Re: [PyMOL] B-factor replacing problem

2010-03-09 Thread Thomas Holder
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

Re: [PyMOL] feature request: supercell construction

2010-04-14 Thread Thomas Holder
, 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

Re: [PyMOL] feature request: supercell construction

2010-04-15 Thread Thomas Holder
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

Re: [PyMOL] Fwd: feature request: supercell construction

2010-04-16 Thread Thomas Holder
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

Re: [PyMOL] Symmetry Expansion

2010-04-16 Thread Thomas Holder
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

Re: [PyMOL] Fwd: feature request: supercell construction

2010-04-17 Thread Thomas Holder
- 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

Re: [PyMOL] Plane Script Updates

2010-06-30 Thread Thomas Holder
.  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

[PyMOL] New script: spectrumany

2010-07-22 Thread Thomas Holder
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

Re: [PyMOL] [PyMol] Changing atom charges using the command line

2010-07-29 Thread Thomas Holder
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

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

2010-09-13 Thread Thomas Holder
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

Re: [PyMOL] Super Bug Report

2010-09-23 Thread Thomas Holder
, 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

Re: [PyMOL] How to measure the angle between two aromatic rings?

2010-09-23 Thread Thomas Holder
, 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

Re: [PyMOL] How to measure the angle between two aromatic rings?

2010-09-23 Thread Thomas Holder
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

Re: [PyMOL] How to measure the angle between two aromatic rings?

2010-09-23 Thread Thomas Holder
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

Re: [PyMOL] how to print out the atom type in a pymol script

2010-09-25 Thread Thomas Holder
Hi Zhijian, it's the at.hetatm attribute. try this: print atoms.atom[0].__dict__ Cheers, Thomas On Sat, 2010-09-25 at 22:56 +0800, zjxu wrote: Dear everyone, I could print the atom properties in a script except the atom type: atoms = cmd.get_model(object) for at in atoms.atom:

Re: [PyMOL] Disappearing right-hand control panel

2010-12-10 Thread Thomas Holder
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

Re: [PyMOL] Atom Numbering

2010-12-14 Thread Thomas Holder
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

Re: [PyMOL] Fab elbow angle

2010-12-15 Thread Thomas Holder
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 -

Re: [PyMOL] Faster way to find polymer chains?

2011-01-23 Thread Thomas Holder
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

Re: [PyMOL] Calculating domain rotations

2011-02-09 Thread Thomas Holder
, 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

Re: [PyMOL] subsequent animated zooms

2011-02-15 Thread Thomas Holder
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

Re: [PyMOL] RMSD and Helices in a Protein

2011-03-10 Thread Thomas Holder
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:

[PyMOL] BiologicalUnit/Quat

2011-03-12 Thread Thomas Holder
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

Re: [PyMOL] protein interaction surface

2011-03-14 Thread Thomas Holder
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

Re: [PyMOL] protein interaction surface

2011-03-14 Thread Thomas Holder
, 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

Re: [PyMOL] symexp

2011-03-22 Thread Thomas Holder
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

Re: [PyMOL] alter_state

2011-03-23 Thread Thomas Holder
 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

Re: [PyMOL] Logging the sculpt wizard

2011-03-24 Thread Thomas Holder
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

Re: [PyMOL] Logging the sculpt wizard

2011-03-24 Thread Thomas Holder
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

Re: [PyMOL] Calling pymol from python - access to global variables

2011-03-29 Thread Thomas Holder
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

Re: [PyMOL] RES: radius of gyration

2011-03-31 Thread Thomas Holder
)**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

Re: [PyMOL] Spectrumany bug?

2011-04-06 Thread Thomas Holder
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

Re: [PyMOL] Convert pml script to Pymol Python script

2011-04-09 Thread Thomas Holder
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

Re: [PyMOL] Convert pml script to Pymol Python script

2011-04-09 Thread Thomas Holder
, 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

Re: [PyMOL] Convert pml script to Pymol Python script

2011-04-09 Thread Thomas Holder
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

Re: [PyMOL] How to color in a different way different helix types?

2011-04-12 Thread Thomas Holder
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

Re: [PyMOL] labeling dna residues

2011-04-14 Thread Thomas Holder
)-- 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

Re: [PyMOL] change of color of dashed line in distance command

2011-04-16 Thread Thomas Holder
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

Re: [PyMOL] Get Protein Dimension

2011-04-26 Thread Thomas Holder
://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

Re: [PyMOL] Downloading the biological assembly from the PDB

2011-05-04 Thread Thomas Holder
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

Re: [PyMOL] Simultaneous fading in and out of different representations

2011-05-04 Thread Thomas Holder
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

Re: [PyMOL] nucleic acid (one or two letter) residue names

2011-05-18 Thread Thomas Holder
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

Re: [PyMOL] nucleic acid (one or two letter) residue names

2011-05-18 Thread Thomas Holder
. 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

Re: [PyMOL] nucleic acid (one or two letter) residue names

2011-05-18 Thread Thomas Holder
=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

Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7

2011-05-18 Thread Thomas Holder
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

Re: [PyMOL] How to display clashes

2011-06-06 Thread Thomas Holder
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

Re: [PyMOL] Generating Image of Periodic System

2011-06-14 Thread Thomas Holder
://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

Re: [PyMOL] How to avoid the message ObjectMoleculeGuessValences in pymol1.4.1?

2011-06-16 Thread Thomas Holder
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

Re: [PyMOL] Polar Contacts printed to text file.

2011-06-24 Thread Thomas Holder
(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

Re: [PyMOL] next resi

2011-06-26 Thread Thomas Holder
, 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

Re: [PyMOL] Secondary structure bug?

2011-06-28 Thread Thomas Holder
structure over all states. You may produce distorted intermediates with g_morph, so that consensus might not be appropriate. To only consider first and last state, do this: dss movie, state=-4 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

[PyMOL] personal plugin directory

2011-06-30 Thread Thomas Holder
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

Re: [PyMOL] Delete frames in movie

2011-07-10 Thread Thomas Holder
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

Re: [PyMOL] Superimposing 2 or more Selections PyMOL GUI

2011-07-12 Thread Thomas Holder
, 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

Re: [PyMOL] save new coordinate

2011-07-20 Thread Thomas Holder
.] 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

Re: [PyMOL] save new coordinate

2011-07-20 Thread Thomas Holder
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

Re: [PyMOL] euler-rod axis

2011-07-24 Thread Thomas Holder
, 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

Re: [PyMOL] save new coordinate

2011-07-24 Thread Thomas Holder
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

Re: [PyMOL] Help for surface coloring

2011-07-28 Thread Thomas Holder
-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

Re: [PyMOL] Extending PyMOL or Plugins

2011-07-31 Thread Thomas Holder
python files (this will most likely change in the future). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got Input? Slashdot Needs You. Take our quick survey online

Re: [PyMOL] Help

2011-07-31 Thread Thomas Holder
#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

Re: [PyMOL] radio buttons does not work (Plugin)

2011-08-03 Thread Thomas Holder
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

Re: [PyMOL] Saving each residue to file

2011-08-15 Thread Thomas Holder
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

Re: [PyMOL] Dynoplot : Interactive plot

2011-08-16 Thread Thomas Holder
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

Re: [PyMOL] Dynoplot : Interactive plot

2011-08-16 Thread Thomas Holder
-- 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

Re: [PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?

2011-08-16 Thread Thomas Holder
but it do not work. are you sure? What happens if you try this: alter all, ss='H' as cartoon rebuild Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- uberSVN's rich system

Re: [PyMOL] loading gro files

2011-08-18 Thread Thomas Holder
-- Thomas Holder 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

Re: [PyMOL] Multiple Structure Superposition

2011-08-29 Thread Thomas Holder
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

Re: [PyMOL] Mutagenesis script

2011-09-04 Thread Thomas Holder
-- 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

Re: [PyMOL] (no subject)

2011-09-04 Thread Thomas Holder
) 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

Re: [PyMOL] add polar/aromatic hydrogen

2011-09-06 Thread Thomas Holder
for any suggestions, -- 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

Re: [PyMOL] Mutagenesis script

2011-09-06 Thread Thomas Holder
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

Re: [PyMOL] Mutagenesis script

2011-09-06 Thread Thomas Holder
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) -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download

Re: [PyMOL] add polar/aromatic hydrogen

2011-09-06 Thread Thomas Holder
, 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

Re: [PyMOL] print hydrogen bonds involved residues

2011-09-10 Thread Thomas Holder
suggestions, -- Best Regards, lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Malware Security Report: Protecting Your Business, Customers, and the Bottom Line. Protect your business

Re: [PyMOL] Writing a script yo pymol

2011-09-12 Thread Thomas Holder
://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

Re: [PyMOL] print hydrogen bonds involved residues

2011-09-12 Thread Thomas Holder
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

Re: [PyMOL] compare crystal packing of two different Space Groups

2011-09-12 Thread Thomas Holder
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

Re: [PyMOL] compare crystal packing of two different Space Groups

2011-09-13 Thread Thomas Holder
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

Re: [PyMOL] pymol wildcards usage

2011-09-13 Thread Thomas Holder
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

Re: [PyMOL] refresh molecule display in python script

2011-09-14 Thread Thomas Holder
-- 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

Re: [PyMOL] regarding the dssp plugins

2011-09-16 Thread Thomas Holder
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

Re: [PyMOL] regarding the dssp plugins

2011-09-16 Thread Thomas Holder
the -na option, thus will fail with my script without modifying it. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA http

Re: [PyMOL] how to organize those .py

2011-09-19 Thread Thomas Holder
, lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg

Re: [PyMOL] How to print sequence based on structure

2011-09-19 Thread Thomas Holder
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

Re: [PyMOL] Dynoplot : Interactive plot

2011-09-20 Thread Thomas Holder
, 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

Re: [PyMOL] A quick Q: zoom

2011-09-21 Thread Thomas Holder
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

Re: [PyMOL] Write in a file the number of water at a distance from a protein surface

2011-09-22 Thread Thomas Holder
), 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

Re: [PyMOL] help needed

2011-09-23 Thread Thomas Holder
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

[PyMOL] comparison of distance operators

2011-09-23 Thread Thomas Holder
, 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

Re: [PyMOL] how to change atom name

2011-09-27 Thread Thomas Holder
: 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

[PyMOL] Fwd: Rendering 3D Surveys with Pymol

2011-10-06 Thread Thomas Holder
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

Re: [PyMOL] Rotation of a Protein

2011-10-10 Thread Thomas Holder
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

Re: [PyMOL] How did they generate this figure

2011-10-10 Thread Thomas Holder
? 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

Re: [PyMOL] how can quickly make a fractional atoms into one

2011-10-11 Thread Thomas Holder
-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

Re: [PyMOL] Ray Trace Mode 1 and Labels

2011-10-15 Thread Thomas Holder
? 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

Re: [PyMOL] how to activate pymol from remote server

2011-10-15 Thread Thomas Holder
, 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

Re: [PyMOL] how to activate pymol from remote server

2011-10-17 Thread Thomas Holder
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

Re: [PyMOL] about Display CCP4 Maps

2011-10-25 Thread Thomas Holder
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

Re: [PyMOL] about Display CCP4 Maps

2011-10-25 Thread Thomas Holder
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

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