Hi Colin, I don't know what phenix.development.optimize_model is. Perhaps one of developers added it for testing/development purposes not for end-users. I suggest you use phenix.refine in the GUI or command line, which is well tested both by time and extensive sets of tests. You cannot combine TLS and individual anisotropic ADP refinement, so regardless what tool you used it's either TLS or individual anisotropic ADP refinement, not both. Pavel On 3/18/15 8:51 AM, Colin Levy wrote:

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