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Re: [ccp4bb] DANO from PDB |
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CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 07 June 2007Subject: Re: DANO from PDB From: James Holton JMHolton {- at -} LBL {- dot -} GOV Date: 2007-06-07 http://bl831.als.lbl.gov/~jamesh/mlfsom/ano_sfall.com The script is actually based on a CCP4BB reply from Elanor I found in the archives. It does Elanor's jigery-hokery, and a few other things. The script is meant to be the front-end for a simulator so I did a number of things to make the output "data" more "realistic". You run it like this: ano_sfall.com model.pdb sites.pdb P212121 2A fpp=4 fp=-8 sigma=1 or ano_sfall.com model.pdb 2A wave=0.98 where: model.pdb is a brookhaven file of the protein structure optional: sites.pdb is a second brookhaven file containing position/occupancy/B of anomalous scatterers P212121 is the desired space group 2A render to a desired resolution wave=0.98 calculate the anomalous f' and f'' contribution at 0.98 A energy=12680 calculate the anomalous f' and f" contrubution at 12680 eV fpp=4 sets the anomalous f'' contribution to 4 electrons fp=-8 sets the dispersive f' contribution to -8 electrons grid=0.3 use a particular grid spacing in sfall sigma=1 gives a value of 1 to the sigma of each column nohydrogen do not add hydrogens first What the script does: 1) add hydrogens with "hadd" yeah, you can't "see" them at 3A, but i.e. a methylene carbon has 8 electrons, not 6. 2) calculate f' and f" for each atom type in the PDB at the wavelength provided using "crossec" unless there is a user-defined f' and f" on the command line 3) calculate a solvent mask with "sfall" 4) smooth the solvent mask with "mapman" (if it is available) this avoids series-termination errors from the "sharp" solvent edge 5) convert everything into HKL and F using "sfall" 6) apply the f' and f" to the contribution of each atom type using "sftools" (this is the jigery-hokery) 7) add up all the (phased) partial structure factors using "sftools" 8) output FP PHIP FH PHIH FPH DANO Fplus Fminus Fmean (with "sigmas") into "ideal.mtz" I add a fake "sigma" column for each "data" column because so many programs require one. FP PHIP is the contribution of the protein (and solvent) FH PHIH is the vector sum of all the f' and f" contributions FPH is the vector sum of FP with all the f' contributions Fplus is FPH + all the f" contributions Fminus is FPH - all the f" contributions Fmean is the mean of Fplus and Fminus DANO is the difference between Fplus and Fminus Comments and questions are always welcome. DISCLAIMER: I do not consider this script ready for "prime time" yet. I'm sure there are quite a few entries in the PDB that will break it. If it works for you, great. If it doesn't work for you, sorry. I'm still working on it. If you use it to publish some fake results, then this is your fault, not mine. If it does something "wrong" that makes you have to retract your structure then this is also your fault, not mine. Why did you trust me anyway? END DISCLAIMER -James Holton MAD Scientist Santosh Panjikar wrote: >Hi all, > > Does anybody have a program which can calculate anomalous differences or > F+ and F- from a refined structure at given wavelength and resolution ? > > Thanks > Santosh > > >Santosh Panjikar, Ph.D. panjikar@embl-hamburg.de >Staff Scientist >EMBL Hamburg outstation http://www.embl-hamburg.de/~panjikar/ >DESY, Notkestrasse 85 Tel.:+49-40-89902-141 >22603, Hamburg, Germany Fax: +49-40-89902-149 > > CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 07 June 2007 |
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