[Chimera-users] saving pdb with transformed coordinates

Michael Elbaum michael.elbaum at weizmann.ac.il
Thu Dec 1 10:23:45 PST 2016


Dear Chimera people,

I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates.

I've tried the following:
for i in xrange(0,90,10):
    rc("rock " + "y " + str(i) + " 1")
    fn = basefn + str(i) + '.pdb'
    rc("write format pdb 0 " + fn)
and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11.

thanks for your help,
Michael
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