[phenixbb] pdb waters

Pavel Afonine pafonine at lbl.gov
Thu Mar 15 12:41:22 PDT 2007


yes, the waters in your file do not match the Monomer Library 
definition. If you simply replace O1 with O that will fix the problem.
For example:

GOOD record:
ATOM  22792  O   HOH X   1      37.309  34.504 -14.174  1.00 
38.28           O

BAD record:
ATOM  22792  O1  HOH X   1      37.309  34.504 -14.174  1.00 
38.28           O

> I have tried running elbow on my pdb already with no luck.  using your 
> command I get the error message: elbow.builder: error: no such option: 
> --do-all

That makes me thinking that you are using an old version of CCI Apps or 
PHENIX. Are you using the latest one?
Is the command you run looks like:
% elbow.builder x.pdb --do-all

Nigel: do you have any comments?


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