Re: [PyMOL] Change default read position of .pymolrc and .pymolrc.py

. We have builded svn pymol at our unilabs linux computers. Is there a way to tell pymol it should look for .pymolrc and .pymolrc.py other places than the users home library? Or can you run the commands in these files in another way? Best Troels -- Thomas Holder MPI

Re: [PyMOL] Update Selection From Frames

-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ''' Show water atoms within some radius of a reference atom during a movie. ''' from pymol import cmd obj = 'myobj' natoms = 50 # create water for i in range(natoms): cmd.pseudoatom(obj, pos=[i*3,0,0], resn='HOH', name='O

Re: [PyMOL] list of polar contacts

-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99

Re: [PyMOL] list of polar contacts

-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99

Re: [PyMOL] list of polar contacts

', list_dist) -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers

Re: [PyMOL] Missing residues in PDB

I put a script on the PyMOLWiki that does renumbering based connectivity: http://pymolwiki.org/index.php/Renumber Cheers, Thomas On 01/30/2012 02:52 PM, Thomas Holder wrote: On 01/30/2012 02:24 PM, gontchar andrey wrote: Thanks a lot! A very useful script, but not exactly that I need

Re: [PyMOL] Missing residues in PDB

set_sequence CDEFGHIKL, myobj Cheers, Thomas On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote: Hi Andrey, I have a script that updates the sequence based on residue numbering (resi). See attachment. Usage: set_sequence sequence [, selection [, start ]] Example: # import

Re: [PyMOL] Editing of the pdb structure

, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99

Re: [PyMOL] Set values for dihedral angles

to work with selections. Note that you can quickly query phi/psi angles with phi_psi command. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen set_phipsi.py Description: application/chimera

Re: [PyMOL] morphing

with the morphing and refinement scripts in pymolv1.5 (both windows 64 and/or linux 64 version is fine). With my very best regards. Hasan- -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ''' Simplified morphing workflow (c) 2011 Thomas Holder License: BSD-2-Clause

Re: [PyMOL] Set values for dihedral angles

of the alpha helix was distorded. Is there any possible ways to make this conversion ? James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current

Re: [PyMOL] Distance measurement between atom groups

. In addition I'd like to measure potential H-bond distance between above residues (polar contacts between electronegative groups) as well as tight packing forces ( distance between non-polar residues). Is there any simplest method for that purpose ? Thanks, James -- Thomas Holder MPI

Re: [PyMOL] Protein-ligand interactions

onlyvisible.pdb, visible Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library

Re: [PyMOL] Protein-ligand interactions

environment which has only short pieces of the polymer. PyMOL sees chain breaks there. You can suppress TER records by: unset pdb_use_ter_records Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Addition of the missing hydrogen atoms

flexibility. Thanks, James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft

Re: [PyMOL] Protein-ligand interactions

set h_bond_cutoff_edge, 4.0 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning

Re: [PyMOL] Rebuild/install of pymol after svn up ?

2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27

Re: [PyMOL] Using super correctly

-- RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Using super correctly

that for align, the default value of seq was -1 and for super, the default value was 0. Executive.c, line 8062 /* negative seq_wt means sequence only! */ Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

[PyMOL] First pre-release of new plugin architecture

. In particular if something does not work as expected. Incompatible with: http://pymolwiki.org/index.php/Plugindirectory See also: http://pymolwiki.org/index.php/PluginArchitecture Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] First pre-release of new plugin architecture

. And the scripts i download from the git repository is placed here. Are you sure about that? Can you please copy/paste this to the PyMOL command prompt and send me the output? import pymol print pymol.__path__ import pmg_tk print pmg_tk.__path__ print cmd.__name__ Thanks, Thomas -- Thomas Holder

Re: [PyMOL] Mutagenesis and states

states? Anyone know to accomplish what I'm setting out to do? Justin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools to simplify cross

Re: [PyMOL] Import MRC files from http://3vee.molmovdb.org/index.php to pymol

the representation, so use the 'isolevel' command (http://www.pymolwiki.org/index.php/Isolevel). This should be documented on the PyMOLWiki somewhere under 3rd Party Tools (or web servers). Cheers, -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] POV-ray

setting in the *.inp file. The bmp output from POV-ray looks worse than the preview window in PyMOL. Is there something I need to change in the *.inp file or configure in POV-ray? Thanks, Corey -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] about super_all.py Plugin installation.

in Pymol wherein one can align 4-5 structures at a time (with low sequence identity). Pavan Payghan On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder spel...@users.sourceforge.net mailto:spel

Re: [PyMOL] about super_all.py Plugin installation.

Hi, I put a new script on the PyMOLWiki that is more flexible than the other all-to-one solutions: http://pymolwiki.org/index.php/Extra_fit Cheers, Thomas Thomas Holder wrote, On 12/30/11 10:50: Dear Pavan, I'm sorry that this appears to be so complicated. The super command in PyMOL

Re: [PyMOL] Transformation Matrices

the states' interelations. Jacob -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources

Re: [PyMOL] about super_all.py Plugin installation.

sequence identity). Pavan Payghan On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net mailto:spel

Re: [PyMOL] alignment by residue

-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell

Re: [PyMOL] about super_all.py Plugin installation.

wrote, On 12/27/11 13:27: Dear Mr. Thomas Holder , Thanks for the reply .According to you the plugin has been installed properly.Can you briefly mention 1.how to define the reference object for using super command 2.how to use super command with multiple structures to align

Re: [PyMOL] about super_all.py Plugin installation.

*** -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps

Re: [PyMOL] about super_all.py Plugin installation.

Dear Pavan, 2. Then super_all xyz.pdb Not the filename, but the name of the loaded object (by default this is the filename without .pdb suffix). super_all xyz Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] How to overcome bond length restriction to build a general stereo geometric model

. The bonds do not show up in pymol. How to solve this problem? Thank you very much. Teddy -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools

Re: [PyMOL] Color states as rainbow

%02x00ff % (i * 255 / (2 + cmd.count_states())) part. Best regards, Takanori Nakane -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools

Re: [PyMOL] Color states as rainbow

On 12/20/2011 11:49 AM, Thomas Holder wrote: On 12/19/2011 11:20 PM, Jason Vertrees wrote: Cleaned up a little, this would make a nice simple addition to the PyMOLWiki script library. I can do it, on the basis of spectrumany. there it is: http://pymolwiki.org/index.php/Spectrum_states

Re: [PyMOL] Color states as rainbow

better, can you tell me the most efficient way to color the states by some color pattern (presumably I will just use the spectrum). This kind of thing should have been used in NMR or MD figures all the time, no? Thanks very much, Jacob Keller -- Thomas Holder MPI for Developmental Biology

Re: [PyMOL] Center of screen?

at the center of the viewing area that always shows where the center is? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Color states as rainbow

. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event

Re: [PyMOL] Problem with distance command(?)

and registration details link at the bottom of the page.. __ -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 10 Tips

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

if not succeeded. do you have a graphics driver with direct rendering support installed? glxinfo | grep direct Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Cloud Services

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

installed this way before adding it to the wiki. I guess yumex is not necessary, does this command work as well? yum --enablerepo=epel install pymol Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Electron Density

PM, Manas Sule wrote: Is there a difference in the sigma values assigned by pymol and coot I am able to see the density at 8 sigma in coot for the Fo-Fc map but can go to maximum at 4.5 sigma in pymol after which it disappears -- Thomas Holder MPI for Developmental Biology Spemannstr

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

in $HOME/pymol-svn - Original log has some Japanese messages so I added /* means ... */ Regards, Masataka -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously

[PyMOL] frames around code in PyMOLWiki

can we have frames around code blocks like before? Or am I the only one who misses them? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously

Re: [PyMOL] frames around code in PyMOLWiki

ago. Check out the options here: http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi. I just modified the extension to allow this. If you want it then change: source lang=python to source lang=python enclose=div Cheers, -- Jason -- Thomas Holder MPI for Developmental Biology

Re: [PyMOL] RMSD between two structures

matches. Cheers, Tsjerk On Wed, Nov 30, 2011 at 11:05 AM, Martin Hedigerma@bluewin.ch wrote: How does PyMOL calculate the RMSD between two structures where the number of atoms is different? Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] H-bonds representation

, James -- 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 performance

Re: [PyMOL] H-bonds representation

residues of the ligand binding pocket) just like before, but with ligand as selection 1 and receptor as selection 2. Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] creating PDB structure

this: edit first (name N) Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record

Re: [PyMOL] Expose PyMOL API

of PyMOL? An example, the below is a script (inspired by Thomas Holder) which saves down to disk all amino acids of a protein structure into separate PDB files. # * from pymol import cmd from pymol import stored from

Re: [PyMOL] Expose PyMOL API

? Could it be that the 'pymol/pymol_path' call is not exactly right? In the modules/pymol directory, there is a module 'pymol/launch_pymol', but I have a similar error (No module named _cmd) when I try to import it. Martin Am 22.11.11 09:47, schrieb Thomas Holder: Hi Martin

Re: [PyMOL] measuring helix angle

: Hi, Can anyone guide me how to use the pymol script to calculate the angle between two helices? Where and how to edit the script? I have 2 helices in a pdb file as follows: protein.pdb hel1 is chain A: 6-20 hel2 is chain A: 26-39 Thanking you in advance... Hena -- Thomas Holder

Re: [PyMOL] Torsion angles

on the ramachandran map values for each structure ( by points or other markers) Finaly could you show me some tutorials wich could help me working with torsions in pymol? Thanks for your help, James -- Thomas Holder MPI for Developmental Biology

Re: [PyMOL] Fwd: Torsion angles

could mark Chi-1 angle for all my structures and plot in on Rama map? I don't know of any easy solution to that, sorry. Maybe someone else? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology DynoPlot.py Description: application/chimera

Re: [PyMOL] Fwd: Torsion angles

with the modifications (but markers by secondary structure are disabled by default to not change the previous behaviour). http://pymolwiki.org/index.php/DynoPlot Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] RMSD between two structures

without aligning? Thanks for hints Martin -- Thomas Holder MPI for Developmental Biology -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1

Re: [PyMOL] Put scripts in a svn folder

the scripts from the subversion folder. How does this idea sounds? Bes Troels -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http

Re: [PyMOL] Filled rings for cyclic molecules?

cartoon_ring_mode, 3 as cartoon It's a bit hidden in the PyMOLWiki: http://pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons#Cartoon_ring_finder Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Editing of the pdb structure

, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1

Re: [PyMOL] Pymol movie

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 -- Get your Android app more play: Bring

Re: [PyMOL] Putting a protein molecule into a grid and traversing through the grid

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

Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

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

Re: [PyMOL] about Display CCP4 Maps

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

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

Re: [PyMOL] about Display CCP4 Maps

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

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

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] Ray Trace Mode 1 and Labels

? 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

, 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 can quickly make a fractional atoms into one

-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] Rotation of a Protein

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

? 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

[PyMOL] Fwd: Rendering 3D Surveys with Pymol

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] how to change atom name

: 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

Re: [PyMOL] help needed

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

, 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] Write in a file the number of water at a distance from a protein surface

), 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] A quick Q: zoom

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] Dynoplot : Interactive plot

, 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] how to organize those .py

, 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

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] regarding the dssp plugins

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] refresh molecule display in python script

-- 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] compare crystal packing of two different Space Groups

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

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] Writing a script yo pymol

://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

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

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] print hydrogen bonds involved residues

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] add polar/aromatic hydrogen

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

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

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

, 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] Mutagenesis script

-- 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)

) 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] Multiple Structure Superposition

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] loading gro files

-- 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] Dynoplot : Interactive plot

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

-- 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] Saving each residue to file

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] 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

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