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] Volumes video

e rendering rocks! I tried it with APBS electrostatic maps. This gives a quite intersting representation mode. Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich,

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

- > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > ___ > PyMOL-users mailing list (Py

[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 Lech

Re: [PyMOL] cartoon_sidechain_helper

n.png. > You just have to color by atom type after coloring by secondary > structure: > > set cartoon_sidechain_helper, on > > C > Color > by ss > Helix (red) Sheet (yellow) Loop (green) > > C > Color > by element > ... > > Cheers, > > --

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On 13.02.2012 20:27, Jason Vertrees wrote: > Greetings, > > It is my pleasure to announce the release of open source PyMOL > v1.5.0.1. The source code has been committed to the open-source > repository. It is revision 3976. An svn tag and downloadable bz2 > source file were also created. All of th

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

Re: [PyMOL] Open Source PyMOL v1.5.0.1

re precise, it seems that this only occurs with sticks representation. All others are nice and super fast. 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:

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On 14/02/12 10:44, fukami...@chugai-pharm.co.jp wrote: > set cylinder_shader_ff_workaround thanks for that trick. It solved the problem. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2

[PyMOL] cartoo_transparency per selection

g changes visually. Bug of feature? Thanks for help, 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 Crypt

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

27;t compile IDTFConverter *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 pr

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

-- 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 -- See everything from the

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 Sys

Re: [PyMOL] commands history

ou type will be saved, as well as actions > from menus (not sure how many, but I think most of them). > Hi, I have this as the first lines in my ~/.pymolrc import datetime _logdate = datetime.datetime.strftime(datetime.datetime.now(), "%y%m%d%H%M%S") cmd.log_open(filename="py

[PyMOL] Font problem

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

also depends on use_shaders. I am using rev. 4052 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 Des

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 Resea

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 Sys

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 tr

Re: [PyMOL] cartoon_transparency issue

//tv.slashdot.org/ > > > > ___ > 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.n

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

wwpdb.org/documentation/format33/sect9.html#MODEL 2) http://wwpdb.org/documentation/format33/sect9.html#ENDMDL -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description

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 gith

Re: [PyMOL] PyMOLWiki Update

esn't look like pymol stuff. Cheers, 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

[PyMOL] Pymol wiki search is not working

was before also 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 Cryptogr

Re: [PyMOL] Compile Errors on SVN 4111

On 19/03/15 16:52, Tim Travers wrote: > > Hi, > > I also had problems compiling this last night. According to the > following (see "Compile and install" towards the bottom), > you have to callfirst: > export CPPFLAGS="-std=c++0x" > before doing the build call. > > I used: > export CPPFLAGS="-std

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 distutil

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

On 28/05/15 19:26, Thomas Holder wrote: > Hi Brenton, > > the logo is currently not available under any license, it's a trademark of > Schrödinger. This means you can't upload it on Wikimedia Commons. > > Cheers, > Thomas > Hi Thomas, That brings up an interesting question about the usage i

Re: [PyMOL] Using Python 3.4.3 Shell

le "", 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 Structural B

Re: [PyMOL] PyMOL with Python 3

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 once this gets merged to SVN. > I think, we can make most of the scripts wo

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] 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 > wrote: > > >> Dear all, >> >> I'd like to very accurately calcul

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 > <>< Graduat

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 ru

[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

[PyMOL] python traceback from apbs plugin

7;type' and 'str' I am not that familiar with python, so that I couldn't 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

Re: [PyMOL] writing selection to a external file

/wiki/index.php?page=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] (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 Ju

[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] GitHub for pymol-scripts

like 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,

Re: [PyMOL] GIT'r Done

origin"] url = g...@github.com:jlec/Pymol-script-repo.git fetch = +refs/heads/*:refs/remotes/origin/* and everything is fine. Thanks, justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52

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] 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 Descripti

[PyMOL] graphic bug?

setup? 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 di

Re: [PyMOL] Problem Compiling Pymol 1.2.x

u past, it looks 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 Cen

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

ble manner! For all gentoo user, 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 b

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] subversion 3897 compile error in Cmd.c

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

[PyMOL] PYNMR or NMR support in Pymol

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] Please remove my emal address from your bulletin board

On 23/04/10 06:00, Charles David Stout wrote: > Dear PyMol developers, > > PyMol is an awesome program, but I'm a casual user. Please remove my > email address from your bulletin board. > Thanks > Dave Stout > 4-22-10 > > d...@scripps.edu > > ---

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

On 23/04/10 10:04, Greg Landrum wrote: > The best part is that you sent this message, where you tell Dave that > he shouldn't post unsubscribe requests to the list, to the list. > > I recognised that it is a common problem with unsubscriptions from mailing lists, so a public reminder how to unsu

Re: [PyMOL] pymol fetch

ile for this example is in which > directory under pymol ? > > 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, 5242

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

umped version. thanks justin [1] http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-msms Might take some hours to appear there -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juel