Re: [PyMOL] PyMOL with Python 3

of the scripts work on py2 and 3 simultaneously. I will create a new branch in the repo. I someone likes to help, you are very welcome to send PRs. Please send one PR per script for the ease of reviews. Justin smime.p7s Description: S/MIME Cryptogr

Re: [PyMOL] PyMOL with Python 3

On 07/12/15 10:42, Justin Lecher wrote: > On 07/12/15 10:23, Spencer Bliven wrote: >> Nice work! It will be very nice to have python3 compatibility in the future. >> >> It would be nice to organize a section of the pymol-script-repo for >> python3-compatible scripts o

Re: [PyMOL] Using Python 3.4.3 Shell

ot;<pyshell#12>", line 1, in > import pymol > ImportError: No module named 'pymol' > > I would very appreciate your help. > Hi, simply you can't right now as pymol is not python3 ready yet. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structur

Re: [PyMOL] What legal license does PyMOL's logo available under?

in distro packages. At least Fedora and Gentoo are using it separately from the svn repo. Cheers, Justin smime.p7s Description: S/MIME Cryptographic Signature -- ___ PyMOL-users

Re: [PyMOL] Compile Errors on SVN 4111

to CXXFLAGS would be more appropriate. Works here on Gentoo systems flawlessly. Justin smime.p7s Description: S/MIME Cryptographic Signature -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored

Re: [PyMOL] Compile Errors on SVN 4111

On 19/03/15 20:45, Thomas Holder wrote: Hi Justin, unfortunately, not everyone is on Gentoo... see comment about distutils and CXXFLAGS here: https://sourceforge.net/p/pymol/bugs/159/#58a5 Hi Thomas, absolutely right, scipy is also suffering from this. There is an open bug at distutils

[PyMOL] Pymol wiki search is not working

in the Pymol wiki. Could this be fixed? thanks, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature

Re: [PyMOL] PyMOLWiki Update

, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature

Re: [PyMOL] Making nmr-like ensemble from several pdbs

On 27/08/14 07:43, James Starlight wrote: and than how to quick merged aligned conformers back to the NMR ensemble including TER record between each model in it? Hi James, in addition you need the MODEL # [1] - ENDMDL [2] entry. Justin 1) http://wwpdb.org/documentation/format33/sect9.html

Re: [PyMOL] Making nmr-like ensemble from several pdbs

On 27/08/14 07:56, James Starlight wrote: Hi both of them are present in my ensemble. the problem is not here- if it possible i could upload the ensemble.pdb to some server if someone could check it. James Hi, Go for some paste bins or do a gist on github. Justin -- Justin Lecher

Re: [PyMOL] cartoon_transparency issue

/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Hi markus, just raytrace you figure using the ray command. Justin

[PyMOL] Error with volume representation of difference maps

,\ 13.251377106, 22.765058517, -20.0 ) Sincerely, Justin T. Biel Graduate Student University of California San Francisco -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms

[PyMOL] Contouring isomesh to absolute values

Is it currently possible to contour map representations (i.e. isomesh) by absolute values (electrons per cubic angstroms) rather than by the map's sigma value? For example, this is useful when making figures comparing maps from two different structures. Sincerely, Justin T. Biel Graduate

Re: [PyMOL] Font problem

On 11/03/14 07:52, Justin Lecher wrote: On 10/03/14 21:52, Thomas Holder wrote: Hi Justin, this is fixed in SVN rev 4070, sorry that it took so long. Cheers, Thomas Hi Thomas, Thanks a bunch. I will try it out tomorrow on my 3D machine. Cheers, Justin Looks beautiful now

Re: [PyMOL] Font problem

On 10/03/14 21:52, Thomas Holder wrote: Hi Justin, this is fixed in SVN rev 4070, sorry that it took so long. Cheers, Thomas Hi Thomas, Thanks a bunch. I will try it out tomorrow on my 3D machine. Cheers, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural

Re: [PyMOL] Font problem

On 22/11/13 17:44, Jason Vertrees wrote: Hi Justin, We'll fix that, too. Cheers, -- Jason Hi Jason, did you find time to look into that? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone

[PyMOL] Font problem

the font rendering during shader activated mode? thanks Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature

Re: [PyMOL] Font problem

Regards, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature

Re: [PyMOL] Stereo (quad-buffered) and fixed object (Sequence, Sidebar) are suboptimal

On 15/07/13 18:56, Thomas Holder wrote: Hi Justin, we fixed this in sourceforge SVN today. Please recompile and check if it works for you. Thanks. Cheers, Thomas Thanks Thomas, works perfectly now! Cheers, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural

[PyMOL] Stereo (quad-buffered) and fixed object (Sequence, Sidebar) are suboptimal

Hi, Static objects like the sidebar and the sequence are only rendered for one eye. This results in some unpleasant optical effects due to one eye seeing different things as the other when having stereo switched on. Is it possible to render those objects for both eyes? Thanks Justin

Re: [PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

*on linux 64.* I have made this progress http://pymolwiki.org/index.php/3d_pdf#Linux_install But when I compile, I get. Hi, try this one http://www2.iaas.msu.ru/tmp/u3d/u3d-1.4.3.tar.gz it only has problems with gcc-4.7 but I can provide a patch if needed. Justin -- Justin Lecher Institute

Re: [PyMOL] Open Source PyMOL v1.5.0.1

Hi Jason, I found a bug. If you set Display - Quality - Maximum Quality turns the display around. That means the back is in the front and small, and the front, larger parts are in the back. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On 14/02/12 09:29, Lecher, Justin wrote: Hi Jason, I found a bug. If you set Display - Quality - Maximum Quality turns the display around. That means the back is in the front and small, and the front, larger parts are in the back. justin To be more precise, it seems that this only

Re: [PyMOL] Open Source PyMOL v1.5.0.1

: ‘molfile_qm_metadata_t’ has no member named ‘have_npa’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11: error: ‘molfile_qm_metadata_t’ has no member named ‘have_internals’ error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1 Thanks, justin smime.p7s Description

[PyMOL] Mutagenesis and states

individually. Maybe I need more knowledge on what is going on when I modify states? Anyone know to accomplish what I'm setting out to do? Justin -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app

Re: [PyMOL] cartoon_sidechain_helper

Strange, yesterday I did a quick test and it didn't work. But here on my main machine everything is fine. Sorry for the noice. jsutin On 13/11/11 17:48, Jason Vertrees wrote: Hi Justin, It works; see http://www.pymolwiki.org/index.php/File:Cartoon_side_chain_helper_on.png. You just have

[PyMOL] cartoon_sidechain_helper

Hi, while trying this http://kpwu.wordpress.com/2011/11/12/pymol-sidechain-helper-in-the-cartoon-view/ I recognised that the color by atom type function doesn't work anymore if the sidechain helper is on. Bug or feature? Could we enable it? Thanks justin -- Justin Lecher Institute of Complex

[PyMOL] Antw.: Put scripts in a svn folder

I started this some time ago and also announced it on the mailing list. But it didn't caught much interest. https://github.com/jlec/Pymol-script-repo So if there is interest, please feel free to check in your scripts. Justin - Reply message - Von: Thomas Holder spel

Re: [PyMOL] Antw.: Put scripts in a svn folder

the main repo can be forked, modified and request pull (http://help.github.com/fork-a-repo/). justin On 11/10/11 5:45 PM, Troels Emtekær Linnet wrote: I personally think git hub is a good suggestion. And we need you wikiguys (Jason etc. ) to catch the idea and implement it. :-) Security

Re: [PyMOL] Volumes video

. Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature

Re: [PyMOL] PyMOL Project Updates Open Source PyMOL v1.4b1

Hi Jason, could you please use PYMOL_DATA to determine the location of the shaders dir? it is actually stored in PYMOL_DATA/shaders and with PYMOL_DATA != PYMOL_PATH/data it fails. Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich

Re: [PyMOL] New plugin: MSMS plugin for PyMOL

, it is officially included in Gentoo Linux now [1]. It would be nice, if you could drop me a mail, in case you changed something, so that I can create a bumped version. thanks justin [1] http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-msms Might take some hours to appear

Re: [PyMOL] pymol fetch

? The fetch command directly fetches the pdb file from the online database. -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP

Re: [PyMOL] Please remove my emal address from your bulletin board

to unsubscribe is included in every mail inside the header List-Unsubscribe: https://lists.sourceforge.net/lists/listinfo/pymol-users, mailto:pymol-users-requ...@lists.sourceforge.net?subject=unsubscribe justin signature.asc Description: OpenPGP digital signature

[PyMOL] PYNMR or NMR support in Pymol

this idea? Perhaps it is a small fix to get the pyNMR code working with the newer versions of pymol. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385

Re: [PyMOL] subversion 3897 compile error in Cmd.c

Hi Hari, the distutils based build is fine. justin signature.asc Description: OpenPGP digital signature -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs

Re: [PyMOL] CEalign - PyMOL Build

+1 from me -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature

Re: [PyMOL] Pre-release version of the PyMOL-APBS plugin

, you can find the plugin in the sci overlay as sci-chemistry/pymol-apbs-plugin. There is a version for revision 11 as well as a live ebuild available. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich

Re: [PyMOL] Problem Compiling Pymol 1.2.x

succesfull. So please try to provide us the log, in worst case compress it and attach it to your mail. What exactly is the output if you start it in a shell? Justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH

[PyMOL] graphic bug?

? pymol HEAD of svn linux-2.6.30 xorg-server-1.6.3 intel-driver-2.8.0 Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB3 - structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital

Re: [PyMOL] Error: unknown type

I've updated it on the Wiki. So anyone likes to try git and update the repo? -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP

Re: [PyMOL] GIT'r Done

/cy7wj8 If anyone has suggestions feel free to edit the howto. Questions about unresolved things are also welcome. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385

Re: [PyMOL] GIT'r Done

Jason Vertrees schrieb: Justin, Thanks for taking the initiative to import the Script Library into git. It's great to see more and more of the PyMOL community giving back. Now users can simply get a copy of all the scripts with one easy git command. I posted some details below

[PyMOL] GitHub for pymol-scripts

everyone to check out the repo and contribute. http://github.com/jlec/Pymol-script-repo/tree/master If you have problem with git, just mail me. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425

[PyMOL] image on pymol.org

Hi Warren, some time ago I asked for the script you used for the image on pymol.org and I lost it somewhere. Could you post it again, please? Thanks, justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institue for structural biochemistry Research Centre Juelich GmbH

[PyMOL] (no subject)

Hello all especially Warren, What does Sorry, time-sequential stereo 3D not available mean. It is printed out when I start pymol. I am using current HEAD. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH

Re: [PyMOL] apbs plugin for MacPyMOL?

Paul Shannon schrieb: I've installed apbs and used it from the command line. Now I'd like to run it (more conveniently) as a MacPyMOL plugin. Anybody know how I can set this up? Thanks! - Paul - This SF.Net email is

Re: [PyMOL] writing selection to a external file

=ReplyToListThunderbirdExtension Justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature

[PyMOL] python traceback from apbs plugin

figure out where it comes from. Thanks for help, jusitn -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature

[PyMOL] [SOLVED] python traceback from apbs plugin and one more question

Justin Lecher schrieb: Hi all, I am using the latest svn version of Pymol with python 2.5.2. Now I get following traceback when clicking the set grid button of the apbs plugin: Traceback (most recent call last): File /usr/lib/python2.5/site-packages/pmg_tk/__init__.py, line 35, in run

[PyMOL] pymolrc

Hi all, Just want to know if there are only per user pymolrc files at ~/.pymolrc or could there be a system wide configuration e.g. /etc/pymolrc. or somewhere else? Thanks, justin signature.asc Description: OpenPGP digital signature

Re: [PyMOL] How to use PyMOL without GUI ?

Yang, Zheng schrieb: Dear All, Would you please remind me how to start PyMOL in Linux, without the GUI, only command lines? Just like Matlab, we using ‘matlab -nojvm’ to disable the graphic interface. I am running PyMOL to ray-trace a figure. But the protein is too big. It always

Re: [PyMOL] problem with .pml file

type @yourpmlfile.pml Hally Shaffer schrieb: I installed pymol onto a linux system. I can open the program, open the pdb file, and open a .pse file, but I cannot open the .pml file which contains the manipulations that I've already made. Any suggestions? -- Hally Shaffer Graduate Student

Re: [PyMOL] Calculation of Domain Volume in Pymol

For all the gentoo guys out there: I wrote an ebuild for msms. Any Bugs and suggestions should be reported to me for further improvement. Robert Campbell schrieb: Dear Buz, On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow b...@mac.com wrote: Dear all, I'd like to very accurately

Re: [PyMOL] Anybody remember Molmol?

Jurgen F. Doreleijers schrieb: Sorry if it's a bit off topic but I need some Molmol features Pymol simply hasn't come around to implement yet. Anybody know how to compile Molmol on the Mac OS X? There is a packages in the fink database. So you could easily install and compile it via fink.

Re: [PyMOL] pymol in the background

HI! I tried it with the latest version in the portage in an login shell and both went fine, working in the shell and using pymol. I'm using eterm. What about using screen? justin Gordon Wells schrieb: Hi I seem to be having trouble running pymol (v1.0, gentoo) in the background from

[PyMOL] unnatural aminoacid

Good morning everyone! I want to build a modell with an unnatural aminoacid inside. I'm using a system wich allows me to incooperate a Coummarinderivatet aminoacid at speziel positions in my protein. For my talks I want to create some nice pictures. so how can mutate the sequence in my