[PyMOL] Re: Slowwwww ray
Stuart, Stuart Endo-Streeter Default view, white with black background (sticks): Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.) Surface ray (white w/ black background): Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.) thanks a lot for the test. I guess I'm in the right spot. Warren, Did you just migrate from an older version? yes sir, set orthoscopic =3D>2.58 seconds on 2 X 2 Ghz opteron load 1alk.pdb show surface set hash_max=3D160 =3D>10.7 seconds on 2 x 2 Ghz opteron that explains it. I did the same test and it "went back" to the speed I remember. How do you determine the hash_max, 160? just by testing it? Thanks Michele
[PyMOL] Slowwwww ray
Hi, I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server. I started doing some modeling after about 6 months hiatus. I'm using MacPymol 0.99b29 (no flickering with this). But it's slower than molasses. I get: Ray: total time: 16.16 sec. = 222.8 frames/hour (32.15 sec. accum.). This is simple white surface on white black background, nothing changed from default. It a fairly small molecule, 600 resi, 5400 atoms. My card is the stock ATI Radeon 9800 Pro. Could it be I messed up something with OpenGL? Why is it so slooow Thanks Michele PS: would anybody with a similar setup try 1ALK.pdb show surface in white and tell my the time to ray? Mine is: Ray: total time: 25.45 sec. = 141.4 frames/hour (57.60 sec. accum.).
[PyMOL] Re: PyMOL-APBS os x
Hi, I compiled APBS successfully. Now when I try the plugin and click on Set Grid I get: --- Error: 1 ValueError Exception in Tk callback Function: at 0x81205f0> (type: ) Args: () Traceback (innermost last): File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", line 153, in None File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand None File "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1046, in execute self.runPsize() File "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1087, in runPsize size.runPsize(pdb_filename) File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line 257, in runPsize self.parseInput(filename) File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line 106, in parseInput self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00103.81 --- any help? Thanks Michele -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Department of Surgery Department of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfuor...@med.cornell.edu
[PyMOL] Re: MacPyMOL Beta 2 Announce/Caveat (Warren L. DeLano)
Hi, >However, since I promised a public MacPyMOL announcement by late >January, I am hereby announcing that MacPyMOL Beta 2 can now be >downloaded from the following public URL: > >But first, a word of caution -- YOU MAY WISH TO WAIT for a later >release. > >Why? Because MacPyMOL Beta 2 is VERY BUGGY and largely UNTESTED. In >addition to Mac-specific Aqua GUI, image copy & paste, and QuickTime >export, it contains a whole bunch of brand new cross-platform user >interface code that will soon be in the open-source release as well. Warren this is great software! Thanks for making the beta Mac version available. I could not find a GUI way to run script though. Am I missing the right place or is still not there. Do NOT tell me ;-) that I have to navigate thru all my Mac folder structure with cd/ls/ and mile long pathways. Michele
[PyMOL] Re: PyMOL 0.93 and MacOS X
Hi everybody, I know I'm an idiot, but I cannot build pymol 0.93 on Mac OS 10.3 to save my life. After getting and resolving a lot of gl.h and glut.h complaints now I'm stuck with: building 'pymol._cmd' extension . -L/usr/X11R6/lib -lGL -lGLU -lglut -lpng -o build/lib.darwin-7.2.0-Power_Macintosh-2.3/pymol/_cmd.so ld: can't locate file for: -lglut Any kind soul there willing to help me? Thanks Michele -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Departments of Surgery and of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfuor...@removethismed.cornell.edu
RE: [PyMOL] electrostatic surface
Todd Geders said: >Hello all, > >Here is a simple script that automates the electrostatic potential >surface generation using Gromacs, MEAD, and Pymol for visualization. >It's exclusively based off of the post by Esben Peter Friis: >It requires you to massage your pdb file a bit, but it gets the job >done. Please glance at the comments in the script to see what I mean. Thanks Todd for the script. I installed Gromacs 3.2 beta, MEAD 2.2.3 on Mac OS 10.3. The only change is that the $PDB.mdp file has to contain: cpp = /usr/bin/cpp to specify the cpp location in OS X. Run the script, seems to work. Now the question is how do I go about validating the results? I tried to compare one image I get with the one published for 1ALK.pdb but there were some differences :-(. Would anyone in the list be willing to send me the files for one of their proteins, so I can re-run the calculations and compare what I get? Thanks Michele Fuortes -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Departments of Surgery and of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfuor...@med.cornell.edu
[PyMOL] Pymol 0.93 and OS X - X 11
Hi all, I'm using a G4 and so far i have been using the GNU-Darwin version which is the CD I bought. I use it starting from X11 in Panther and it worked well. Now it seems that the new Mac version 0.93 is much faster. But no GUI menu :-( What I tried to do is to copy all the new modules files from the new version in the old version and it seems to work well, the display is now REALLY fast. The only problem is that python starts as a separate application instead of starting into X11. What would be the way to have python start inside X11 instead of its? Thanks a lot Michele -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Departments of Surgery and of Cell and Developmental Biology Cornell University Medical College E-mail: mfuor...@med.cornell.edu
