[PyMOL] Is it possible to tell if a loaded PDB file contains secondary structure records?
I'm writing a script that writes a Python script that loads PDB files and displays them in cartoon representation. The problem is that, if the PDB file doesn't contain secondary structure records, you get a ribbon-like representation rather than a proper cartoon. The obvious way to fix this is to run util.ss but this can be slow if you have a lot of structures. Is there a way in the API to tell whether a PDB file you've loaded contains secondary structure records, so that you can avoid an unnecessary call to util.ss? Tom Walsh
[PyMOL] Re: Is it possible to tell if a loaded PDB file contains secondary structure records?
Okay, this comes from a script I wrote a while ago to create selections for individual helices etc: stored.ss = [] cmd.do(iterate %s and name ca,stored.ss.append(ss)%yourmodel) then check all stored.ss[] == or some such. There is probably a less clumsy way though. Hope it helps. On Wednesday, 22 October 2003 12:49, Tom Walsh wrote: I'm writing a script that writes a Python script that loads PDB files and displays them in cartoon representation. The problem is that, if the PDB file doesn't contain secondary structure records, you get a ribbon-like representation rather than a proper cartoon. The obvious way to fix this is to run util.ss but this can be slow if you have a lot of structures. Is there a way in the API to tell whether a PDB file you've loaded contains secondary structure records, so that you can avoid an unnecessary call to util.ss? Tom Walsh --- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- |\ /---\| | -/ o \ \\/ __/ | -\ \__-/__|__/ |/ \---/ _/_\__/ |_ |_ ___/ ~~~ Gordon Wells Department of Biochemistry University of Pretoria
[PyMOL] local PDB updates
Hello, There is a script which accesses a PDB server to get the weekly update lists of PDB structures. It downloads the new and modified structures and can be run as a cronjob under Linux. The script is freely accessible from http://www.rubor.de/bioinf/ Cheers, Kristian Rother
RE: [PyMOL] Off screen drawing bug on a nForce 2 computer
Paulo, As far as I know, what you're reporting is a platform-dependent OpenGL bug (or feature). Many graphics cards don't support rendering to display context that is not visible. Ray-tracing doesn't have this limitation of course, but in theory we could teach PyMOL how to use auxillary buffers to enable off-screen OpenGL rendering as well. Unfortunately there isn't any way to color bonds independent of atoms in PyMOL. The closest thing you can do is create a new object consisting of just those to bonds and to color that object separately. 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 Paulo Lai Sent: Tuesday, October 21, 2003 7:55 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Off screen drawing bug on a nForce 2 computer Hi, I have added a very limited SOAP interface to PyMol and I've found that when the viewer window is covered there are errors in the png files it generates. For example if I load a structure and rotate it, it will save the image of the structure in its new orientation overlaid on top of its original position. It works fine on my laptop which uses the ATI Mobility Radeon 7500, and I can get it to work on my nForce 2 desktop, if I use the minimal level of hardware acceleration (when using the latest version of the NVIDIA drivers). The other issue I've had is PyMol freezes if I have it open normally, and then I use remote desktop to connect to that computer, neither of these are critical. If anyone is interested, the SOAP libraries for Python (SOAPpy and ZSI) are still quite rough with many relatively simple things not functioning correctly, I've resorted to passing lists around. Final thing, is there a way to colour a single bonds in sticks view without affecting the colour of the other bonds the atom is connected to? Cheers, Paulo --- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] atom sphere radius
Hi there, I would like to show an active site metal but the sphere radius is too big. Is there a way to change the sphere radius for an atom or display it otherwise with a radius of say 1A. thanks, robert --- Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637
RE: [PyMOL] atom sphere radius
Robert, alter selection, vdw=number for example: alter elem fe, vdw=1.0 rebuild 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: Robert Schwarzenbacher [mailto:robe...@sdsc.edu] Sent: Wednesday, October 22, 2003 1:43 PM To: Warren L. DeLano Cc: pymol-users@lists.sourceforge.net Subject: [PyMOL] atom sphere radius Hi there, I would like to show an active site metal but the sphere radius is too big. Is there a way to change the sphere radius for an atom or display it otherwise with a radius of say 1A. thanks, robert --- Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637
RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
Fred, The tkinter dependency is missing. RPM is supposed to check that, but I forget to add it to the list. Look for the tkinter RPM on your RH9.0 CDROM (or on the net). 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 fr...@mit.edu Sent: Wednesday, October 22, 2003 3:33 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window Hi PyMOLers, Can someone tell me why I don't get the Tk window with all of the menus when I start PyMOL under redhat 9.0? I installed the RPM file pymol-0.90-1.rh90.py22.i386.rpm and got no errors during installation. Here's the content of the shell window after starting PyMOL: Xlib: extension XFree86-DRI missing on display :0.0. PyMOL(TM) Molecular Graphics System, Version 0.90. Copyright (C) 1998-2003 by DeLano Scientific LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. Other Major Authors and Contributors: Ralf W. Grosse-Kunstleve, Ph.D. PyMOL is user-supported open-source software. Although most versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing campaign to create open and affordable software for molecular research. Updates and other information can be found at http://www.pymol.org;. Please cite PyMOL in publications and presentations: Warren L. DeLano The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org Enter help for a list of commands. Enter help command-name for information on a specific command. Hit ESC anytime to toggle between text and graphics. OpenGL based graphics front end: GL_VENDOR: Mesa project: www.mesa3d.org GL_RENDERER: Mesa GLX Indirect GL_VERSION: 1.3 Mesa 4.0.4 Traceback (most recent call last): File modules/pymol/__init__.py, line 177, in exec_str exec s in globals(),globals() File string, line 1, in ? File modules/pymol/__init__.py, line 292, in launch_gui __import__(invocation.options.gui) File modules/pmg_tk/__init__.py, line 22, in ? # as /usr/lib/python2.1/site-packages File modules/pmg_tk/PMGApp.py, line 15, in ? ImportError: No module named Tkinter Thanks everyone. --- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
