<FONT face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=2>Hi Vincent,<br><br>I think the consensus often varies on what is considered high resolution, though I have heard that anything better than 2A is considered high resolution. I suppose if ask 10 different people, you may get 10 different answers :)<br><br>As for refinement strategies, I think the main thing to consider is maintaining a proper data-to-parameter ratio with a safety factor around 3. With that said, you should be able to do rigid-body refinement with group ADPs and simulated annealing at 3.7 A. You should be add in TLS groups at the end as well. Given that the refinement will be done in "groups", you can easily manipulate the number of groups to maintain a legal data-to-parameter ratio. For example, one rigid group requires 6 parameters, and a single TLS group requires 20. All of this can be done easily in Phenix.<br><br>I hope this helps. I'm sure Pavel or someone else from the Phenix group will add their expertise.<br><br>Best regards,<br><br>Jason Porta<br>Graduate Student<br>Eppley Structural Biology Facility<br>Dept. Biochemistry & Molecular Biology<br>University of Nebraska Medical Center<br>Omaha, NE 68198<br>402-559-5533<br><br><br><div><br><div><br></div><font color="#990099">-----phenixbb-bounces@phenix-online.org wrote: -----<br><br></font><blockquote style="border-left: 2px solid #000000; padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;">To: PHENIX user mailing list <phenixbb@phenix-online.org><br>From: vincent Chaptal <vchaptal@mednet.ucla.edu><br>Sent by: phenixbb-bounces@phenix-online.org<br>Date: 04/09/2010 12:35PM<br>Subject: [phenixbb] refinement at 3.7A<br><br><font face="Courier New,Courier,monospace" size="3">Hello list,<br><br>i would like to add a following discussion to yesterday's low resolution<br>refinement question: What is low res? at what resolution should we use<br>only rigid body refinement or can we use minimization as well?<br><br>In my case, i have a 2.7A and a 3.7A structures, of 2 different mutants,<br>in the same space groups and cell parameters. After refining the high<br>res one, i'm wondering what is the best strategy to refine the low res one?<br>If i do a simple rigid body refinement, I have R=32.1, Rfree=35.8. If i<br>use individual site refinement, i have R=30.7, Rfree=35.8. (both with<br>group ADP, TLS and NCS).<br>The statistics look good and the maps look great. There isn't any<br>feature in the difference map so i'm guessing i'm done with refinement?<br>(I'm afraid of over-refining it as the map look too good for this<br>resolution. )<br><br>I was also advised to add hydrogen bond restraints to maintain secondary<br>structures, I guess upon using minimization refinement?<br><br>Basically, could you update me on what's today's dogma on what type of<br>refinement we should use at what resolution?<br>( i couldn't find this info on the phenix web site, sorry if i missed it)<br>thank you very much.<br>vincent<br><br><br><br><br>Pavel Afonine wrote:<br>> Hi,<br>><br>> rigid body refinement does not employ any restraints. You can use<br>> secondary structure restraints in refinement of individual coordinates.<br>><br>> Actually, you can use secondary structure restraints in constrained<br>> rigid body refinement (SA in torsion angle space).<br>><br>> To use secondary structure restraints:<br>> "secondary_structure_restraints=true". phenix.refine GUI should have<br>> an option for this too.<br>><br>> Pavel.<br>><br>><br>> On 4/7/10 4:38 PM, r n wrote:<br>>> Hi<br>>> I wanted to do low resolution rigid body refinement with secondary<br>>> structural restrain. I have not seen<br>>> any command or information in the phenix document?<br>>> any help<br>>> Thanks<br>>> ram****<br>>><br>>><br>>><br>>> ------------------------------------------------------------------------<br>>><br>>> _______________________________________________<br>>> phenixbb mailing list<br>>> phenixbb@phenix-online.org<br>>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>>><br><br>--<br><br>Vincent Chaptal<br><br>Dept. of Physiology at UCLA<br><br><a href="http://www.physiology.ucla.edu/Labs/Abramson/index.html">http://www.physiology.ucla.edu/Labs/Abramson/index.html</a><br><<a href="http://www.physiology.ucla.edu/Labs/Abramson/index.html/">http://www.physiology.ucla.edu/Labs/Abramson/index.html/</a>><br><br>Phone: 1-310-206-1399<br><br><br>IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.<br>_______________________________________________<br>phenixbb mailing list<br>phenixbb@phenix-online.org<br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></font>
</blockquote><br></div></FONT>