[phenixbb] symmetry related bond restraint in R3 space group

Pavel Afonine pafonine at lbl.gov
Fri Jan 11 00:44:49 PST 2013

Hi Xiang,

could you please send me PDB file and parameter file that you used, and 
that you believe does not do what you want.
Also, what you mean by "it did not work in Phenix refine"? The way to 
know if custom restrains that you specified were actually used is to 
look in .geo file to check if bonds in question are there. Anyway if you 
send me the files I will have a look. At this stage I don't need 
reflection data file.


On 1/8/13 2:23 PM, Xiang Li wrote:
> I am trying to add some restraints between symmetric molecule with symmetry operation. However, I found it is not correct to use the operation information directly provided in Coot.
> The crystal I worked on has R3 symmetry. The symmetry operation in Coot shows to be -x+y,-x,z+ (1,1,0) and it did not work in Phenix refine. I read one previous email on this topic about the difference of symmetry operation in Coot and Phenix. However, I do not know how to do the conversion between the two when the numbers changed. Could you help me to work out on correct the symmetry operation in Phenix and talk some more on how to do the conversion please? I really appreciate your help!
> Sincerely,
> Xiang
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