>Alwyn, > >I don't know if I should ask these from you directly, I guess some of >the below are of general interest so I will do this through O-info: > >1) Are there any plans on updating O for high resolution refinement i.o. >display hydrogens (maybe someone out there has an adequate all.dat >including shelxl definition of hyrdrogens. If so, please share) and >anisotropic B-factors? Yep, myself and Mike Word made a full set of these. They are available from our ftp site at ftp://kinemage.biochem.duke.edu/UNIXprograms/probeScripts/OwithHydrogens.ta r This package was put together as part of an effort to interface some of our software with O, which requires hydrogens. In the end we went with a method that adds the hydrogens on-the-fly, so it contains some extra scripts you may not want, but they're flagged as obsolete in the README. Things you should know about: There were a couple of bugs that we could never track down. Particularly to do with the refi commands not finding the backbone NH. My best guess is that this is our fault rather than O's, but we tried pretty hard to fix it. If anyone finds (or even better fixes) the problem, please let me know. The rotamer file included is our new rotamer file (publication in press), not the standard O one. It assumes PDB standard atom names. These are NOT the same as the atom names used by XPLOR, although the tar file includes a script that converts them. PDB standard atom names have four characters, which are handled well internally in O, but one character gets lots when you write out the file, so you won't be able to read them straight back into most programs. Our program REDUCE can be used to add hydrogens with standard names, and it can be found at: http://kinemage.biochem.duke.edu/website/programs.htm#REDUCE. If my understanding is right, SHELX allows you call your atoms whatever you like. There are enough files (six or so, I think) that making them with different names is a real nuisance, so I'm not volunteering. If someone would like to tell me how to contribute these files to the standard O repository, I'd be happy to do it. Gratuitous advertisement: also on our web site is our non-hydrogenated (oxidised?) rotamer library, and the probe package which allows you to analyse van der Waals overlaps and display them in O, allowing you to quickly find and correct errors as you rebuild. Feel free to poke around starting at http://kinemage.biochem.duke.edu. Regards, Stan Simon Lovell, Biochem Dept, Duke University Tel (919) 684-2217
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