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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..." http://www.phenix-online.org/documentation/refinement.htm#anch354 Pavel On 8/14/13 11:18 AM, [email protected] 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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