Re: [phenixbb] phenixbb Digest, Vol 117, Issue 9

Hi Mark! Anybody for the 24th trip to Alba? I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving. César. ------------------------------------------------------------------ Cesar Santiago, Ph. D. Dept. of Macromolecules Structure at CNB, CSIC. X-ray Crystallography Facility. Campus Universidad Autónoma. Madrid, 28049 [email protected] On Aug 27, 2015, at 6:42 AM, [email protected] wrote:

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Today's Topics:

1. Re: phenix.refine automatic linking options (Engin ?zkan) 2. external passive 3D monitor with macbook pro or imac for coot and pymol stereo view (Xiao Lei) 3. Rank-scaled map (Jianghai Zhu) 4. Re: Rank-scaled map (Pavel Afonine) 5. Re: on the starting mtz file for phenix refine (Pavel Afonine) 6. Ligand addition in COOT for later refinement in Phenix.refine (Manoj saxena) 7. Re: Ligand addition in COOT for later refinement in Phenix.refine (Oleg Sobolev) 8. Computational Crystallography Newsletter - Volume 6, Number 2 (Nigel Moriarty) 9. Starting structure as reference model - crashing in 1.10-2142 (Tristan Croll) 10. Re: Starting structure as reference model - crashing in 1.10-2142 (Pavel Afonine)

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Message: 1 Date: Thu, 20 Aug 2015 15:41:31 -0500 From: Engin ?zkan To: Billy Poon Cc: PHENIX user mailing list Subject: Re: [phenixbb] phenix.refine automatic linking options Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear Billy and Nigel,

Thank you. Phenix.refine GUI in the latest nightly/release candidate no longer has the master enable/disable button, and so the problem is resolved.

Engin

On 8/13/15 11:28 AM, Billy Poon wrote:

...

Hi Engin,

Thanks! We updated that part of the GUI so that it should be more intuitive. There is now a button that lets you apply automatic linking to all the components and a button that disables all automatic linking. You can, of course, still pick which components to enable by checking the specific boxes.

On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan mailto:[email protected]> wrote:

Dear Developers,

Using the latest phenix nightly, I observed something odd in the phenix.refine UI, and I thought I should report it. If one unchecks Automatic ligand linking, this seems to not override its options, as the instructions in the Options window suggest. Specifically, if "Automatic Ligand Linking" is unchecked, but the "Link metals" is checked within its Options window, metal link restraints are still created.

I checked the .geo file to confirm this.

Thanks, Engin

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