity(4)
R[0:3,0:3] = M[0:3,0:3]
T[0:3,3] = t
# should print two times the same matrix
print M
print matrix(T) * matrix(R) * matrix(T).I
Hope that helps.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
the script
transform_by_camera_rotation # call the new command
save /tmp/withneworientation.pdb # save the file
Is that clear?
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
-6103-77-1255
--
Thomas Holder
MPI for Developmental Biology
distancecoloring.py
Description: application/chimera
--
Got Input? Slashdot Needs You.
Take our quick survey online. Come on, we don't ask for help often.
Plus
python files
(this will most likely change in the future).
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Take our quick survey online
#Translate_or_rotate_individual_objects
If this is not precise enough for you and you want real beta-sheet
modeling, you should use something like modeller.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
two radio button looks gray and checked. (I think the
correct behavior should be; only one checked and none gray) setting a
different default value (using ref_value.set()) does not change anything.
2) I always get the default value (1 in this example) when hit the
submit button.
--
Thomas
res-f002
where 'a' and 'f' where the residue type and the number is the residue
number in the chain.
Any hints are very welcome.
Martin
--
Thomas Holder
MPI for Developmental Biology
--
uberSVN's rich system
traceback or error reported on the console.
Do you have experienced similar problems ?
I can confirm that DynoPlot does not work. This needs to be fixed.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
Thomas Holder
MPI for Developmental Biology
--
uberSVN's rich system and user administration capabilities and model
configuration take the hassle out of deploying and managing Subversion and
the tools developers use
--
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MPI for Developmental Biology
--
Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
user administration capabilities and model configuration. Take
the hassle out of deploying and managing Subversion
wrote:
Hi,
I would like to know how to do structure based superposition using PyMol for
3 or more structures. Please help me out.
Thanks,
-Suda
--
Thomas Holder
MPI for Developmental Biology
--
EMC VNX: the world's
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll
) and
you don't need an alignment, you can use rms_cur.
http://pymolwiki.org/index.php/Rms_Cur
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Special Offer -- Download
for any suggestions,
--
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MPI for Developmental Biology
--
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get
is 1334
output file - kill.pdb - atom number 36:B:CA 1380
log.pml - ...byresi((1shr`1380))...
Why does it tag the atom number from the output file? Shouldn't it tag
the atom number from the input file (1shr)?
--
Thomas Holder
MPI for Developmental Biology
On 09/06/2011 03:43 PM, Thomas Holder wrote:
Try this:
cmd.save(kill.pdb, test)
sorry, forgot quotes, must be:
cmd.save(kill.pdb, test)
--
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MPI for Developmental Biology
--
Special Offer -- Download
,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free Love Thy
suggestions,
--
Best Regards,
lina
--
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Spemannstr. 35
D-72076 Tübingen
--
Malware Security Report: Protecting Your Business, Customers, and the
Bottom Line. Protect your business
://pymolwiki.org/index.php/Util.mroll
http://pymolwiki.org/index.php/Property_Selectors
http://pymolwiki.org/index.php/Selection_Algebra
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
You have to make .pml file and put the python commands inside pymol
blocks.
it's python blocks, see:
http://pymolwiki.org/index.php/Python
... do I need to put those code in another .py file?
That's also possible, yes.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
structures then save the moved
molecules, but the space group changed to the target structures. I also
tried the matrix_copy command with failure.
Does anyone know how to do this? Thanks in advance.
Best,
Shukun
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076
was introduced after 0.99!
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA
Learn about the latest advances in developing
but this expression does not works as expected...
Is there a way in pymol to delete all except [something]?
In selections these experssions work. But in object names they don't.
--
Andrew Gontchar
--
Thomas Holder
MPI for Developmental Biology
--
Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford
http://sbcb.bioch.ox.ac.uk/schmidt.php
--
Thomas Holder
MPI for Developmental Biology
--
BlackBerryreg; DevCon
for any advice,
--
Best Regards,
lina
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
(c) 2010 Thomas Holder, Max Planck Institute for Developmental Biology
PyMOL wrapper for DSSP and STRIDE
'''
from pymol import cmd, stored
from subprocess import Popen, PIPE
,
lina
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Learn about the latest advances in developing for the
BlackBerryreg
Hi Lina,
Another question here,
can I show the whole residue as a ball, and different residues connect
by (virtual) bonds.
combine ribbon and CA spheres:
hide everything
show ribbon
show spheres, name CA
set sphere_scale, 0.5
set ribbon_width, 5
Cheers,
Thomas
--
Thomas Holder
MPI
,
Thomas
Thomas Holder wrote, On 08/16/11 15:51:
On 08/16/2011 03:16 PM, Joseph André wrote:
Hi everybody,
I want to build an interactive plot I tried to use and tweak dynoplot
but DynoPlot doesn't work properly : I can display the Tk window but
points aren't plotted. However the dihedrals
Cheers,
Thomas
On 09/21/2011 04:47 PM, lina wrote:
Hi,
I tried to zoom in, make it large,
but seems not work, neither,
zoom
zoom complete 1 or 0
zoom center
Thanks for some suggestions,
--
Best Regards,
lina
--
Thomas Holder
MPI for Developmental Biology
), for example like this:
## At x Ang of the protein surface there are XX water molecules
## Water ID are
Thanks in advance for your help.
Stephane
--
Thomas Holder
MPI for Developmental Biology
--
All the data continuously
around 9.0) and not ZONE1
# save to files
save zone1.pdb, ZONE1
save zone2.pdb, ZONE2
Have a look at
http://pymolwiki.org/index.php/Selection_Algebra
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application
:
http://pymolwiki.org/index.php/Alter
Cheers,
Thomas
On 09/27/2011 09:35 AM, lina wrote:
Hi,
how can I change the atom such as
H01 to H22 in command
Thanks ahead,
--
Best Regards,
lina
--
Thomas Holder
MPI for Developmental Biology
Dear PyMOL users,
I don't know how many cavers are in this audience, but if you are
curious what PyMOL can be used for apart from displaying molecules, have
a look at the post below!
Cheers,
Thomas
Original Message
Subject: Rendering 3D Surveys with Pymol
Date: Wed, 5 Oct
in PyMol that can do that?
Best,
Kanika
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure contains
?
Thanks for any hint.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application
-0.18 -0.01 .122
C
to:
ATOM822 H01 PDB 1 32.103 36.531 -0.203 -0.11
0.02 H
ATOM823 C12 PDB 1 34.140 35.147 -0.218 -0.18
-0.01 C
only the last field.
How can I quickly achieve it.
Thanks,
--
Thomas Holder
MPI for Developmental
?
Although the outline looks quite good for the graphics, especially once they
are printed, it makes the text look like blocky typewriter font. Any advice
appreciated.
Thanks
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
, and TCL_LIBRARY are correctly defined, then
you can launch PyMOL from an external Python program
But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY
Regards,
Masataka
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
the same with PyMOL.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance
density map?
Seems those questions are not so-pymol-related, but I wish if someone
are familiar with this, can give me some advice??
Those questions might be easy, but to me at present it seems very confusing.
Thanks with best regards,
--
Thomas Holder
MPI for Developmental Biology
On 10/25/2011 02:27 PM, lina wrote:
On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Lina,
do you already have any electron density or reflection file (*.map, *.mtz,
...) or do you want to create a fake density from your structure? It's not
I don't
And read the help for the map_new command (there is no wiki page yet):
PyMOLhelp map_new
now the wiki page is there:
http://pymolwiki.org/index.php/Map_new
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
file correctly?
Thanks in advance for answers!
Cheers,
Alexander
--
Thomas Holder
MPI for Developmental Biology
--
The demand for IT networking professionals continues to grow, and the
demand for specialized
on?
If you have selections for each cube, try this to lookup cubes that
contain atoms of residue number 10:
print cmd.get_names('public_selections', 0, 'resi 10')
Can all this be done in a single pymol window/script?
please let me know.
Thanks
-Anasuya
Cheers,
Thomas
--
Thomas Holder
90 degrees with respect to their-axis.
How can i solve this problem?
Guridis Georgios
Post-doc
IMBB,Crete,Greece
--
Thomas Holder
MPI for Developmental Biology
--
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