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 with 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 On Tue, 20 Jan 2004 18:35:07 -0800 "Warren L. DeLano" 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 > https://lists.sourceforge.net/lists/listinfo/pymol-users > Morri Feldman
Re: [PyMOL] controlling atom sphere radii
to make all spheres smaller, try something like this: set sphere_scale, 0.3 play around with the 0.3 bit to get the size you want. last time i checked, you could only have one sphere_scale per object, so if you want different sized spheres in the same picture (i don't think you do), you may need to do something like this: # show normal spheres for ARGs show spheres, resn arg # show small spheres for ILEs create iles, resn ile show spheres, iles set sphere_scale, 0.3, iles (i'm on a windows box with an old version of PyMOL right now, so i don't know if that last bit has changed recently) -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Tue, 20 Jan 2004 rbax...@uchicago.edu wrote: > Dear All, > > I have some residues shown as sticks and a heteroatom shown as a sphere. > I woul dlike to make the sphere a little smaller compared to the sticks. > How can I control the radius of the sphere? > > Any help appreciated, snippet of script below, > > Richard Baxter > > select pocket3=((s;RCVL and i;189,190,212,213,222,223,224)) > select fe2=(r;FE2) > ... > show sticks,pocket3 > show spheres,fe2 > > > --- > 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 >
Re: [PyMOL] controlling atom sphere radii
rbax...@uchicago.edu wrote: Dear All, I have some residues shown as sticks and a heteroatom shown as a sphere. I woul dlike to make the sphere a little smaller compared to the sticks. How can I control the radius of the sphere? Hi Richard - Add the following lines (suitably modified) to your script: alter (elem Fe), vdw=3.5 rebuild I used this trick to make a "lipid bilayer" composed of an array of heteroatoms (I chose cesium) which were then expanded beyond their original van der Waals radii to make a hexagonal grid. - Matt -- Matthew FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080
[PyMOL] controlling atom sphere radii
Dear All, I have some residues shown as sticks and a heteroatom shown as a sphere. I woul dlike to make the sphere a little smaller compared to the sticks. How can I control the radius of the sphere? Any help appreciated, snippet of script below, Richard Baxter select pocket3=((s;RCVL and i;189,190,212,213,222,223,224)) select fe2=(r;FE2) ... show sticks,pocket3 show spheres,fe2
RE: [PyMOL] Ray Tracing Crash
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
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
[PyMOL] Ray Tracing Crash
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
RE: [PyMOL] Cartoon does not display properly
Dan, Thats what happens when there is no secondary structure information defined. PyMOL's dss command will solve this, but note that dss will not give identical results to DSSP (the closest thing to a standard for secondary structure assignment). 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 Daniel Moriarty Sent: Tuesday, January 20, 2004 10:41 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Cartoon does not display properly Hello everyone, I have a generated PDB file which gives very thick ribbons when I try to do the cartoon display. Apart from that, it seems fine. I remember seeing this problem once before with a file I downloaded from the PDB, and I couldnt resolve the problem then. Any ideas on what to do? Thanks, Dan
[PyMOL] Cartoon does not display properly
Hello everyone, I have a generated PDB file which gives very thick ribbons when I try to do the cartoon display. Apart from that, it seems fine. I remember seeing this problem once before with a file I downloaded from the PDB, and I couldn¹t resolve the problem then. Any ideas on what to do? Thanks, Dan
