Greetings everyone: I have been dealing with a structure of a protein that has a Cys residue covalently modified with a peptide fluromethyl ketone. Can someone tell me how to include this ligand in phenix.refine? In the past, I have used CNS for this purpose. I created a topology and parameter file (using ProDrug server) and modified a patch in the refine script in CNS to establish a covalent connection between an atom in the ligand and gamma sulfur of the protein in question. Thanks. Chitta
Hi Chitta, Please look for "CIF modifications and links" here: http://www.phenix-online.org/documentation/refinement.htm You may also want to look at the elbow documentation: http://www.phenix-online.org/documentation/elbow.htm Ralf
Hi all, I am wondering why I am getting a large coordinate error of 2.17A in the phenix refinement of the structure that I earlier refined in CNS (2.4A resolution). Is it normal or why is it happening? How to fix it? Rwork and Rfree are 18% and 22%. Maia
Hi Maia, the R-factors seem good at this resolution. If the other validation criteria, local and global, are ok, then I wouldn't worry too much about this error anyway, since its estimation is not always reliable. For example, as local validation use phenix.real_space_correlation to plot map CC for each atom - this will give you the ideal local fit of your model into electron density map. Use Molprobity for geoemtry validations, etc. Cheers, Pavel. On 3/14/09 12:24 PM, Maia Cherney wrote:
Hi all, I am wondering why I am getting a large coordinate error of 2.17A in the phenix refinement of the structure that I earlier refined in CNS (2.4A resolution). Is it normal or why is it happening? How to fix it? Rwork and Rfree are 18% and 22%.
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participants (4)
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cdas＠purdue.edu -
Maia Cherney -
Pavel Afonine -
Ralf W. Grosse-Kunstleve