[PyMOL] python command to get b-factor and occupancy of a single atom?
Dear PyMOLers, I have trouble to find out, which command I could use in a python script to get the b-factor and occupancy of a single atom. In the script library, I only found examples getting b-factors iterating over a selection. Although, I could iterate over one atom, only, is there a more 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 Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ___ 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
[PyMOL] Python from PyMOL or PyMOL from Python?
Dear PyMOLers, I want to modify atomic coordinates in a python program and make pictures with PyMOL for making a movie. In your experience, is it better to call the python program from PyMOL or to call PyMOL from the python program? And could you please give me any good pointer for your 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: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ___ 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
Re: [PyMOL] Electron Density
Hi Manas Sule, this is a bit more complicated: For PyMOL, you usually calculate an electron density map covering your molecule. As far as I understand PyMOL, the sigma is taken directly from your input map. For Coot, this is completely different. Coot tries to reconstruct from your input map the complete map for the unit cell taking the crystallographic symmetry into account (using it for displaying an "infinite" map), and calculates the sigma from the unit cell map. This already might be different to the sigma within the box that you used to cover your molecule. However, if the reconstruction fails, either because the symmetry of your map is wrong (i.e., P1), or the input box is too small to allow reconstruction of the whole unit cell, the rest of the unit cell is filled with "0", resulting in much smaller sigma values! If this happens, you have to display the input map at a much higher sigma level in Coot to get the same absolute electron density value and thus appearance. Apparently, this is the case for your map. To get the sigma value right, you should calculate a map covering either the asymmetric unit with the right symmetry or covering the whole unit cell. Then, run a peak search program, like CCP4 peakmax, or play visually with the sigma value using that map - it should be same in PyMOL and in Coot, then. Best regards, Dirk. Am 06.12.11 15:12, schrieb Manas Sule: Is there a difference in the sigma values assigned by pymol and coot I am able to see the density at 8 sigma in coot for the Fo-Fc map but can go to maximum at 4.5 sigma in pymol after which it disappears On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett <mailto:rrowl...@colgate.edu>> wrote: I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the selection about which you would like to see the electron density mesh. I haven't tested the contour limits, but it's larger than 10. ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu <mailto:rrowl...@colgate.edu> On 12/5/2011 12:49 PM, Manas Sule wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer mailto:pame...@mcw.edu>> wrote: isomesh [mesh name], [map name], 6.0 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <mailto: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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <mailto: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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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 -- **
Re: [PyMOL] [ccp4bb] Snow leopard + NVidia quadro FX4500
Dear Deena, yes, I have a Mac Pro with an Nvidia FX 4500 running under 10.6.3. For me, all programs work more or less fine in hardware stereo (Pymol, Coot, Moloc, Chimera). I've done the following to get it working: 1. Connect the CRT monitor to the first DVI socket of the graphics card (the one further away from the 3-pin Mini-DIN) 2. Connect the TFT to the second DVI socket (in the middle) 3. Connect the emitter to the 3-pin Mini-DIN socket 4. Choose a resolution for the CRT that allows a refresh rate of 120 Hz 5. I've arranged the monitors such that the menu bar is on the TFT (you might want to change this, if you like) 6. Not necessary since 10.6, but I've installed the most recent X11 from xquartz.macosforge.org You can start MacPyMOL or PyMOLX11Hybrid with the parameters "-X 1800 -Y 200 -S" (you might want to play with the X,Y position) and switch pymol to stereo in the application (still required despite -S). For me, it is necessary to start pymol on the CRT monitor with suitable X,Y parameters, since dragging a X11 stereo window from the TFT to the CRT could lead to a crash of your whole session. Good luck, Dirk. Am 14.06.10 21:35, schrieb Deena Oren: Hi all, Does anyone have this combination of Nvidia FX4500 in a mac machine running 10.6 and if so is stereo working? I am getting a messed up screen when using either coot in hardware stereo or pymol -S even without invoking the stereo command. Yet ccp4mg is working 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 Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ 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
Re: [PyMOL] stereo issue on OS X 10.6.3 with PyMOL 1.2r3
Hi Patrick and Ben, Am 14.06.10 18:15, schrieb Ben Eisenbraun: > Hi Patrick, > > >> I invoke the stereo version with this command: >> >> /Applications/PyMol/MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1250 -Y 100 -S >> >> The X/Y placement is to ensure that the window falls on my CRT, and the >> -S seems to be necessary to force stereo (if I just run regular MacPyMOL, >> selecting the quad-buffered option has no effect). >> > > Yes, we had to use the -S to force stereo mode as well. I have an OS X > 10.5.8 machine with a Quadro 4500 that works fine with MacPyMOL and > PyMOLX11Hybrid once stereo mode is forced. It won't turn on the emitter > without it. > For the MacPyMOL version, the "-S" flag is _not_ necessary for quad-buffered stereo, if you go to the monitor settings and drag 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 of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ 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
Re: [PyMOL] [ccp4bb] Stereo flipping in coot and pymol
Am 28.09.2009 um 16:25 schrieb Joachim Reichelt: I said, we are on Linux. Uups, yes, you are right - may fault. But you may try the new driver installation and the minizing/maximizing, anyway. Good luck, Dirk. But I did not say: We are using Stereographic glases and emiter 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 which emitter and glasses you are using. I've seen this behaviour long time ago with very old Nvidia graphics card drivers under Linux. Sometimes, I still see this behaviour with new drivers but with old computer hardware. Here are a few hints that might be worth trying: - Install the most recent Nvidia driver. If it happened after updating, it might be worth to go back 1-2 versions. - If you use the emitter from NuVision, you can simply invert left and right with a small switch. - Sometimes, it helps to minimize the application and maximize it again. Good luck, Dirk. Am 28.09.2009 um 15:48 schrieb Joachim Reichelt: Dear all, our users complain that during there graphics session front and back are switched. We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors. So it seems that you see sidechains behind a sheet, that are in realety front of a sheet. If they were behind it, you should not see them at all. -- Joachim -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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 *** 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.lmu.de WWW: www.genzentrum.lmu.de *** -- *** 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.lmu.de WWW:www.genzentrum.lmu.de *** -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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
Re: [PyMOL] Stereo flipping in coot and pymol
Dear Joachim, you don't say whether its Linux, Windows or Mac OS X and which emitter and glasses you are using. I've seen this behaviour long time ago with very old Nvidia graphics card drivers under Linux. Sometimes, I still see this behaviour with new drivers but with old computer hardware. Here are a few hints that might be worth trying: - Install the most recent Nvidia driver. If it happened after updating, it might be worth to go back 1-2 versions. - If you use the emitter from NuVision, you can simply invert left and right with a small switch. - Sometimes, it helps to minimize the application and maximize it again. Good luck, Dirk. Am 28.09.2009 um 15:48 schrieb Joachim Reichelt: Dear all, our users complain that during there graphics session front and back are switched. We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors. So it seems that you see sidechains behind a sheet, that are in realety front of a sheet. If they were behind it, you should not see them at all. -- Joachim -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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- us...@lists.sourceforge.net *** 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.lmu.de WWW:www.genzentrum.lmu.de *** -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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
Re: [PyMOL] Smooth fading of surface in movie?
Dear PyMOLers, thanks a lot to all of you for your helpful suggestions! I will try Tsjerk's way that probably keeps me from writing an external Fortran program for generating pymol commands ;-) Best regards, Dirk. Am 01.09.2009 um 20:42 schrieb Tsjerk Wassenaar: Hi :) Some people are just not lazy enough ;) Lazy people like me spend a good deal of effort thinking about how to avoid efforts like writing repetitive lines :p And then you could come up with: from math import sin,pi mset 1 x300 for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" % ( math.sin( math.pi*(i-200)/(2*100) ) ) ) The fuzz with the sine is of course to have a smoother fade. One could also take the simpler linear fade, but mind that the either numerator or divisor (or both) have to be float in order to end up with a float: for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" % ( (i-200)/100.0 ) ) With a bit more scripting, you can easily use this to define functions for fading properties from one value to another over a given range of frames. As a side note, if the fade is part of a more complex movie, hide the surface one frame after the fade has completed. Possibly it's also best to explicitly show it again in the first frame, in case you have Pymol cycle through the movie. In case the purpose is fading in the surface, start with surface view hidden and turn on the surface the frame before you start the fade. This way you avoid Pymol calculating its way through a null surface, possibly even coming up with some artefacts... Hope it helps, Tsjerk On Tue, Sep 1, 2009 at 5:01 PM, Matthew D. Hogg wrote: I use a clunky set of mdo commands to do this. mdo 266: set transparency, .1, (palm+linker+Nterm) mdo 267: set transparency, .2, (palm+linker+Nterm) mdo 268: set transparency, .3, (palm+linker+Nterm) mdo 269: set transparency, .4, (palm+linker+Nterm) mdo 270: set transparency, .5, (palm+linker+Nterm) mdo 271: set transparency, .6, (palm+linker+Nterm) mdo 272: set transparency, .7, (palm+linker+Nterm) mdo 273: set transparency, .8, (palm+linker+Nterm) mdo 274: set transparency, .9, (palm+linker+Nterm) mdo 275: set transparency, 1, (palm+linker+Nterm) If the surfaces are turned on for objects palm, linker and Nterm, then this will fade out the surface over frames 266 to 275. Setting the transparency to 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 out a surface of, say, a ligand, between scenes? 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.lmu.de WWW: www.genzentrum.lmu.de *** -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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- us...@lists.sourceforge.net *** 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.lmu.de WWW:www.genzentrum.lmu.de *** -- Let Crystal Reports handle the reporting - Free
Re: [PyMOL] Smooth fading of surface in movie?
Dear Carsten, yes, thanks. However, for a smooth fading, that would require a lot of scenes. Is there a simple python loop, that would create scenes with smooth transparency fading-in from 0 to 1 and that I could use in my pymol-scripts? Unfortunately, I'm not familiar with python, 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, September 01, 2009 8:57 AM To: PyMOLBB Subject: [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 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** *** 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.lmu.de WWW:www.genzentrum.lmu.de *** -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
[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 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
[PyMOL] Wrong session viewport and sudden ray tracing crop in 1.2r1
Dear Warren, I just started to work with session files in addition to scripts, so maybe, these are known issues. In version 1.2r1 for Mac, I notice a strange behavior when saving and re-opening sessions: (1) the session file apparently doesn't store the "viewport"-setting (2) when I re-open a session, restore the viewport-setting by hand (which results in the same view as when I stored the session) and issue a "ray" command with pixel sizes greater than the viewport- setting, the resulting image is suddenly cropped at the edges, although, in the original 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 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ___ 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
[PyMOL] Difference between create and select?
Dear Warren & PyMOLers, I notice that "create" is needed to make objects that can have different transparency settings. But what exactly is the difference between "create" and "select", since both commands seem to make a new object from the atom 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.lmu.de WWW:www.genzentrum.lmu.de *** -- ___ 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
[PyMOL] Dashed loops in cartoon?
Dear PyMolers, I want to show a tentative trace through very weak electron density in a cartoon representation with dashed loops, along with the usual helices, sheets and solid loops for the reliable part of the structure. I could not find a description for this task - is this possible? 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:+49-89-2180-76999 E-mail: kostr...@lmb.uni-muenchen.de *** -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] 3D Glasses, which ones are the best ?
Dear David, I don't know where the price differences come from, but it's really worth to try different systems on you own, say, in a lab where different ones are used. In our group, most people use the Nuvision system because of the low price. Personally, I use the stereographics/ real-d system because of the better wearing comfort. How important this is, and whether it's worth the price difference is of course completely up to the individual user ... Best regards, Dirk. Am 15.11.2007 um 13:46 schrieb David McGiven: Dear Pymol Users, Sorry for getting back to this topic, but it's the only place I know about where I can find scientific colleagues using pymol and 3D Glasses. I've seen very big differences between prices of 3D Glasses, being the crystal eye the most expensive (~800 US$), the Nuvision almost half the price (~400US$) and the eDimensional for almost nothing! (~100 US$) Is it really worth paying the price of the real-d glasses ? Does anybody know why this big price differences ? Thanks in advance. Best Regards, David McGiven -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ PyMOL-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 Fax:+49-89-2180-76999 E-mail: kostr...@lmb.uni-muenchen.de ***
Re: [PyMOL] between views
Hi Andreas, thanks for that pointer - sounds pretty easy. I'll give it a try next time! Best regards, Dirk. Andreas Forster wrote: Tassos, Dirk, sorry for the very late reply, but I've just now finished going through a few hundred list mails that had accumulated. For converting scenes to movies, Joel Bard's slerpy is really shweet. Check it out at http://www.pymolwiki.org/index.php/Slerpy. What I do is the following - after putting slerpy's two scripts into the current directory and opening pymol: - load session.pse - import slerpy - F1 (or wherever your first scene resides) - sscene (makes slerpy understand scene 1) - F2 - sscene (makes slerpy understand scene 2) - swrite arbitraryName (saves parameters for interpolation) - srecord (does the interpolation) - set ray_trace_frames, 1 (makes sure your images are ray-traced before they are saved) - mpng 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 Kostrewa wrote: Hi Tassos, I found the following article, but haven't tried it on my own: http://www.pymolwiki.org/index.php/Scene I hope this helps! Best regards, Dirk. Anastassis Perrakis wrote: > Dear pymolers - > > One can store 'Scenes' and then switch between them; the algorithm > that goes from one scene to each other is very nice. > > Can one ask Pymol to write frames going from one scene to another to > png files to make a movie ? > > or does anyone have python code that can render the transitions > between views/scenes in a different way ? > > best - tassos > -- 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] ray-traced stero figurea
Hi Richard, to change wall-eyed stereo figures to cross-eyed, you can simply exchange the left and right images (in wall-eyed, the left picture is for the left eye, the right picture for the right eye, whereas in cross-eyed, the left picture is for the right eye and vice versa). Warren once explained to me the two stereo angle definitions PyMOL uses. Here is en excerpt of what he wrote: " ... stereo_shift is the separation between the two cameras observing the image, expressed as a % of the distance from the objective. stereo_angle is a scaling factor applied to the natural angular difference which would occur between two eyes at that distance, both looking at the objective. Generally speaking stereo_shift is the main depth control parameter, and stereo_angle should remain close to 2 in order to generate "correct" stereo geometry. However, adjusting stereo_angle can reduce ghosting and change the apparent Z location of the objective. Detting stereo_shift to zero makes you a Cyclops (you're basically telling PyMOL that your eyes are superimposed). ... The actual translation(+/-) and rotation(+/-) of the camera at "distance" are: translation = distance * (stereo_shift/100) rotation = (stereo_angle/2) * (arctan(stereo_shift/100)) (default = ± 1.2 deg) ..." In my ~/.pymolrc, I've put these two values for getting +/- 3 degree rotations for hardware (quadbuffered) stereo: set stereo_angle = 2.0 set stereo_shift = 5.24 I hope, this helps. Best regards, Dirk. Richard Baxter wrote: Dear All, I used the following commands to generate a nice wall-eye stereo figure (at least it seems to work for me): ray 600,900,-1,-3; png stereo_right.png ray 600,900,-1,3; png stereo_left.png figures are combined in photoshop at 300dpi with an extra 5mm between, so that images are 2 inches across separated by ~55mm. My question, how to convert this to a cross-eye stereo figure, do I just switch the sign of the angle, or should I also multiply/divide by some amount? I don't understand the shift argument, how I should 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
Hi Tassos, I found the following article, but haven't tried it on my own: http://www.pymolwiki.org/index.php/Scene I hope this helps! Best regards, Dirk. Anastassis Perrakis wrote: Dear pymolers - One can store 'Scenes' and then switch between them; the algorithm that goes from one scene to each other is very nice. Can one ask Pymol to write frames going from one scene to another to png files to make a movie ? or does anyone have python code that can render the transitions between views/scenes in a different way ? best - tassos - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=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 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
[PyMOL] [Re: Help for X.org-based Stereo 3D on Linux?]
Dear Warren and PyMOL users, we have a current Scientific Linux 4 (a non-commercial Red Hat Enterprise Clone) with X.org installed at PSI, and stereo works fine with an Nvidia Quadro card with 3-pin mini-DIN connector by just adding a "Stereo 3" option in /etc/X11/xorg.conf (and I've added a modeline with 120 Hz for stereo, but this is not required). Best regards, Dirk. DeLano Scientific wrote: PyMOL Users, We have gotten a couple of questions recently regarding running nVidia-based Stereo 3D under the "X.org" X-server instead of using XFree86. We don't have X.org set up in house yet, so I was hoping someone else might be able to provide a definitive answer as to whether or not it works, and if so, some information on how to get it to work. According to reports, simply adding Option "Stereo" "3" to Xorg.conf (as we have done for XFree86 in the past) isn't sufficient... Thanks in advance for any help you can offer! Cheers, DeLano Scientific LLC Email Support Services - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ 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:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch **** -- 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] RE: making a movie from saved scenes
Dear Warren, this little thread points nicely to the major problem that I have quite often with PyMol: it is a really powerful program, but the documentation is somewhere scattered between various incomplete sources (manual, reference list, wiki, bulletin board, user home pages, ...). This makes it very difficult for the average user like me to make full use of PyMol's capabilities. I would _really_ prefer to have a good and up-to-date documentation available, at least for the last official version, rather than more and more improvements with poor documentation. Best regards, Dirk. Seth Harris wrote: Hi Sun, Warren (and others?) has posted some text before about this. A simple template for it is as follows with the key being that mview interpolate command at the end. This works, but I haven't been through it recently to remind myself of the nuances of the animate=0 options and the view=0 options at their respective occurences, but if you play around with it I think you'll find it a treat. Don't forget that the mset 1 x180 should be replaced by however many total frames you want in the movie, and repeat the little blocks for however many scenes you have. If you don't mind equal sized steps between scenes you can automate the whole thing in a little python loop for X number of scenes. Also replace 001, 002, etc. with whatever your scenes are stored as. Use the mview store, YY to pinpoint at which frame you want that scene to be set. mset 1 x180 scene 001, animate=0 mview store, 1 scene 002, animate=0 mview store, 60 mview interpolate mdo 1: scene 001, view=0 mdo 2: scene 002, view=0 There are other non-scene based movie mechanisms that allow fancier fades and things, but this way is certainly much easier 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
Hi Warren, the new version works fine without flicker on my iBook,1.2 GHz G4, ATI Mobility Radeon 9200 with 32 MB. Thanks a lot! Cheers, Dirk. Am 06.11.2005 um 04:32 schrieb Warren DeLano: Mac users: We lucked out and obtained a little help from an off-duty Apple engineer today who figured out how to work around the issue in 10.4.3. It was one of these combined bugs -- we weren't doing things sensibly in PyMOL, and the ATI driver wasn't quite complying with normal OpenGL behavior with respect to screen updates. They changes seem to have done the trick, so I have posted an updated MacPyMOL build at: http://delsci.com/beta Please let me know if this does NOT solve the issue on your machine. Also, since I had to change the lighting and draw-buffer code, please let me know right away if anything strange or new surfaces. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ 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: +41-56-310-5288 E-mail:dirk.kostr...@psi.ch http://sb.web.psi.ch
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: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D "in a window" down near the bottom. this is really great - stereo was the most missing features for me with Macs! But what about stereo support of the monitors? Would this already work with Apple's TFT screens? Are their refresh rates fast enough for that, or does one still has to buy a CRT monitor? Amazing! The "Stereo 3D Matters to Me" campaign actually worked. 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 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch -- **** 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] PyMOL featured on Apple Store site?
Hi Warren and PyMol users, Warren DeLano wrote: They've got MacPyMOL two places on this site: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D "in a window" down near the bottom. this is really great - stereo was the most missing features for me with Macs! But what about stereo support of the monitors? Would this already work with Apple's TFT screens? Are their refresh rates fast enough for that, or does one still has to buy a CRT monitor? Amazing! The "Stereo 3D Matters to Me" campaign actually worked. 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 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] lcd stereo
And what about the ever faster LCD screens designed for gamers? With refresh times appraching 8 microseconds, hardware stereo with 2x 60 Hz on LCD screens seems to come into reach. Best regards, Dirk. William Scott wrote: I just noticed that the price on the Sharp LCD stereo monitor is now $600. http://store.sharpsystems.com/product.asp?sku=2555920 Is it possible to run pymol on linux in stereo on this? --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. 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 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] From scenes to movies?
Hi Martin, your script works beautifully!!! Thank you very much!!! I would like to understand two commands that you use in your script, for which I couldn't find any infos, neither in the manual, nor in the reference nor in the WiKi. Could you please tell me: - what does "set scene_animation,-1" mean? - what do the "mview store" and "mview interpolate" commands mean? Thanks again!!! Best regards, Dirk. Martin Nervall wrote: Dirk, Actually there is a way to render a movie from predefined scenes. I created a .pse-file with my desired scenes and then made a movie from the extrapolations between the scenes. It will look pretty much as an ordinary scene_animation in Pymol. From the movie I rendered lots of .png-files which I finally merged into a .mpg or .avi movie. It's time consuming but it works. Here is a sample script that will render a 50 frame movie from two scenes stored in movie.pse: '' load movie.pse set scene_animation,-1 set scene_animation_duration,0 mset 1 x50 scene F1 mview store, 1 scene F2 mview store, 30 mview store, 35 scene F1 mview store, 50 mview 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 to show in a movie describing a protein structure. Is there a way in PyMOL to export the individual frames for a movie from scenes? If not, this would be my most desired 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 --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Martin Nervall Molecular Biotechnology Program Dept. of Cell & Molecular Biology Biomedical Center Box 596 SE-751 24 Uppsala Sweden Phone +46 (0)18 471 5058 http://xray.bmc.uu.se/~aqwww/ --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ 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:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] From scenes to movies?
Hi Warren & Pete, Warren DeLano wrote: Pete & Dirk, Actually, I think Dirk is looking for something to convert the automatic scene-to-scene camera interpolation into movies...the immediate answer is no -- it isn't yet trivial to do, but we will be working on making that easier before the next release. yes, Warren is right - this is exactly what I would like to have. I'm looking forward to getting this feature! Cheers, Dirk. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.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 movie from scenes? If not, this would be my most desired missing feature in PyMOL! Yes. What I do is to use a script to step through each frame of the movie (rotation by 1 degree, zoom in slightly, change transparency slightly, etc), ray-trace (optional), and dump the png. From there, ffmpeg will combine all of these into a single movie file (memcoder is supposed to do this as well). I'm not entirely sure what you mean by frames from scenes, though. Hope this helps, Pete Pete Meyer Fu Lab BMCB grad student Cornell University --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ 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:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] From scenes to movies?
Hi Warren, the scenes feature in PyMOL is _really_ nice! By choosing appropriate scenes, it does exactly what I would like to show in a movie describing a protein structure. Is there a way in PyMOL to export the individual frames for a movie from scenes? If not, this would be my most desired 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
Hi Jie Yang, it's getting harder to buy a stereo-capable CRT monitor with all the fancy TFTs. One monitor that I know to be still available is the iiyama Vision Master Pro 514 (HM204DT). It is a 22'' CRT with a maximum horizontal refresh rate of 140 kHz (!) and a maximum vertical 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 trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (>100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang -- **** 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] Pymol on MacMini: performances
Dear Luca, I own a current G4 iBook, and the Mac mini is in principle an iBook in cubuoid form (but without display and keyboard). I don't know how demanding your pymol sessions are, but I'm quite happy with the MacPyMOL version on my iBook, which seems to be subjectively a little 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 everyone, I'm thinking of buying a Mac mini to use as minimal computer for home, and will need it to run pymol smoothly. is this the case, or the little machine doesn't have enough juice to handle, let's say, visualisation of a protein active site and ligand docked into it, with different level of transparence and such? I need pymol essentially to look at my structure and generate pretty pictures for my phD thesis... many thanks to anyone can give insights... luca -- **** 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] keynote and pymol
Hi Rick, I want to join Bill's experience with keynote. What I usually do, is to read the series of pymol pictures into Quicktime Pro and export them as movie (you can save the series of pictures directly as "slide show" without any quality loss; however, such a "movie" often halts for a fraction of a second during a presentation). I haven't tried all movie export options, but the one that I currently prefer is the "Sorensen 3" codec with maxium quality (and maxium file size!): it runs smoothly from within a keynote presentation on my 1.2 GHz G4 iBook. Best regards, Dirk. William Scott wrote: I was wondering if anyone out there has any experiance with usuing Apple's Keynote to display animated pymol gif's. I've had a look in the archives and couldn't find anything. On a second note (and sorry to open up this debate again), What is the consensus for displaying a pymol movie in a presentation package such as powerpoint? i've tried avi and mpeg but i find that there is a loss in the quailty when compared to the sharpness of a animated gif. Many Thanks Rick Young Hi Rick: I use pymol movies in keynote all the time. It seems to work well with either animated gifs or quicktime movies. If you dig around inside your presentation you will see the animated gifs get converted to quicktime movies. My experience is it doesn't blow chunks quite as much as powerpoint. HTH, Bill --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. 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 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] BEWARE: recent nVidia drivers
Yes, I've also downgraded from the 7174 driver to the 6629 driver because of huge performance problems with another open source density fitting program. We are using Scientific Linux, another RedHat Enterprise Clone, as operating system. Cheers, Dirk. Warren DeLano wrote: Folks, You may have seen some related messages go by on the PyMOL and/or VMD mailing lists, but just to reiterate: If you have nVidia graphics hardware, PLEASE avoid updating your nVidia graphics drivers for the time being. The 7-series (e.g. 71.74) simply do not work with PyMOL, VMD, and other tools on many (but not all) system configurations. We are working to understand just what the problem is... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ 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:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
Hi, > AFAIK, Debian's glibc uses tls/nptl only on Linux-2.6, not on Linux-2.4. > So using a 2.6 kernel should be fine. However, I do not have Nvidia > hardware to test this. Yes, I'm using the Nvidia driver 1.0-6111 on a Debain Sarge with the 2.6.7 kernel without any problems. 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?
I wanted to have a program that can easily calculate cavities in proteins to be displayed with pymol (see e-mails below for details). Thanks to Gareth and Lari I've got two pointers to such programs: I've tried PASS, recommended by Lari and got a surface picture of my cavities within literally a few minutes, as Lari already wrote. I've ordered SURFNET, recommended by Gareth and will also try it (it needs a signed license agreement returned by mail). Many thanks again! Best regards, Dirk. Gareth Stockwell wrote: > One program which can do this is SURFNET: > > http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html > > There are two ways in which cavities can be displayed: > > i) SURFNET can write out PDB format files containing the atoms/residues > lining each cleft, which you can view directly > > ii) If linked with the CCP4 libraries when compiled, SURFNET can write > CCP4 format density maps which describe the shape of each cavity. These > can be loaded into PyMOL and contoured to show the location of each > cleft. > > HTH > Gareth Lari Lehtiö wrote: > I was looking for such a program couple of days ago, and I found "pass". > > http://www.ccl.net/cca/software/UNIX/pass/overview.shtml > > I saw the cavities in couple of minutes in pymol :) I'm not familiar with > voidoo, so I don't know if you will find this usefull or not... > > My current problem is related to this one, so I'll post it here also. > I would like to calculate surface of the cavity with pymol and show this as > a cavity going in to the protein. But the surface is all grey, because it > is the "inside". Is there a way to map the colours also to the other side > 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 > »» > Quoting Dirk Kostrewa : > > # Dear PyMol users, > # > # I'm looking for a program that can calculate and write out cavities in a > # > # format that can be converted such that I can display it with PyMol (I'm > # not > # satisfied with the results from VOIDOO). Could you please send me any > # pointer > # to a program that you found useful? 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...@psi.ch > # http://sb.web.psi.ch > # > # > # > # > # --- > # This SF.Net email is sponsored by BEA Weblogic Workshop > # FREE Java Enterprise J2EE developer tools! > # Get your free copy of BEA WebLogic Workshop 8.1 today. > # http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > # ___ > # 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:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] Cavity display?
Dear PyMol users, I'm looking for a program that can calculate and write out cavities in a format that can be converted such that I can display it with PyMol (I'm not satisfied with the results from VOIDOO). Could you please send me any pointer to a program that you found useful? 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...@psi.ch http://sb.web.psi.ch
[PyMOL] Still stereo inversion problem
Dear PyMol users, I still have the problem, that rather frequently the hardware stereo is inverted on my linux box (RedHat 9.0/XFree86 4.3.0/Nvidia Quadro4 980 XGL with Nvidia driver 1.0-4496). I thought that I have solved the problem by setting and exporting the environment variable __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 **** 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
[PyMOL] Stereo inversion problem "solved"
Dera PyMol users, it seems that I've "solved" the stereo inversion issue: I've errornously set and exported __GL_SYNC_TO_VBLANK environment variable in my .bash_profile (assuming it will be inherited to all sub-shells). Setting and exporting it in my .bashrc solved this 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: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] stereo inversion?
Dear PyMol users, I've got an annoying effect under RedHat 9.0 with a Nvidia Quadro4 980 XGL graphics card, the most recent Nvidia driver and Stereographics glasses & emitter: occasionally, the hardware stereo is inverted (back appears in front and vice versa) and doesn't come back to normal mode. I've already set the environment variable "__GL_SYNC_TO_VBLANK=On", and in the XF86config I've defined the Device as follows: Section "Device" Identifier "Nvidia1" BoardName"Quadro4 980 XGL" Driver "nvidia" Option "stereo" "3" Option "NvAgp" "1" Option "UBB" "On" Option "PageFlip" "On" Option "WindowFlip" "On" 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 not simpler." Albert Einstein 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
[PyMOL] individual surfaces?
Dear PyMol users, I'm currently trying to display individual surfaces around different selections of a molecule to show how they contact each other. However, either I get only the last surface displayed or a joined surface using the command examples below: this one gives only the surface of residue 440 show surface, ( resid 431 ) flag ignore, ( not resid 431 ) show surface, ( resid 440 ) flag ignore, ( not resid 440 ) rebuild whereas this one gives the joint surface of residues 431 and 440 show surface, ( resid 431 or resid 440 ) flag ignore, ( not ( resid 431 or resid 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 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] stereo parameters?
Dear PyMol users, my subjective stereo impression with pymol in window stereo mode is too "flat", both on SGI and on Linux, at least when I compare it with my ~10 years or so experience using other applications. I started to fiddle around with the stereo parameters "stereo_angle" and "stereo_shift", but the results were not as expected from the presumed meaning for these parameters. Could anyone (maybe Warren?) please explain to me what the exact meaning of these two parameters IN PYMOL is? If I will find a subjectively better set of parameters I will 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?
Dear pymol users, in your experience, how does the graphical performance of pymol (or any other graphical program) on a PC running under Linux with a good stereo-capable graphics card (Nvidia Quadro, ATI FireGL) compare to a stereo-capable SGI workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450 MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein sketch at 800x800 resolution and maximum display quality requires on the SGI 3 minutes for 180 frames, i.e. 1 frame/sec, whereas the same movie requires on the PC 20 seconds, i.e. 9 frames/sec. I wonder how this can be and would like to hear about your experiences. I've compiled pymol from the source file with the mips pro compiler from SGI. Results were comparable with the previous pymol version for which I've installed directly the binaries. Thus, I don't think that the speed difference is due to a compiler problem on the SGI. I've got another graphics program for protein modelling, Moloc, that runs on both platforms. There, I've observed similar subjective speed differences 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: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch
Re: [PyMOL] graphics performance
Dear Gordon, I assume that you changed the default "nv" driver in your XF86config(-4) file to the Nvidia driver "nvidia". I've replaced on my private Pentium III (733 MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less improvement than expected. Here are my observations: 1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is probably okay. 2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchmark program "gears" in full-screen mode and somewhat less than this in the Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23). 3. But, puzzlingly with pymol and on-screen rendering of a complex secondary structure sketch (without ray-tracing) I only get a moderate increase (~ 10 %, or so) of the movie frame rate compared to a Geforce2MX440 running on a Pentium III (450 MHz) in my office! Here, I would really expect a huge difference in frame rate. I also don't understand this. A possible explanation would be that pymol, upon automatic detection of the graphics card, internally changes the complexity of the calculations resulting in a slower but improved image? Best regards, Dirk. On Wednesday 08 January 2003 09:40, gordon wrote: > Hi > I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't > really notice a performance improvment (running linux). I judge this > based on how smoothly large sized proteins can be rotated with spheres > 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 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] Disable shadows in ray tracing
Dear PyMol users, do you know a way to disable shadows in ray tracing? Although shadows look beautiful in cartoons and ball-and-stick models, I think they are irritating when electron density maps are displayed as isomeshes. 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
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. -- *** Dirk Kostrewa Paul Scherrer Institut E-mail: dirk.kostr...@psi.ch Life Sciences, OSRA/007 Phone: +41-56-310-4722 CH-5232 Villigen PSI Fax: +41-56-310-4556 Switzerland Internet: http://www.sb.psi.ch *** On Wednesday 02 October 2002 14:31, Daniel John Rigden wrote: > Hi everyone > > I'm trying to install version 0.82 to replace 0.78. The relevant rpms are > pymol-0.82-1.rh70.py152.i386.rpm and pymol-0.78-3.rh70.py152.i386.rpm. > > However, I get a load of messages of the following type > > [r...@dodo progs]# rpm -ivh pymol-0.82-1.rh70.py152.i386.rpm > Preparing...### > [100%] > file > /usr/lib/python1.5/site-packages/pymol/examples/package/redhat/pymol-0.78-2 >.rh72.py21n.spec from install of pymol-0.82-1.rh70.py152 conflicts with file > from package pymol-0.78-3.rh70.py152 file > /usr/lib/python1.5/site-packages/pymol/modules/ExtensionClass.so from > install of pymol-0.82-1.rh70.py152 conflicts with file from package > pymol-0.78-3.rh70.py152 > file /usr/lib/python1.5/site-packages/pymol/modules/_cmd.so from install > of pymol-0.82-1.rh70.py152 conflicts with file from package > pymol-0.78-3.rh70.py152 > file /usr/lib/python1.5/site-packages/pymol/modules/_glu_nummodule.so from > install of pymol-0.82-1.rh70.py152 conflicts with file from package > pymol-0.78-3.rh70.py152 > file /usr/lib/python1.5/site-packages/pymol/modules/_glumodule.so from > install of pymol-0.82-1.rh70.py152 conflicts with file from package > pymol-0.78-3.rh70.py152 > etc etc > > I tried renaming the /usr/lib/python1.5/site-packages/pymol/ directory, > but that didn't help. > > I believe I can force rpm to install the new stuff anyway, but is it safe > to do so in this case? > > Thanks for your help > > Daniel > > > +-+ > > | Dr Daniel John Rigden | > | CENARGEN/EMBRAPA | e-mail: dan...@cenargen.embrapa.br | > | Parque Estacao Biologica | http://www.cenargen.embrapa.br | > | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741| > | 70770-900, Brasilia-D.F.-BRAZIL | Fax:+55 (61)340-3658| > > +-+ > > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Suggested stereo parameter settings
Dear PyMOL users, in case that you may find the current stereo parameters not optimal, here are my suggestions: put the following lines in your .pymolrc file (copy from /pymol/sample.pymolrc): set stereo_angle=6.0 set stereo_shift=0.0 At least on our SGIs these settings produce a significantly 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 Life Sciences phone: +41-56-310-4722 OSRA/007fax: +41-56-310-4556 CH-5232 Villigen PSIWWW: http://sb.web.psi.ch Switzerland *
