Hi Young-Jin, For the second one you can try lower the scale factor of wxu and wxc from default (1 and 0.5) . Is it the first round to run phenix? If not better to go back and rerun it again. See the manual for details: http://www.phenix-online.org/documentation/refinement.htm And for the first one |I have no experience on that and no idea at all. Hope other guys will help you for that. Good luck! leo Young-Jin Cho wrote:
Hi, my current wonderings are as below: First, how can I add H atoms into nucleotide ligands in pdb file? I did 'phenix.reduce model.pdb > model_h.pdb', but as I see it didn't add H's of sugar (1', 2', 3' 4' and 5'). Once I had this kind of problem before, I was suggested to use phenix.ready_set command but seemingly this does not work any longer with last version that I am using now. Also, is it possible to add H into phosphate group?
The second very general question is about getting over overfitting problem. My phenix runs gave me too much difference between R and Rfree about .7 w/o adding H atoms. I assume it came from water molecules because it(huge gap) just starts to happen after 1_bss stage. If anybody can suggest a good way to get over this problem, you will save my tremendous times and useless efforts.
Big thanks in advance,
Young-Jin
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb