[phenixbb] pdbtools atom_selection behavior

[wtempel]

Hello all,
suppose I would like to remove one alternate conformation B from residue 1
in chain A and set the occupancy of remaining atoms in that residue to 1.

phenix.pdbtools alts_minim.pdb occupancies.set=1 \
  occupancies.atom_selection=”chain A and resid 1” \
  keep=”not (chain A and altid B and resid 1)” \
  output.file_name=alts.out.pdb


There are better methods to achieve that, but I eventually would like to
expand this command to do other “things” to my coordinates.
Well, so far I have failed to have the atom_selection to work the way *I*
expect. stdout reveals that the program fails to apply a common scope to
the command switches, and proceeds to reset occupancies of all atoms. Can
this be done on the command line? A minimal (not) working example is
attached, and your feedback appreciated.
Best regards.
Wolfram Tempel

​
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170207/92b3f25b/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: set.out
Type: application/octet-stream
Size: 12013 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170207/92b3f25b/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: alts.out.pdb
Type: chemical/x-pdb
Size: 244 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170207/92b3f25b/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: alts_minim.pdb
Type: chemical/x-pdb
Size: 315 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170207/92b3f25b/attachment-0003.bin>