[phenixbb] pdb waters
mwb at mrc-dunn.cam.ac.uk
Fri Mar 16 08:03:22 PDT 2007
Thanks for all help so far.....
OK, renaming the water to O from O1 worked fine, I also updated CCI
Apps, now --do-all works. It only picked out one hetatm though so
then I ran elbow naming the residues and it produced cif files for
all my ligands - Hooray!
Then I put all these files into the command line with model and
structure factors and get:
Sorry: Fatal problems interpreting PDB file:
Number of atoms with unknown nonbonded energy type symbols: 51
Please edit the PDB file to resolve the problems and/or supply a
CIF file with matching restraint definitions, along with
apply_cif_modification and apply_cif_link parameter definitions
if necessary (see phenix.refine documentation).
Also note that elbow.builder is available to create restraint
definitions for unknown ligands.
Again! Even though I now have cif file for all.
Any thoughts greatly appreciated.
BTW refinement without ligands has provided a great map and v.good
stats! Really want to refine with ligands though, cheers, Matt.
On 15 Mar 2007, at 19:41, Pavel Afonine wrote:
> 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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