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[ccp4bb] pdbset surprise ? |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 18 February 2008Subject: pdbset surprise ? From: "Ingo P {- dot -} Korndoerfer" korndoerfer {- at -} CRELUX {- dot -} COM Date: 2008-02-18 i just noticed a to me somewhat unexpected behaviour of pdbset. as it turns out, it seems to make a difference whether i do run pdbset all in one go, changing the cell and applying transformations at once: pdbset XYZIN ... << eof-pdbset cell spacegroup ... rotate euler shift fractional eof-pdbset or split it up into two steps, where i first change the cell pdbset XYZIN ... XYZOUT tmp1.pdb << eof-pdbset1 cell spacegroup ... eof-pdbset1 and then apply the transformations pdbset XYZIN tmp1.pdb XYZOUT ... << eof-pdbset2 spacegroup ... rotate euler shift fractional eof-pdbset2 the second option works fine, with an r-factor in refmac rb refinement that corresponds to my amore result, while in my special case the first option results in a pdb file that does not refine in refmac. my impression is that the pdbset "cell" card somehow does not properly override the original, old, cell from the pdb file throughout ... or is this maybe an implicit feature, something to do with the order in which pdbset processes the input pdb and input cards ??? no big problem, easily worked around ... once you are aware of it, that is ... possibly worthy of a short warning in the documentation ? cheers ingo CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 18 February 2008 |
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