[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.
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 r...@email.unc.edu 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=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[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
[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
