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

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] Extending PyMOL or Plugins

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

#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] Help for surface coloring

-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] euler-rod axis

, 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

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] save new coordinate

.] 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

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] Superimposing 2 or more Selections PyMOL GUI

, 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] Delete frames in movie

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

[PyMOL] personal plugin directory

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] next resi

, 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] Polar Contacts printed to text file.

(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] How to avoid the message ObjectMoleculeGuessValences in pymol1.4.1?

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] Generating Image of Periodic System

://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 display clashes

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] nucleic acid (one or two letter) residue names

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

. 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

=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

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] Downloading the biological assembly from the PDB

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

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] Get Protein Dimension

://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] change of color of dashed line in distance command

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] labeling dna residues

)-- 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] How to color in a different way different helix types?

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] Convert pml script to Pymol Python script

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

, 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

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] Spectrumany bug?

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] RES: radius of gyration

)**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] Calling pymol from python - access to global variables

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] Logging the sculpt wizard

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

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] alter_state

 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] symexp

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] protein interaction surface

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

, 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

[PyMOL] BiologicalUnit/Quat

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] RMSD and Helices in a Protein

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:

Re: [PyMOL] subsequent animated zooms

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] Calculating domain rotations

, 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] Faster way to find polymer chains?

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] Fab elbow angle

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] Atom Numbering

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] Disappearing right-hand control panel

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] Super Bug Report

, 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?

, 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?

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?

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] Mutagenesis How many rotamers per amino acid

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] [PyMol] Changing atom charges using the command line

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

[PyMOL] New script: spectrumany

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] Plane Script Updates

.  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

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

- 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] Fwd: feature request: supercell construction

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

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] feature request: supercell construction

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] feature request: supercell construction

, 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] B-factor replacing problem

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

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