[phenixbb] phenix.development.optimize_model

Hi, I am running a Phenix development installation (dev_1977) and used the phenix.development.optimize_model option on a project of mine refined at 1.9Å. The output has certainly improved the R factors but I was curious as the refined model which is a rather globular structure has been refined utilising 17 TLS groups and anisotropic B factors. In its current state of development, how robust are these refinement choices and on what basis are they being determined? They differ somewhat from what I might have invoked manually? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 [email protected] On 12/03/2015 15:19, "[email protected]" wrote:

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Today's Topics:

1. Announcement and call for abstracts: Structural Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia (Capitani Guido (PSI)) 2. how to correct residuess with missing atoms (Smith Liu) 3. Re: how to correct residuess with missing atoms (Joel Tyndall) 4. RESOLVE density modification (Mark A Saper) 5. Re: RESOLVE density modification (Terwilliger, Thomas Charles) 6. Nitric Oxide metal.edits not working? (Yarrow Madrona) 7. Re: Nitric Oxide metal.edits not working? (Edward A. Berry) 8. Group B factor refinement not working for low resolution data (??) 9. Re: Group B factor refinement not working for low resolution data (Pavel Afonine) 10. Re: Group B factor refinement not working for low resolution data (Phoebe A. Rice)

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Message: 1 Date: Fri, 6 Mar 2015 13:29:51 +0000 From: "Capitani Guido (PSI)" To: "[email protected]" Subject: [phenixbb] Announcement and call for abstracts: Structural Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia Message-ID: Content-Type: text/plain; charset="us-ascii"

Dear Colleagues,

The 29th European Crystallographic Meeting (ECM29), to be held on August 23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics microsymposium (http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural bioinformatics topics with relevance to macromolecular crystallography are welcome. Abstract submission (for oral or poster presentation) is available at http://ecm29.ecanews.org/participate/abstract-submission/, with deadline March 23. The final program will encompass two 30-min talks from invited speakers, three 20-min talks chosen from the submitted abstracts, and poster presentations. Looking forward to many interesting contributions; with best regards,

Guido Capitani

Dr. Guido Capitani Paul Scherrer Institute OFLC/110 5232 Villigen PSI Switzerland [email protected] Tel. +41 56 310 47 22 http://www.psi.ch/lbr/capitani_-guido http://www.eppic-web.org

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Message: 2 Date: Sun, 8 Mar 2015 18:11:19 +0800 (CST) From: "Smith Liu" To: "[email protected]" Subject: [phenixbb] how to correct residuess with missing atoms Message-ID: <[email protected]> Content-Type: text/plain; charset="gbk"

Dear All,

Is any function of Phenix or some other software which can be used to correct residuess with missing atoms in the PDB file?

I am looking forward to getting your reply.

Smith