[PyMOL] pymol and EM 'models'
hi all - could one use pymol to read in EM/Tomography images in one the formats below: stacked images from IMOD .rec format. conversion of this stack of images to meta, patch, rib, or vrml ? Thanks, Tassos
[PyMOL] Question about electron density map with mtz file
Dear all, I am trying to put on the electron density. I only have .mtz file but I have a look at the manual and the program need XPLOR file. How can I get the XPLOR file or do I need to convert the mtz file to this - if so how can I do that? Thank you very much Best Regards Adiphol Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=listsid=396545469
[PyMOL] frozen command line on amd64
Hi, Pymol is behaving interestingly on my amd64 dual core, fedora core6 updated, python2.4. I have tried the precompiled version 0.99rev9 and the latest beta for linux-32bit and the only 64-bit I could see dated may 2006. The binary comes up as usual, but the tcl command line is frozen and will not accept any keyport input. That's obviously not helpful. I wonder if someone else has seen this behavior or has ideas how to go about it. Thanks, Gerwald below more detailed info... this is the pymol output on startup, note the freeglut error: freeglut (/xsoft/pymol-0.99rev9/pymol.exe): Unable to create direct context rend ering for window 'PyMOL Viewer' This may hurt performance. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. This PyMOL Executable Build is exclusively available to PyMOL Sponsors with current PyMOL Maintenance and/or Support Subscriptions. Only designated PyMOL Power, Casual, and Developer Users covered within the scope of such a Subscription may legally use this software product. Any other usage is specifically prohibited and may constitute a violation of United States and international Copyright laws. This Executable Build integrates and extends Open-Source PyMOL 0.99rev9. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: GeForce 7900 GT/GTO/PCI/SSE2 GL_VERSION: 1.4 (2.1.0 NVIDIA 97.55) Adapting to GeForce hardware. Detected 2 CPUs. Enabled multithreaded rendering. In addition (no I don't really have ample time to spend on this), here is how far the simple-minded approach to compile the source code leads on this machine: Comments on this would also be appreciated :-) This is the output from: python setup.py build. gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPI C -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ila yer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/us r/local/include/python2.4 -c layer1/PConv.c -o build/temp.linux-x86_64-2.4/layer 1/PConv.o -ffast-math -funroll-loops -O3 In file included from /usr/local/include/python2.4/Python.h:55, from layer0/os_python.h:28, from layer1/PConv.c:18: /usr/local/include/python2.4/pyport.h:612:2: error: #error LONG_BIT definition appears wrong for platform (bad gcc/glibc config?). error: command 'gcc' failed with exit status 1
Re: [PyMOL] Question about electron density map with mtz file
Hi Adiphol * adi di adipho...@yahoo.com [2007-05-11 10:26] wrote: Dear all, I am trying to put on the electron density. I only have .mtz file but I have a look at the manual and the program need XPLOR file. How can I get the XPLOR file or do I need to convert the mtz file to this - if so how can I do that? Thank you very much Actually PyMOL can read ccp4 format maps, but they have to be maps, not the mtz reflection file with the columns h, k, l, FWT, PHWT etc. as output by refmac and other programs. If you ask refmac to output a CCP4 format map, then PyMOL can read it: load filename.map, map_obj, format=ccp4 will load the map and create an object called map_obj. The latter then needs to be contoured by PyMOL. For example: isomesh lev1, map_obj, selection=molecule c. a resi 100, level=1, buffer=8. would create an object called lev1 with a contour level of 1 in a box of 8Angstroms around residue 100 of chain a of molecule. Hope that helps, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
[PyMOL] Reading .MOE files in PyMOL 1.0 beta 23
This message is for PyMOL users who also use the Molecular Operating Environment (MOE), a commmercial molecular modeling package published by the Chemical Computing Group (CCG). Incentive builds of PyMOL 1.00beta23 include the latest version of what will hopefully prove to be a broadly useful capacity for reading .MOE files in PyMOL. The basic idea is that you can do all sorts of fancy molecular calculations in MOE (an expert package) and then easily share those results with your non-computational colleagues via PyMOL session files, shows, or rendered movies simply by reading your .MOE file into PyMOL. The way it works is that each .MOE file becomes a group object in PyMOL containing multiple objects with each of the individual chains and graphics you have defined in MOE. PyMOL then attempts to mimic MOE appearance as much as practical. Note that multiple .MOE files can be loaded into a single PyMOL session, enabling you to combine and display results from an assortment of related calculations. Current PyMOL sponsors are welcome to download and try this build (1.00b23) from http://delsci.com/ip/beta using the access credentials provided on their latest invoice receipt. Please let us know how well it works with your own .MOE files -- we absolutely need more feedback on this feature! If you do experience problems, please send us your (non-proprietary!) .MOE files for troubleshooting and test-case development. Cheers, Warren PS. Although the PyMOL .MOE reader itself is not open-source, PyMOL session files and shows containing converted MOE content can be opened by open-source PyMOL builds. PPS. If you're not familiar with MOE, read more at http://www.chemcomp.com -- though it is proprietary, it has a very open architecture, well-suited for methods development. PPPS. Maestro users, stay tuned... dot-MAE is next as soon as .MOE reading proves stable and complete. - DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD
