Re: [PyMOL] Pymol crash when deleting callback object

awesome, thanks On Tue, Sep 29, 2015 at 7:39 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Spencer, > > This was a threading issue, I have fixed the script. > > Passing a wrong name to PutCenterCallback results in the same threading > issue. Should also be fixed. > > Cheers, >

Re: [PyMOL] Pymol crash when deleting callback object

Hi Spencer, This was a threading issue, I have fixed the script. Passing a wrong name to PutCenterCallback results in the same threading issue. Should also be fixed. Cheers, Thomas On 29 Sep 2015, at 10:47, Spencer Bliven wrote: > I'm using the callback version of the Axes script (third sc

[PyMOL] Pymol crash when deleting callback object

I'm using the callback version of the Axes script (third script at http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython, deleting the constructed axes object causes Pymol to crash. It's an old script and I'm guessing not well maintained, but the crash is still unfortunate. As an

Re: [PyMOL] Pymol crash when raytracing empty graphics

Thanks for the quick fix! I would love to get a hotfix if possible. The PDBe API is a nice solution. I think that detecting CA traces will fix 90% of the cases. There are still a few edge cases besides CA which don't have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer type

Re: [PyMOL] Pymol crash when raytracing empty graphics

Hi Spencer, Thank you for the bug report. We could reproduce and fix the crash, if you want I can send you a hotfix build. I will also push the fix to the open source SVN repository soon. I second John's suggestions to query the "ca_p_only" property from the PDBe API. Also, the next PyMOL vers

Re: [PyMOL] Pymol crash when raytracing empty graphics

Dear Spencer It is possible to work this out using the PDBe API. for our interactive API see: http://www.ebi.ac.uk/pdbe/api/doc/ The molecules url will give you this information: http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q entity 1 has "ca_p_only": true, which means cartoon will not

[PyMOL] Pymol crash when raytracing empty graphics

We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA at

Re: [PyMOL] pymol crash when ray

one more thing… Delete all objects that you are not using for this particular rendering (save it as a separate file). I have found this speeds up rendering times. > On Apr 14, 2015, at 7:49 PM, H. Adam Steinberg > wrote: > > For an instantaneous rendering of any PyMOL scene that won't crash

Re: [PyMOL] pymol crash when ray

Hi Wenfu, Did you get the same error if you do the raytraicing from a script? Probably you could try with this approximation to render your molecule. Cheers, Osvaldo. On Tue, Apr 14, 2015 at 5:12 PM, wrote: Hi pymol users, > > I am just usi

[PyMOL] pymol crash when ray

Hi pymol users, I am just using pymol to open one super big molecular model (20 megadaltons). My pymol1.7 is on linux system and the computer has 32 CPU with 62GB memory storage. When I try to use command ray to make a high quality image, the pymol crash with error message like this: Pymol ran

Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5

Hi William and Warren, I've also updated to OSX 10.5.2, and any issues that I had with Pymol seem to have been resolved, even when running under conditions that would previously have caused a crash. I'm going to keep my fingers crossed for now. Thanks! and all the best, --Buz On Feb 12

Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5

I've noticed after updating to X11 2.1.3 that X11 crashes reproducibly if I (for example) resize coot's window before it finishes loading. I don't recall having X11 crash ever with 2.1.1 or earlier. Fortuitiously, the 10.5.2 update reverts X11 to 2.1.1, so updating that might solve the problem

Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5

ts.sourceforge.net] On Behalf > Of Buz Barstow > Sent: Monday, February 11, 2008 8:55 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Pymol Crash in X11 on MacOSX 10.5 > > Hi All, > > I've been having a lot of trouble with Pymol since upgrading to the >

[PyMOL] Pymol Crash in X11 on MacOSX 10.5

Hi All, I've been having a lot of trouble with Pymol since upgrading to the X11 included with MacOS 10.5. Of late (using X11 2.1.3), Pymol built with fink, and ipymol 1.0 have been crashing after a small amount of viewing and rotating an object in the program (a few rotations and zooms).

RE: [PyMOL] pymol crash!

> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Ramesh Sistla > Sent: Wednesday, July 14, 2004 7:25 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol crash! > > Dear List! > > I grabbed 0.96and installed. It is a beauty. Only that whe

[PyMOL] pymol crash!

Dear List! I grabbed 0.96and installed. It is a beauty. Only that when I clicked on getview button, it copied the matrix to clipboard and crashed. The error it returned is: PyMOL: Viewing matrix copied to clipboard. unable to alloc 1869182081d bytes /usr//bin/pymol: line 14: 24056 Aborted

[PyMOL] pymol crash on linux opening a .pse saved session file

Hi Warren and all, My student is experiencing a crash every time she attempts to open a .pse saved session file. The file is of a large trimeric molecule in a cartoon and space fill representation with different coloured domains Hardware: PC, Athalon, 1gb ram, ATI radeon 8500 video card, 2 mo