Re: [PyMOL] New MacBook

You can rotate > the ribosome in real time. > > Mike > > On Fri, May 19, 2006 at 09:24:02AM +0200, Marc Saric wrote: > >>>I'm very interested in knowing whether PyMOL is usable on the new >>>MacBook considering that it has Intel integrated graphics. >

Re: [PyMOL] New MacBook

n a MacBook with Pymol in action though. -- Bye, Marc Saric

Re: [PyMOL] Pymol Query

ther/older programs like O, where it is considered a feature NOT to center the display (i.e. you see nothing after loading)). -- Bye, Marc Saric

[PyMOL] Re: New user needs help! (Michael Morbious)

s and can be downloaded as command-line exe-file for Windows. There is certainly a more elegang Pymol-only sollution for this. -- Bye, Marc Saric

Re: [PyMOL] Pymol and batch-queue jobs

ossible), which gets sent to a batch-queueing-system from a Tk-GUI or offline (save script for later execution). - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFBKuf2

[PyMOL] Pymol and batch-queue jobs

something like that on my own and contribute it, but maybe someone allready has done it (don't want to reinvent the wheel)). Thanks in advance. - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Mozilla -

Re: [PyMOL] A couple of quick PyMOL + APBS notes

ing APBS-computation over to a remote machine, possibly one, which has access to the same filesystem)? - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFA95

[PyMOL] Re: PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

course) and it *works out of the box*. Really, really great stuff (no more GRASP/DELPHI!!!)! Bottomline: (you could add a hint on the rpm to your site stating, that they work with SuSE 9.0/9.1 (32 bit) also). Thanks for that great tool! And thanks to Warren for giving Pymol free to the world. -

[PyMOL] spectrum

would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric

RE: [PyMOL] embeding pymol in a web page

d Mac users and the happy few using Mozilla can't use this tool. Therefore an alternative to Chime, which would support Mozilla and the other OS-platforms should be preferred. Keep up the good work! - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: Gnu

Re: [PyMOL] 2 Questions for the User Community

ribbon is essentially a C-alpha trace. Due to a bug in 0.93, this was a locked seting anyway, so any recent scripts probably already make this assumption. Would also be ok. No objection unless you make this a hard-coded option (which is not the case). -- Bye, Marc Saric http://www.marcsaric.de

[PyMOL] Need advice on graphic card

I know, nVidia claims, that their driver can do that though (but I haven't tested it, due to lack of a second screen and a dual-head graphics-card. -- Bye, Marc Saric http://www.marcsaric.de

[PyMOL] Release in progress...

od without another security-measure: Typing "q" (will immediately quit Pymol). - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQE/m7VYvKxJUF29wRIRArhbAJ928s/6nrRnCqg4mfEEAPO4WarTMQCgx08I wyMNr7nlUUmDsIJh4tvv1pk= =rsZP -END PGP SIGNATURE-

[PyMOL] Re: PyMOL-users digest, Vol 1 #381 - 4 msgs

from what you would expect from a look at the OpenGL-window). - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQE/L1aqvKxJUF29wRIRAl9aAKCL5Tg15FaMCzgMPv9zHCeWKxK9GwCgpdKc

[PyMOL] Re: New Map Formats Coming...

FLD (AVS Field) map formats in the current development version. | Are there any other map formats which people would use heavily if PyMOL | were able to support them? APBS Open DX? See http://agave.wustl.edu/apbs/ Molmol mol ? - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE

RE: [PyMOL] Further functionality

elphi should work too in theory, but | we're currently working to resolve a few problems with the | approach... - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozi

[PyMOL] Roving-problems in 0.88

mputing Gaussian map for 1025 atom positions. ObjectMap: Normalizing: mean = 0.079996 & stdev = 0.284775. /tuxprog/bin/pymol: line 12: 6303 Segmentation fault $PYMOL_PATH/pymol.exe $* Besides that, everything seems to work fine. -- Marc Saric http://www.marcsaric.de

[PyMOL] Re: PyMOL-users digest, Vol 1 #271 - 4 msgs

Having a fully integrated set of tools which are shipped together with the main program would make life much easier. -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] hbond from rTools 0.5.2.menu on Linux does not work

works fine. Any suggestions? I don't have the exact output of the error-message here unfortunately, but I could provide it if needed. -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Again: Content of unit-cell

Pointing out that object has to be the object you wan't to rotate/translate, and that it has to be on the list on the right side would be nice (or am I wrong with that?). Keep up the good work. -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Content of unit-cell

at possible? I have tried to remove parts manually after adding symmetrie-mates, but this is painfull for very large structures (I have one with a 700 A-axis...). Thanks in advance! -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Pymol 0.82-Error

ximum Performance" and back to "Maximum Quality, Pymol crashes with the following error-message: """ PyMOL>rebuild NULL-POINTER-ERROR: in RepSphere.c line 379 PyMOL: abrupt program termination. """ This could be reproduced, so it might be worth looking at it

[PyMOL] Again: How does the density wizard works?

ng to update an existing isomesh created at the commandline. So maybe I'm overlooking something really simple, but it did not work at all so far. If someone could point out how this thing is supposed to work??? Thanks in advance! -- Bye, Marc Saric Max-Planck-Institut fuer molekulare

[PyMOL] Density wizard

rsion 1010. import sglite OpenGL based graphics front end: GL_VENDOR: VA Linux Systems Inc. GL_RENDERER: Mesa DRI G400 20010622 AGP 1x x86 GL_VERSION: 1.2 Mesa 3.4.2 -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Re: Stereo3D hardware recommendation

t also be a bit less heavy. If you want the cheapest "pro"-sollution, I would go for the Nuvision, they are good enough. If -for some reason- you really want maximum-sized shutters, you need Crystaleyes. Maybe you can test at least one of the two at your next crystallography department or CA

[PyMOL] Re: NVidia Linux Stereo Drivers

NuVision)?? 4. Does this emitter allow for stereo in a window (instead of fullscreen-stereo)? -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Pymol 0.82 and Python 2.2

, might be due to python itself, checking for versions. I think, for the time beeing, one could either install a separate Python2.1 for Pymol or just ignore the messages. And you could recompile Pymol from source I think. In this case, it should not complain anymore. -- Bye, Marc Saric Max

[PyMOL] Pymol 0.82 Redhat7.2 rpm on SuSE 8.0

r/bin/python to /usr/bin/python2.1 to make Pymol think it has found the right version. Of course one could recompile from source, but... -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] RE: pymol-on-linux questions

st in the consumer-sector) normaly arise from the surrounding stuff, i.e. type of graphics-memory, clockspeeds (memspeed beeing more important than GPU-speed, as the GeForce is bandwith-limited) etc. Bottomline: I would not expect a huge performance-improvement. Hope this helps. -- Bye, Marc S

[PyMOL] RE: easy (?) question (DeLano, Warren)

To get a linear C-alpha trace (no smoothing), "set ribbon_sampling 1" This is a bit unobvious (at least for me) wouldn't it be good to have this as an extra menu-point (i.. CA-trace)? -- Bye, Marc Saric

[PyMOL] Video

tools.com/ -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Some experiences with the new 0.78-rpms

. The only disatvantage is the somewhat too small font in the Tk-log-window. So in essence: The Redhat72-rpms work on SuSE 7.3 also. --- Marc Saric

[PyMOL] Re: Installing Pymol on SuSE 7.3 again (Andrey Khavryuchenko)

if installed on SuSE (for example it seems that the package expects python to be in a different path or under a different name (I have a working python 2.1.1, but one package complains, that python > 2.1 is neccessary). Pymol now runs (compiled from source) so anyway. -- Bye, Marc Saric M

[PyMOL] Installing Pymol on SuSE 7.3 again

compiled Python 2.1.1 it is ok. Cheers! -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

[PyMOL] Installing Pymol on SuSE-Linux 7.3 fails

x27;t tested it further though), but pymol won't start. 3D-acceleration works with a lot of other programs, and I use python as a scripting language now and then, so it should work in principle. Can anybody point me to a possible sollution for this problem? Thanks in advance! -- Bye, Marc Saric Max-Planck-Institut fuer molekulare Physiologie Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168