RE: [PyMOL] Ray Tracing Crash
Morri, The RH9 Patch is described and published on: https://rhn.redhat.com/errata/RHBA-2003-136.html I would not expect Debian to suffer from the same crash. If it does, then we may be dealing with a genuine bug in PyMOL (assuming that you're not simply running out of RAM). With respect to Debian, in order to debug the problem, you might want to send me a PyMOL session file which crashes on your system when the next command issued is ray. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Morri Feldman [mailto:morrifeld...@yahoo.com] Sent: Tuesday, January 20, 2004 10:36 PM To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman' Cc: 'pymol-users' Subject: RE: [PyMOL] Ray Tracing Crash Warren and Matt, Thanks so much for your help. I must be using the stock glibc because set max_threads, 1 allows me to ray trace without crashing. I will tell my system administrator to patch glibc. Do you know where I should look for the patch? My debian/testing system at home also has trouble ray tracing especially sticks. When it fails I get a segmentation fault. Is my problem at home also due to an unpatched glibc? The error message is: /usr/bin/pymol: line 7: 32460 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* Thanks for creating such a great program, Morri --- Warren L. DeLano war...@delanoscientific.com wrote: Morri, (First, thanks Matt for the great diagnostic advice!) This sounds to me like a potential threading deadlock, possible due to the broken threading in RedHat 9. Are you using the stock version or have you patched glibc? If you haven't patched your RedHat 9, then one way to be sure this is the problem is to set max_threads, 1 before issuing the ray command. If PyMOL doesn't hang, then you've found the culprit. If have already patched your RH9, then let's do some more work to determine what's going on... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Matt Franklin Sent: Tuesday, January 20, 2004 6:25 PM To: Morri Feldman Cc: pymol-users Subject: Re: [PyMOL] Ray Tracing Crash Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4 processors. Has anyone else experienced this problem? Do you have any solutions? This message may double post because I accidentally tried to post it from my other email account. Sorry Thanks, Morri Morri Feldman Hi Morri - The progress bar for raytracing doesn't move linearly - the first half of the bar is covered fairly quickly, then more slowly, then very slowly, then the last fifth is usually covered in one jump. Are you sure you just aren't being impatient? Try raytracing a very simple scene, like a single amino acid in spheres mode, to see if it hangs then. Also try raytracing parts of your scene in case some funny bit of your molecule is causing this problem. Finally, try reducing the complexity of your surfaces and/or spheres: set surface_quality, -1 (0 is the default). Feel free to contact me directly - I'm local! (Although Warren will be more helpful...) - Matt -- Matthew FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080 --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net
Re: [PyMOL] Ray Tracing Crash
On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: My debian/testing system at home also has trouble ray tracing, especially with sticks. When it fails I get a segmentation fault. What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? Is my problem at home also due to an unpatched glibc? glibc in debian/testing should be fairly recent. Perhaps it suffers from a different bug, but the one described earlier should be fixed by now, if it ever pertained to Debian. The error message is: /usr/bin/pymol: line 7: 32460 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* As Warren said, a detailed description of the scene you were trying to raytrace would be welcomed. Michael
[PyMOL] How to send pymol command to pymol by python interpreter
Dear Pymol users I launch Pymol in my python program. After that, I can't change objects in pymol in my python program. In short I do not know how to send pymol command (ex cmd.do(show cartoon)) to Pymol not by directly input in pymol external command line but by python interpreter. Does anybody know how to do this ? Thank you. Takefumi SORA
[PyMOL] Re: Problems with PyMOL + XIG Summit2.2
Warren, XiG would like to know what is happening with PyMOL and Accelerated-X. We are not experts with PyMOL so we may need help reproducing the problem. WLDWhat numeric version of Summit are you using? WLDWhat Summit series do you have (LX, DX, CX, WX, etc.)? WLDWhat operating system, distro, and version are you running? Most of this information can be generated by running the 'Xsupport' script and sending the the output. For instance send the file 'xsupport.txt' that is made by running the command: # /usr/X11R6/lib/X11/AcceleratedX/bin/Xsupport xsupport.txt This output also contains other information that we might need to reproduce the problem here. What GL render mode does PyMOL use while picking objects? Sincerely, -- Mike Ginis mgi...@xig.com http://www.xig.com On Wed, 21 Jan 2004, Warren L. DeLano wrote: WLDPyMOL Users, WLD WLDIt appears that some PyMOL users are having trouble with Xi WLDGraphics' Summit line of OpenGL graphics drivers, version 2.2. WLD WLDAtom picking (which uses glReadPixels with color-encoded pixel WLDbuffers) fails with these drivers. It's unclear right now whether WLDthe problem is due to the XiG OpenGL implementation or with the WLDdefault keyboard modifier event mapping. WLD WLDIf you are both a PyMOL and Summit user (any version), please help by WLDresponding to me directly with information about: WLD WLDWhat numeric version of Summit are you using? WLDWhat Summit series do you have (LX, DX, CX, WX, etc.)? WLDWhat operating system, distro, and version are you running? WLDDoes atom picking and mouse selection work for you in PyMOL? WLDDoes PyMOL work fine under XFree86 with the identical hardware setup? WLD WLDOnce we understand the extent of the problem, we'll try to set up our WLDown Summit install here and then track down the problem... WLD WLDCheers, WLDWarren WLD WLD-- WLDmailto:war...@delanoscientific.com WLDWarren L. DeLano, Ph.D. WLDPrincipal Scientist WLDDeLano Scientific LLC WLDVoice (650)-346-1154 WLDFax (650)-593-4020 WLD WLD -Original Message- WLD From: Dr. Daniel James White PhD [mailto:d...@chalkie.org.uk] WLD Sent: Wednesday, January 21, 2004 1:20 AM WLD To: t.gran...@ubs.u-bordeaux1.fr; Warren L. DeLano WLD Subject: pymol, with summit2.2 Xserver on linux WLD WLD Hi, WLD WLD I get this problem also. WLD I fear is the the summit Xserver niot handling mouse events properly WLDor WLD something. WLD My mouse is a ps2 logitech with a scroll wheel button. WLD I can't do ctrl-click operations. WLD WLD Have you also noticed that your sound does not work with summit, but WLD does with XFree86? WLD WLD cheers WLD WLD Dan WLD WLD WLD Message: 1 WLD From: Warren L. DeLano war...@delanoscientific.com WLD To: 'Thierry Granier' t.gran...@ubs.u-bordeaux1.fr, WLD pymol-users@lists.sourceforge.net WLD Subject: RE: [PyMOL] mouse WLD Date: Fri, 16 Jan 2004 08:12:42 -0800 WLD WLD Thierry, WLD WLD This behavior could be the symptom of either malfunctioning OpenGL, or WLDa WLD screen with two few colors to support color-encoded picking (which is WLD what PyMOL uses behind the scenes). WLD WLD Please confirm that your display is running in 24 or 32 bit color. If WLD that is the case and picking still fails, then please try saving a png WLD file of what you see on the screen (png filename.png). If that PNG WLD file exhibits any distortion or artifacts, then that's the cause of WLDthe WLD problems. Otherwise, PyMOL may have a bug... WLD WLD Cheers, WLD Warren WLD WLD WLD -- WLD mailto:war...@delanoscientific.com WLD Warren L. DeLano, Ph.D. WLD Principal Scientist WLD DeLano Scientific LLC WLD Voice (650)-346-1154 WLD Fax (650)-593-4020 WLD WLD -Original Message- WLD From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- WLD ad...@lists.sourceforge.net] On Behalf Of Thierry Granier WLD Sent: Friday, January 16, 2004 12:52 AM WLD To: pymol-users@lists.sourceforge.net WLD Subject: [PyMOL] mouse WLD WLD Good morning, WLD WLD I am trying to use pymol on a PC linux RedHat 9.0 using WLD the software summit 2.2 of Xig, and I run into the following WLD problem: WLD after loading a molecule, when I try to click on an atom, for WLD selection, WLD using WLD CTRL shif lb or CTRL shift lb, I get the message WLD no atom found nearby WLD WLD I have tried all the mouse settings from the gui with no success. WLD WLD Any help will be appreciated, WLD thank you WLD WLD Thierry Granier. WLD WLD WLD WLD WLD --- WLD The SF.Net email is sponsored by EclipseCon 2004 WLD Premiere Conference on Open Tools Development and Integration WLD See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. WLD http://www.eclipsecon.org/osdn WLD ___ WLD PyMOL-users mailing list WLD PyMOL-users@lists.sourceforge.net WLD
[PyMOL] c-alpha traces
Hi, Some structure comparison software is only able to generate alignments built of c-alpha atoms of both structures compared. Is Pymol able to visualize such alignment with (faked) backbone shown ? If not what could possibly show it ? Regards, -- Michal Kurowski mic...@genesilico.pl
[PyMOL] translucent proteins
I would like to be able to make the backbone protein in a structure translucent so that the active site is clearly visible through the protein. Any ideas on how to do this? Lesley
RE: [PyMOL] How to send pymol command to pymol by python interpreter
Hi. I appreciate your answer, Warren. Thank you. Please let me ask one more question. You said I need two lines first: import pymol pymol.finish_launching() As long as I use,I can't the role of pymol.finish_launching() if I don't call this, what troubles will happen ? Takefumi SORA
