[phenixbb] a question on LSTc refinement

Nigel Moriarty nwmoriarty at lbl.gov
Mon Aug 19 16:33:51 PDT 2013


Sorry for the delay.

I made some changes to the restraints library to handle SIA and alpha 2-6
linkages in April so it's there in the more recent versions but you may
need to specify the linkage. Could you please send me your problem residues
and I'll provide the exact command.



NB. Any files sent to me will be held in strictest confidence.

On Wed, Aug 14, 2013 at 11:18 AM, <fn1 at rice.edu> wrote:

> Hi all,
> I read some previous post on LSTc [SIA(alpha2-6)GAL(beta1-4)NAG]
> refinement, but i still cannot figure out how to refine it in PHENIX. In
> the current version of phenix, i still could not find the ALPHA2-6 link.
> Does anybody have such experience?
> Another question is that, sialic acid (SIA) is in the monomer library of
> phenix. But when i run on the pdb directly, it will give the error
> information like, "unknown bond type for O1A and O1B".  Though this error
> could be solved by provided the cif file generated by phenix.elbow.
> Thank you very much!
> Fengyun
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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