Re: [PyMOL] sources for PyMOL 2

OK, I found the answer myself, googling in this email list. Sources will be released early next year, I understood. I'll wait patiently :) Cheers, Albert On 22/11/17 11:49, Albert Solernou wrote: Dear All, we have been writing a plugin for PyMOL during the last years, released as G

[PyMOL] sources for PyMOL 2

Dear All, we have been writing a plugin for PyMOL during the last years, released as GPL. I would like to support PyMOL2, but need to know whether the code will be made accessible or not. Is PyMOL2 still free software? And if so, can we get access to the source code? Thanks, Albert

Re: [PyMOL] how to convert .pse to html?

File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py", line 152, in dump_rep int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2]))) IndexError: tuple index out of range Do you have any idea what's the problem? THX again. On 01/25/2017 10:46 PM, Thom

Re: [PyMOL] how to convert .pse to html?

Hi Thomas, Thanks a lot for your information. I know this command and that's what I needed. However, I don't what to open the PyMOL GUI. Is it possible that we run PyMOL with a text mode and convert the .pse file directly to a .html file? Thanks again. Albert On 01/25/201

[PyMOL] how to convert .pse to html?

Hello, I've got a pymol .pse file and I am just wondering how can we convert it with a Linux command line directly to a .html file without opening pymol GUI? Thank you very much. Albert -- Check out the vibrant

Re: [PyMOL] New plugin: PyMOLProbity

fantastic job!! Thanks a lot. Albert On 01/16/2017 10:16 PM, Sampson, Jared M. wrote: Dear PyMOL Users, I am pleased to introduce a new plugin called PyMOLProbity <https://github.com/jaredsampson/pymolprobity> which allows a PyMOL user to visualize MolProbity-style structural vali

Re: [PyMOL] Save command output to a file in pymol

I think you can obtain it from your Linux terminal On 01/13/2017 10:34 AM, Academic Research wrote: Pymol Professionals I need your help, I have the following command: |iterate n. CA, print resi + ':' + ss | I use this command in pymol to print out each residue number and its correspondi

Re: [PyMOL] how to show PBC box?

Dear Tsjerk: Thanks a lot for such prompt reply. It works very well. Cheers. Albert On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote: Hi Albert, You can do: show cell Cheers, Tsjerk -- Developer Access Program

[PyMOL] how to show PBC box?

ank you very much. Albert -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Col

Re: [PyMOL] loading StringIO

That's lovely, David. Thanks, Albert On 10/26/2016 11:56 AM, David Hall wrote: > https://pymolwiki.org/index.php/Read_Pdbstr > > -David > > On Oct 26, 2016, at 3:55 AM, Albert Solernou <mailto:a.soler...@leeds.ac.uk>> wrote: > >> Dear All, >> I wa

Re: [PyMOL] loading StringIO

Hi Jordan, I still don't figure out how to do that with "load_object". What is the "type" for a file handler? Would be "object" the file handler itself? Albert On 10/26/2016 10:58 AM, Jordan Willis wrote: > Probably could use load_object instead. > >

[PyMOL] loading StringIO

Dear All, I was wondering if there was a way to load a PDB file stored in memory instead of disk, i. e., a memory file, defined through StringIO or tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could handle an open file instead of a file? Thanks, Albert

Re: [PyMOL] problem of optirun in Pymol

Hello: I am using openSUSE 13.2 X64 OS. Pymol works fine without optirun in 1.8.4. Here is output from ./pymol -c PyMOL>python end PyMOL: normal program termination. However, when I type optirun ./pymol -c I didn't obtain any information. regards Albert On 10/10/2016

[PyMOL] problem of optirun in Pymol

mol Pymol doesn't start and I didn't get any error messages from terminal either. I am just wondering how can we solve the problem? Thx a lot Albert -- Check out the vibrant tech community on one of the world&#

Re: [PyMOL] problem of internal_gui

I see. It works very well now. Thanks a lot On 10/06/2016 10:32 PM, Thomas Holder wrote: > Hi Albert, > > "internal_gui" is now a blacklisted setting not be stored or restored from > session files. > > You can launch PyMOL without internal gui like this f

[PyMOL] problem of internal_gui

to solve this problem? I am using PyMOL-1.8.2.3. I also tested in the latest 1.8.4, it has the same issue. Thank you very much. Albert -- Check out the vibrant tech community on one of the world's most engaging

[PyMOL] how to hide dashed artificial cartoon?

Hello: I noticed that if I show my structure as cartoon, there would be a "dashed loop" cartoon filling in the missing part of my structure. I am just wondering how can we disable PyMol show the missing part automatically? Thank you very mu

[PyMOL] VR for Pymol?

Hello: Does anybody have any idea whether PyMol support Virtual Reality (VR)? Can we use the following VR devices to visualize PyMOl in computer? http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-reality-performance-power https://www.youtube.com/watch?v=U4JPhUr_d7g If yes, will any VR de

Re: [PyMOL] selecting faces and vertices in CGOs

be very grateful if you could give me some hints on the code structure, and on how to tackle the inclusion of this new feature. Cheers, Albert On 04/08/2016 09:18 PM, Thomas Holder wrote: > Hi Albert, > > This is currently not possible and adding this would be a very major project. &g

[PyMOL] selecting faces and vertices in CGOs

Dear All, I was wondering if there is a way to select faces, vertices and/or edges from a CGO either using the mouse or the command line. How difficult would be to add this, and how would you do that? It would be very useful for us if we could get that working. Thanks, Albert

[PyMOL] why lib/python folder is missing?

Hello: I am using the following command line to compile PYmol: setenv prefix /home/albert/install/pymol/open-1.8 setenv modules $prefix/modules python setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix However, I noticed that there is no the "lib/pyth

[PyMOL] how to get an atom coordinates information

Hello: I would like to know the XYZ information of a specific atom. I am just wondering how can we do this? Is there any command line? thank you very much Albert -- Site24x7 APM Insight: Get Deep Visibility into

[PyMOL] pymol crashed reading any structure file

Dear: I've compiled pymol-1.8.0 under my Linux X64 OS. I found that Pymol can start by command: pymol without any complaints or erros. However, when I try to load a .pdb file into pymol, pymol always failed with following messages:

Re: [PyMOL] how to close displaying a molecule

just click the b.pdb on the Pymol object manager bar to undisplay it. That's the basic of basic usage of Pymol. Wouldn't it be nice if you spend a few minutes to go through Pymol manual? On 12/11/2015 08:19 AM, Smith Liu wrote: Dear All, Suppose by pymol I have opened A.pdb abd B.pdb. Is a

Re: [PyMOL] real time minization in Pymol

Yes, I also really love this function. However, for the sake of accuracy, I believe many users will also strongly demand for introducing forcefield for minimization..I am looking forward to see that "optimize" plugin would somehow merged into "Molecular Sculpting".At least, it is very e

[PyMOL] real time minization in Pymol

for the ligand). There is a "optimize" plugin in Pymol, maybe the developer can consider merge them together? Thank you very much Albert -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your

Re: [PyMOL] default fetch format

Hi Thomas: thanks a lot for helpful advice. May I ask is there any superior features of mmCIF format against PDB format? regards Albert On 11/22/2015 04:15 PM, Thomas Holder wrote: > Hi Albert, > > Unfortunately the default fetch type can't be configured. But you can > o

[PyMOL] can we clone representation?

Thank you very much Albert -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:

[PyMOL] default fetch format

Hello: I noticed that if we run command: fetch 2ac1 to get PDB into pymol in Version 1.8.0, it downloaded .cif file by default. I am just wondering is it possible to change the default format as .pdb file? thanks a lot Albert

Re: [PyMOL] problem of pymol 1.8

otter). I google it, and cannot find any helpful information.... thanks again ALbert On 11/18/2015 11:16 PM, Thomas Holder wrote: > Hi Albert, > > These messages come from third-party plugins that you have installed, see: > http://pymolwiki.org/index.php/MtsslDock > http://pymol

[PyMOL] problem of pymol 1.8

ed wx Unable to initialize plugin 'mtsslTrilaterate' (pmg_tk.startup.mtsslTrilaterate). I am just wondering how can we solve the problem? I've already installed python PMW in my machine.

Re: [PyMOL] Stacking Interactions

I think the major concern is how Pymol depicts the pi-pi stacking Of course we can identify such interaction immediately as soon as we open the system in Pymol. However there is no any components to indicate this, eg: we can depict the H-bond with a dash between two atoms but how could pi

[PyMOL] GTX980Ti for Pymol 3D?

Hello: Does anybody know whether Nvidia GTX980Ti support Pymol active stereo 3D? I saw someone said that some GTX graphic card may also work, but I am not sure for this one. Thx a lot -- ___

[PyMOL] how to enable 3D

://istar.cse.cuhk.edu.hk/iview/ and here is script for this tool https://github.com/HongjianLi/istar/tree/master/public/iview Thank you very much. Albert -- ___ PyMOL-users mailing list (PyMOL

Re: [PyMOL] pymol to webGL?

Dear Osvaldo: Thanks a lot for further information. I just run the command |set pse_export_version, 1.72 | before I load anything to pymol, then followed the step for exporting. But it still failed with messages: Traceback (most recent call last): File "/home/albert/install/

Re: [PyMOL] pymol to webGL?

Thanks a lot for further advice. Here is what I got: PyMOL> run exportToWeb.py PyMOL>exportToWeb my Traceback (most recent call last): File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line 256, in parse self.result=apply(layer.kw[0],layer.args,layer

[PyMOL] pymol to webGL?

Hello: I noticed that there is a plugin called exportToWeb.py I try to rum it with command: python exportToWeb.py test.pse However, no any new file generated I am just wondering how shall we use this script correctly? thanks a lot Albert

[PyMOL] restriction format?

e permission to export them as PDB file or the like Thank you very much Albert -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.

Re: [PyMOL] APBS problem

thanks a lot for reply. Problem solved after I specify the maloc library path explicitly in my tcsh environment. setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib On 10/08/2015 05:02 PM, Andreas Forster wrote: Hi Albert, I apologize that I take your email for a grumpy old

[PyMOL] how to setup environment for APBS?

? thanks a lot Albert -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail

[PyMOL] APBS problem

Hello: I am trying to calculate the protein surface electstatic properities by APBS plugin in pymol. But it always failed with messages: Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist? Does a

[PyMOL] label

Hello: Does anybody have any idea whether pymol could label the absolute configuration (R/S) for a chiarity atom? Thank you very much. Albert -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real

[PyMOL] how can we display properties?

Hello: I've got a ligand .sdf file which contains many informations such as: molecule weight, logP, surface area and so on. I am just wondering is it possible to display those properties in Pymol? Thank you very much A

[PyMOL] can we show ligand in 2D?

Hello: I've got a 3D coordinate in 3D. I am just wondering is it possible to show it in 2D diagram in Pymol for a ligand so that we can get more clear idea how exactly the ligand looks like? thanks a lot A

[PyMOL] any hotkey?

Hello: I am just wondering is there any hotkey in Pymol so that we can center in the Ligand automatically? For instance: If I press keyboard "L", Pymol zoom to ligand binding pocket automatically Thanks a l

[PyMOL] how to copy color?

Hello: I've colored object1 in various color in different regions. I am just wondering how can we copy the color scheme for object1 to object2? Object 2 is the same protein with object1 but with different conformations. Thank you very much A

[PyMOL] how can we change GUI font size?

Hello: I notice that my screen resolution is too high that the font of pymol GUI looks extremely small. I am just wondering is it possible to increase them? thank you very much. -- Don't Limit Your Business. Reach for

[PyMOL] problem of Pymol git install

Hello: I've installed pymol git repo following steps: http://www.pymolwiki.org/index.php/Git_install However, when I start pymol, it always showed the following messages: No module named tkintertable.Tables Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui). No module name

[PyMOL] how can we rotate torsion angle of a molecule?

just wondering is it possible for pymol give alternative rotamer conformation of a protein residue? thanks a lot Albert -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you wit

[PyMOL] opensource for commercial use?

Hello: I just got a question: can we use the open source version of pymol for commercial usage? Or can we develop some commercial tool based on Pymol? thank you very much. Albert -- Don't Limit Your Business.

Re: [PyMOL] RMS over a MD trajectory.

Oh, I see... It looks like I'll need to end up writing a short script that does the loop along the trajectory together with a correct RMS calculation. Thanks for the tip, Carsten. Cheers, Albert On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote: > Hi Al, > > based on

Re: [PyMOL] RMS over a MD trajectory.

Thanks Thomas, I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] (RMSD after refinement) but your "cycles=0" looks cleaner. Cheers, Albert On 05/06/2015 05:14 PM, Thomas Holder wrote: > Hi Albert, > > Please pay attention to the difference between all

Re: [PyMOL] RMS over a MD trajectory.

Terribly useful Carsten! I could easily do a loop and get the RMS along the trajectory: k = [] for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i)) for i in range(100): print k[i][0] Cheers, Albert On 05/06/2015 04:20 PM, Schubert, Carsten [J

[PyMOL] RMS over a MD trajectory.

RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- ----- Dr Albert Solernou EPSRC Resea

[PyMOL] unable to export obj

l versions 1.7.4 and 1.6.0. Saving into an obj file works well when surface_type is set to 0, or 1. Any help? Best, Albert -- ----- Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy,

Re: [PyMOL] rms_cur, rms, fit - No atoms selected

Thanks!! Now it works!! albert En/na Warren DeLano ha escrit: > (Sorry if this is dupe -- my email client is acting up...) > > the rms_* and fit commands required that the atoms in each selection to have > matching identifiers: such as chain, resi, segi, resn, etc. You can use t

[PyMOL] rms_cur, rms, fit - No atoms selected

g with ubuntu, apt-get), and compliling the source code from the svn of the current version, 1.2-x. Same results. Hope someone can help me, albert