Hmmm.I have a question for the experts: It seems to me from the figure (although that is for Tri Ngo to verify), that
these partial occupancies are correlated. When conformation A of TYR (in the green density) is occupied, Phe B in the blue density probably cannot be occupied because of a VdW clash. (Again, caveat that I can't see that exactly from the static image) I recall that Shelxl allows to constrain such occupancies, but how are Refmac and Phenix dealing with that? How would I implement that? Are clashes between partial occs just ignored? Even if I am wrong about the existence of a clash in this particular case, such situations are not uncommon imho. Thx, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine Sent: Friday, July 27, 2012 7:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Alternative conformation of Phe and Tyr? Hi, you can't expect to see something with occupancy ~0.3 at the same cutoff level as you use to see fully occupied sites. So most likely the solution is to use a lower cutoff levels, as many suggested already. Two maps you attached look totally expectable to me. Pavel On Fri, Jul 27, 2012 at 1:01 AM, Tri Ngo <ngoduc...@gmail.com> wrote: Dear ccp4bb, I am working on refinement of an enzyme structure. I notice an alternative conformation (gauche+ and gauche-) on both residues Phe and Tyr. Here is the image of electron density before refinement. Based on the different map intensity, I am quite sure there is an alternative conformation on both positions. http://i50.tinypic.com/29zaoap.jpg However, after running occupancy refinement by Phenix, I don't see the density map at the gauche- conformation of Tyr residue. Please take a look at the image 2. http://i50.tinypic.com/anzfrn.png So do you think the gauche- conformation of Tyr exists in this structure. Should I keep it in the final model because there is no positive map there? Thank you very much for your input. -- Ngo Duc Tri PhD Student Structural Biology Lab School of Medicine - Sungkyunkwan University - Korea Phone: 031-299-6150 - Cell: 010-7774-8210
