Thank you Nigel,
However, your cif file did not help with the problem (carboxylate is not
planar) when using the PHENIX 1.4-3 version that we have now. You
mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get
them both? By the way, phenix.ready_set (in our current version) screwed
up all hydrogens in my other ligand (trimer of ASG-GCU). I think that
the ready.set needs to know that the monomers are linked. With this
particular ligand that is a hexamer, ASG is in the library, but GCU is
not. Should I give a cif_link file for the ready.set, too? After I get a
newer version of phenix, I 'll try it again.
Maia
Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar
groups including the carboxyl group missing from the earlier PHENIX
version I believe you used. I have attached it. There are a few
other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the
model using the data from the Chemical Components database from the
PDB. I would recommend that you use ReadySet! for preparing a PDB
file for refinement. It also adds hydrogens to your model which is
usually a good thing.
Your example does have some nuances. You mention that it is
covalently bound to the CYS. I have attached the two additional files
needed to inform phenix.refine of the covalent bond. I used eLBOW
directly for this but will ensure that ReadySet! will do the same
function in the next release.
An additional function that I have been working on recently is the
removal of the hydrogen in a carboxyl group when the ligand is in the
model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the
carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact
me directly.
Nigel
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