[PyMOL] PyMOL and cctbx
Dear Simon and other pymolers, I have realised that the solution to getting cctbx working with pymol on windows I posted no longer works with recent builds of cctbx. I have found that the following solution works: 1. Download and install python (to the default location - C:\Python24) -- http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi (1a. If you want to use the draw_symops.py or draw_symops_cctbx.py scripts you also need to install numarray after installing python -- http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download) 2. Download cctbx *without* python included and unpack into C:\cctbx_build and C:\cctbx_sources -- http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe 3. Download pymol built against python 2.4 (but not including its own python) and install in the default location -- http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip (You cannot use the latest beta versions which include their own version of python to the best of my knowledge) 4. Create 2 files (use notepad or wordpad or any other text editor) and save in the C:\Program Files\Delano Scientific\PyMOL directory: a) pymol.cmd @python -x %~f0 %* exit /b import cctbx import pymol b) run.cmd CALL C:\cctbx_build\setpaths_all.bat CALL C:\Program Files\Delano Scientific\PyMOL\pymol.cmd 5. One other thing, it's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon. Hopefully this should work OK... I know it is working on at least one other system than my own. Let me know if it works for you. I'll post this up on the wiki ASAP. Cheers Roger begin:vcard fn:Roger Dodd n:Dodd;Roger org:University of Cambridge;Department of Medicine adr:Addenbrooke's Hospital, Hills Road;;CIMR, Wellcome Trust/MRC Building;Cambridge;Cambridgeshire;CB2 2XY;UK email;internet:rb...@cam.ac.uk title:Post-Doctoral Research Associate tel;work:+44-1223-762629 note;quoted-printable:MSN - rogerd...@hotmail.com=0d=0a= ICQ - 100657240=0D=0A= Skype - rogerdodd=0D=0A= Gizmo - rogerdodd=0D=0A= SIP (VoIP) - 17476057995 x-mozilla-html:TRUE url:http://www.cus.cam.ac.uk/~rbd22/ version:2.1 end:vcard
[PyMOL] Help/suggestions for illustrating lattice arrangement
Hi, I am trying to prepare a figure illustrating a fairly complex packing arrangement in a large H32 (R32) unit cell, where the packing may actually have some biological relevance. To try and show the packing I've been generating symmetry related molecules using the symexp command. The problem I've been running into is that things become too complex and cluttered, whether I use lines, ribbons, cartoons, etc. My asymmetric unit contains 2 homo-pentamers and my question is - would it be possible to replace each monomer with, for example, an ellipsoid of roughly the same size centred on the subunit's centre of mass to simplify things? Is this the sort of thing that could be done with a cgo object? Any help or other suggestions would be greatly appreciated. Cheers Roger
[PyMOL] rgb to cmyk woes
Hi all, I'm trying to prepare some figures for publication and of course the journal requires them in cmyk format. I have produced the images in pymol using the cmyk color space and saved them as png files. However, the png files themselves are in 24 bit rgb format if I'm correct. Trying to subsequently convert them to cmyk format tiff files in photoshop or coreldraw results in all the colors being mangled (becoming duller and darker). Is there some trick to converting to the cmyk color space without altering the colors - I assumed working in the cmyk mode in PyMOL would ensure this didn't occur? Thanks in advance for any help Roger Dodd
[PyMOL] Pymol segmentation fault - fedora core 1
Hi everyone, I've recently updated to the 0.97 release of pymol and although it ran fine to start with, it's now generating a segmentation fault. I installed from the * pymol-0_97-bin-linux-libc6-i386.tgz* http://prdownloads.sourceforge.net/pymol/pymol-0_97-bin-linux-libc6-i386.tgz?download file into /usr/local/pymol and ran setup.sh. Then when running the pymol.com script I get the following: ./pymol.com: line 14: 31156 Segmentation fault $PYMOL_PATH/pymol.exe $* I'm not sure exactly what's causing this and any help would be appreciated. I've tried completely removing the pymol directory and reinstalling but I still get the same error. Cheers Roger
[PyMOL] Restrict surface transparency to limited region
Dear PyMOL users/devs, I am trying to produce a figure with a molecular surface and would like to make this surface transparent only covering certain residues. I have tried creating a separate surface for these residues and the rest of the protein and setting transparency for the object covering only those residues, but this gives a very discontinuous looking surface representation. Is it possible to just enable transparency on a limited region of a surface? Thanks Roger -- Roger Dodd CIMR University of Cambridge Wellcome Trust / MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 2XY
