Hi I did get different values in phenix.model_vs_data, after the refinement gave me R and Rfree as 24 and 29% and phenix.model_vs_data gave me R_compute and Rfree-compute as 22 and 26%. Thought that both R-compute and refinement values should be more or less same? any suggestions R
Hi, tiny deviations are expected, but large ones like this - are not. If you want me to explain what's happening in your case - please send me the data and model files, and then I will have a look. Pavel On 5/12/12 4:55 PM, r n wrote:
Hi I did get different values in phenix.model_vs_data, after the refinement gave me R and Rfree as 24 and 29%
and phenix.model_vs_data gave me R_compute and Rfree-compute as 22 and 26%.
Thought that both R-compute and refinement values should be more or less same?
any suggestions
R
A refine input file with strategy selecting individual adp refinement has a selection of excluded residues as follows: adp { individual { isotropic = not ((chain A and resseq 1500:1501) or (chain B and resseq 1500:1501) or (chain X)) anisotropic = none The isotropic B factors of the above excluded residues are however refined. The selection has been ignored. Thanks! Nora On 13 May 2012, at 13:46, Pavel Afonine wrote: Hi, tiny deviations are expected, but large ones like this - are not. If you want me to explain what's happening in your case - please send me the data and model files, and then I will have a look. Pavel On 5/12/12 4:55 PM, r n wrote: Hi I did get different values in phenix.model_vs_data, after the refinement gave me R and Rfree as 24 and 29% and phenix.model_vs_data gave me R_compute and Rfree-compute as 22 and 26%. Thought that both R-compute and refinement values should be more or less same? any suggestions R _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5456 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
On Mon, May 14, 2012 at 11:13 AM, Nora Cronin
A refine input file with strategy selecting individual adp refinement has a selection of excluded residues as follows:
adp { individual { isotropic = not ((chain A and resseq 1500:1501) or (chain B and resseq 1500:1501) or (chain X)) anisotropic = none
The isotropic B factors of the above excluded residues are however refined. The selection has been ignored.
I believe this is because of the overall B-factor for the entire crystal ("Ucryst") being refined, which will happen no matter what. Because phenix.refine reports the total atomic B-factors including all contributions, this change will propagate to the atoms you've excluded, even if their individual B-factors aren't being refined. (Although it is also unclear why you wouldn't want to refine those B-factors too - this is almost always recommended.) I guess we need to add this to the phenix.refine FAQ list. PS. please post with a new subject instead of replying to a previous post, it makes a big difference for some email clients and our mailing list archives. -Nat
participants (4)
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Nathaniel Echols -
Nora Cronin -
Pavel Afonine -
r n