[PyMOL] python command to get b-factor and occupancy of a single atom?

elegant way of getting the b-factor and occupancy of a single atom? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich

[PyMOL] Python from PyMOL or PyMOL from Python?

preferred method (other than the simple scripting tutorial)? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone

Re: [PyMOL] Electron Density

s 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 -- *** Dirk Kostrewa Gene Center Munich Department

Re: [PyMOL] [ccp4bb] Snow leopard + NVidia quadro FX4500

fine in stereo. Thanks, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue, Box 295 New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- ******* Dirk Kostrewa

Re: [PyMOL] stereo issue on OS X 10.6.3 with PyMOL 1.2r3

the menu bar in the monitor arrangement settings to the CRT screen, _prior_ to invoking MacPyMOL (I have probably the same hardware here as described above). Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [PyMOL] [ccp4bb] Stereo flipping in coot and pymol

connected by 3-wire cable to the DIN plug on NVIDIA Quadro FX 3000 NVIDIA GLX Module 173.14.17 Mon Feb 23 16:04:17 PST 2009 If of interest, this is openSUSE 11.1 on i386 Am 28.09.2009 16:21, schrieb Dirk Kostrewa: Dear Joachim, you don't say whether its Linux, Windows or Mac OS X and

Re: [PyMOL] Stereo flipping in coot and pymol

yMOL-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- us...@lists.sourceforge.net *** Dirk Kostrewa Gene Center, A 5

Re: [PyMOL] Smooth fading of surface in movie?

1 and then reversing the order of the values will make the surface fade in. HTH Matthew Hogg University of Vermont Burlington, VT 05405 Quoting Dirk Kostrewa : Dear Warren, using PyMOL without any additional "plug-ins", like slerpy or eMovie, is it possible to fade in or ou

Re: [PyMOL] Smooth fading of surface in movie?

, yet ... Best regards, Dirk. Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]: Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, Sept

[PyMOL] Smooth fading of surface in movie?

Dear Warren, using PyMOL without any additional "plug-ins", like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5

[PyMOL] Wrong session viewport and sudden ray tracing crop in 1.2r1

nal session with the same viewport- and ray- settings, the image was not cropped Could you please check and, maybe, correct this? Best regards, Dirk. ******* Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 8

[PyMOL] Difference between create and select?

m selection? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lm

[PyMOL] Dashed loops in cartoon?

? If not, I will just show dashed bonds between the C-alphas of the tentative trace. Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax

Re: [PyMOL] 3D Glasses, which ones are the best ?

-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 F

Re: [PyMOL] between views

anotherName (writes out 50 images covering the interpolation from scene 1 to scene 2) - go have a coffee - make movie from images in ImageReady I was amazed. This worked exactly as I had expected. The most taxing part was walking to the coffee machine. Thanks, Joel! Andreas On 3/30/07, Dirk K

Re: [PyMOL] ray-traced stero figurea

ould figure out what value to use. Any advice greatly appreciated. sincerely, Richard Baxter -- **** Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch

Re: [PyMOL] between views

ge=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- **** Dirk Kostrewa Paul Scherrer Institut Bi

[PyMOL] [Re: Help for X.org-based Stereo 3D on Linux?]

__ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:

Re: [PyMOL] RE: making a movie from saved scenes

sier to work with. -Seth -- **** Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch

Re: [PyMOL] Mac Flicker Issue Workaround

PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +4

Re: [PyMOL] PyMOL featured on Apple Store site?

Please, forget my questions about stereo-capable monitors - Warren has already answered my questions in another e-mail (that I read too late). Regards, Dirk. Dirk Kostrewa wrote: Hi Warren and PyMol users, Warren DeLano wrote: They've got MacPyMOL two places on this site:

Re: [PyMOL] PyMOL featured on Apple Store site?

ed. Apple really *is* serious about meeting our needs. Yes, apparently. Gives a good feeling with Apple. Cheers, Dirk. -- **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722

Re: [PyMOL] lcd stereo

. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dirk Kostrewa Paul Scherrer Institut Life

Re: [PyMOL] From scenes to movies?

w interpolate set ray_trace_frames = 1 mpng movie '' Hope this is to some help. cheers /Martin At 09:49 2005-09-26, Dirk Kostrewa wrote: Hi Warren, the scenes feature in PyMOL is _really_ nice! By choosing appropriate scenes, it does exactly what I would like

Re: [PyMOL] From scenes to movies?

ourceforge.net] On Behalf Of Peter Adrian Meyer Sent: Monday, September 26, 2005 2:25 PM To: Dirk Kostrewa Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] From scenes to movies? Hi Dirk, a protein structure. Is there a way in PyMOL to export the individual frames for a mov

[PyMOL] From scenes to movies?

missing feature in PyMOL! Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch

Re: [PyMOL] hardware stereo on window XP

ertical refresh rate of 200 Hz, that I use for stereo (1280x960 at 120 Hz). There might be still some other stereo-capable monitors available . . . Best regards, Dirk Kostrewa. jiey...@ucsd.edu wrote: I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am t

Re: [PyMOL] Pymol on MacMini: performances

bit faster than the X11 version (via fink). Make sure that you have enough memory (at least 512 MB), otherwise this will be the bottleneck. Maybe, you find among your colleages somebody who owns an iBook and try your pymol tasks there? Best regards, Dirk Kostrewa. Luca Fenu wrote: Hi ever

Re: [PyMOL] keynote and pymol

Play to win an NEC 61" plasma display: http://www.necitguy.com/?r=20 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dirk Kostrewa Paul Scherrer Ins

Re: [PyMOL] BEWARE: recent nVidia drivers

lists/listinfo/pymol-users -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch

Re: [PyMOL] Warning: Nvidia 6111 drivers for linux

lems. Best regards, Dirk. -- **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch

Re: [PyMOL] Cavity display?

; of the surface? > > best regards, > > ~Lari~ > > > »» > Lari Lehtiö > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland >

[PyMOL] Cavity display?

BTW, this would be my wish for a next release of PyMol! Best regards, Dirk. -- **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@p

[PyMOL] Still stereo inversion problem

__GL_SYNC_TO_VBLANK in my .bashrc file, but this rather annoying problem still persists. So, has anybody else experienced this and maybe found a solution? Best regards, Dirk. -- "Make everthing as simple as possible, but not simpler." Albert Einstein ***

[PyMOL] Stereo inversion problem "solved"

his stereo inversion problem. Good luck, Dirk Kostrewa. -- "Make everthing as simple as possible, but not simpler." Albert Einstein **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-

[PyMOL] stereo inversion?

ot; BusID"PCI:1:0:0" EndSection This happens also without setting the UBB, PageFlip and WindowFlip options. Do you have any idea what's going wrong here? I would be very grateful for any hint! Best regards, Dirk. -- "Make everthing as simple as possible, but

[PyMOL] individual surfaces?

d 440 ) ) rebuild How can I display the individual surfaces separately? Alternatively, is there a command to display atoms in a CPK representation? Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villige

[PyMOL] stereo parameters?

l post them as a suggestion on this board, then. Best regards, Dirk. -- **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch

[PyMOL] Comparison SGI <-> PC?

ifferences in favour to the PC. But I couldn't measure any benchmarks. Best regards, Dirk Kostrewa. -- **** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-

Re: [PyMOL] graphics performance

gt; on. > Just wondering why? > > Thanks in advance > Gordon -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch

[PyMOL] movie maker for linux?

Dear PyMol users, do you have any recommendations for a program under linux that assembles all the individual png pictures into a movie for a PowerPoint/OpenOffice presentation? Any hints are welcome! Best regards, Dirk. -- Dirk Kostrewa Paul

[PyMOL] Disable shadows in ray tracing

. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch

Re: [PyMOL] rpm installation problems

Hi Daniel, AFAIK, rpm complains if you want to install a newer package version over an older one. In the case of an update, just issue the command "rpm -Uhv pymol-0.82-1.rh70.py152.i386.rpm". Best regards, Dirk. -- **

[PyMOL] Suggested stereo parameter settings

better stereo picture than the default values 2.1 and 2.0, respectively. Many thanks to Warren who told me which parameters to change and their default values. Regards, Dirk. * Dirk Kostrewa Paul Scherrer Institut e-mail: dirk.kostr...@psi.ch