<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><P>Thank you very much for your help.</P>
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<P>I just wanted to follow up in how I'm progressing with this. I tried the things you suggested, as well as a variety of others, with no luck. It turns out that my 4mol/AU P41 twinned data is ACTUALLY 8mol/AU P212121. The packing in the AU has an almost 41 screw relating 4 mols to the other 4. When this operation is carried out, 2 mols overlay 2 others almost perfect, while the other 2 overlay the other 2 by 180 degrees. So my AU packing is a pseudo-41 with apparent twinning. (The b dimension did not need halving, so my cell is 2x the size, if that makes sense).</P>
<P> </P>
<P>The data refines very well as P212121, and Rfree drops like a rock.</P>
<P>Again, thank you so much for your suggestions, and Phenix is really wonderful!</P>
<P>Christina</P>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Pavel Afonine <pafonine@lbl.gov><BR>To: PHENIX user mailing list <phenixbb@phenix-online.org><BR>Sent: Tuesday, May 20, 2008 1:51:42 AM<BR>Subject: Re: [phenixbb] problem with high Rfree<BR><BR>Hi Christina,<BR><BR>I usually observe similar R/Rfree behavior when I use LS target instead of maximum-likelihood. In fact, twin refinement in phenix.refine is based on LS target function. This is just to share my observations; it's not necessarily happening in your case.<BR><BR>- How many of test reflections you have and how they are distributed in resolution bins?<BR>- Just out of curiosity: did you try to ignore twinning and run refinement with default target?<BR>- What if you don't run SA?<BR>- Did you try to play with target weights (try different values for wxc_scale and wxu_scale) to see how this affect the R-factors?<BR>- Are
you using the latest (or one of) phenix.refine?<BR>- Did you try to fill in water?<BR><BR>Could you send a log file: may be we could spot something outstanding...<BR><BR>Pavel.<BR><BR><BR>On 5/19/2008 1:32 PM, Christina Bourne wrote:
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<DIV>Hello BB,</DIV>
<DIV>I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A.</DIV>
<DIV>I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms)</DIV>
<DIV>Maps look nice, although I wish my ligand had more/better density.</DIV>
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<DIV>I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong.</DIV>
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<DIV>Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell.</DIV>
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<DIV>Any opinions or suggestions are most welcome as I wait for better xtals to grow...</DIV>
<DIV>Thanks in advance,</DIV>
<DIV>Christina</DIV></DIV><BR><PRE><HR width="90%" SIZE=4>
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