[PyMOL] pymol crashes - segmentation fault
Hi all, Recently I finally managed to install the Nvidia driver (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 Pro/AGP/SSE2) on my Fedora Core 5 box. When I try and run pymol it crashed after I load a pdb file and try and either right or left click on the main display. Here is the output from the pymol run: PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro2 Pro/AGP/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.82 Adapting to Quadro hardware. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. HEADERSCOP/ASTRAL domain d1a5ug2 [29269] 08-MAY-03 CmdLoad: "/home/fauxn/results/SCOP_90_results/d1a5ug2.pdb" loaded as "d1a5ug2". /home/fauxn/software/pymol/pymol: line 14: 7203 Segmentation fault $PYMOL_PATH/pymol.exe "$@" Any pointers welcome! Cheers Noel -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au website: http://vbc.med.monash.edu.au/~fauxn
[PyMOL] kensington three button mouse in mac book pro-issue
Hi, I am using Kensington three-button mouse on a Mac book pro (17") laptop. In pymol, when i press the middle button (for translation), it switches to horizontal scroll. The translation function is not working! Has anyone experienced similar problem?. Any fix or work around? Thanks Murali
Re: [PyMOL] Paths to loaded objects
I think he means for you to have a "Load" button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). On 8/19/06, Ron Jacak wrote: Peter, >> I'm working on a plugin that reads information appended to the end of >> PDB files to draw CGO objects. Right now, I have the user specify >> the >> filesystem path to the currently loaded objects through the >> plugin GUI so that I know where to go to find the file. For one >> object, >> this isn't so bad. But if users load multiple objects that are in >> different directories, I will have to change the GUI so that the user >> has to specify the path to each object loaded. This kind of >> situation >> would quickly become tedious. Does PyMOL store the paths for objects >> that are loaded somewhere? I know I can get the current working >> directory using getcwd(), so I'm hoping there's a way to get the >> path to >> the loaded objects as well. > I don't know of a way to get file information from a pymol object, > but you > could work around this by using a python dictionary (when the pdb > file is > loaded, store the full path to the file in a dictionary using the > pymol > object name as the key). I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Any other ways around this problem? -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill - 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
[PyMOL] discrete helix
Dear Colleagues, I am using PyMOL to show a protein under a series motion. One pretty representation is the cartoon view. However, when the residues become farther and father away, the helix cartoon become discrete, although that structural domain is still a helix. So is there a parameter, which controls the cut-off distance of the helix cartoon? An illustration: Original Helix Cartoon: \/\/\/\/\/\/\/\/\/ After a deformation, the Helix cartoon becomes discrete: \/\/ \/ \/\ /\/\ /\ /\/ Similarly, if I change the view mode to 'ribbon' (or 'lines'), the ribbons (or lines) are also discrete. Thank you so much for your help! Best, Z.Y.
