[phenixbb] a question on LSTc refinement

Pavel Afonine pafonine at lbl.gov
Fri Aug 16 21:19:13 PDT 2013

Hi Fengyun,

since nobody replied with a better suggestion, here is mine.
You can define a bond (and angle, etc) between any two atoms, any number 
of such bonds. Have a look at how-to and let me know if you have any 
problems doing this or any questions:

"Definition of custom bonds..."



On 8/14/13 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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