Group B factor refinement not working for low resolution data
Hi, I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：[email protected]
Hello Xiang, short answer: try refining with all defaults plus weight optimization. If that does not go well please send me data and model files and I will do my best to make it work. Longer answer: the way B-factor restraints are implemented in phenix.refine (that you can learn about in corresponding paper) allows refining individual Bs at any resolution. So this is why this is the first choice to try. If that does not work it's best to a) let us know and b) try group B refinement. Pavel On 3/11/15 7:30 PM, 李翔 wrote:
Hi,
I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please?
Thank you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, University of Michigan Email：[email protected] mailto:[email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
I've been refining a 3.4A structure (now using dev-1951) and find that anything besides TLS (with multiple groups at least) makes Rs go up. A lot. And I am asking it to optimize weights. ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago [email protected]mailto:[email protected] ________________________________ From: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] Sent: Thursday, March 12, 2015 12:35 AM To: 李翔; PHENIX user mailing list Subject: Re: [phenixbb] Group B factor refinement not working for low resolution data Hello Xiang, short answer: try refining with all defaults plus weight optimization. If that does not go well please send me data and model files and I will do my best to make it work. Longer answer: the way B-factor restraints are implemented in phenix.refine (that you can learn about in corresponding paper) allows refining individual Bs at any resolution. So this is why this is the first choice to try. If that does not work it's best to a) let us know and b) try group B refinement. Pavel On 3/11/15 7:30 PM, 李翔 wrote: Hi, I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：[email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]
Hi Phoebe, I'm always interested to have a look at unusual cases... Often this builds knowledge and helps to improve methodology. Would you mind sending me files (data and model) so that I can investigate what's going on? Thanks, Pavel On 3/12/15 8:18 AM, Phoebe A. Rice wrote:
I've been refining a 3.4A structure (now using dev-1951) and find that anything besides TLS (with multiple groups at least) makes Rs go up. A lot. And I am asking it to optimize weights.
++++++++++++++++++++++++++++++++++++++++++
Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago
[email protected] mailto:[email protected] ------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] *Sent:* Thursday, March 12, 2015 12:35 AM *To:* 李翔; PHENIX user mailing list *Subject:* Re: [phenixbb] Group B factor refinement not working for low resolution data
Hello Xiang,
short answer: try refining with all defaults plus weight optimization. If that does not go well please send me data and model files and I will do my best to make it work.
Longer answer: the way B-factor restraints are implemented in phenix.refine (that you can learn about in corresponding paper) allows refining individual Bs at any resolution. So this is why this is the first choice to try. If that does not work it's best to a) let us know and b) try group B refinement.
Pavel
On 3/11/15 7:30 PM, 李翔 wrote:
Hi,
I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please?
Thank you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, University of Michigan Email：[email protected] mailto:[email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe:[email protected]
participants (3)
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Pavel Afonine -
Phoebe A. Rice -
李翔