[phenixbb] [EXTERNAL] Re: red blobs (Andrea Smith)

[Jiang, Jiansheng (NIH/NIAID) [E]]

Hi Andrea,

It might be the B-factor problem.

The "red" densities are negative values that may be caused by neighbour atoms which were over-fitted.  How was the Wilson B-factor value (and resolution) and the B-factor in the model, particularly, around the "red" region.  You may need to reset the B-factor to a lower value (or apply a negative B-factor to the processed data), and refine the model again, to see if the "red" densities could disappear.

Jiansheng.
==================================================
Jiansheng Jiang, Ph.D.
Molecular Biology Section
Laboratory of Immune System Biology, NIAID/NIH
Building 10, Room 11D07
10 Center Drive
Bethesda, MD 20892-1892
U.S.A.
Phone: 301-761-6760
E-mail: jiangji at niaid.nih.gov
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________________________________________
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Andrea Smith <andrea.smith at uochb.cas.cz>
Sent: Friday, March 15, 2024 3:27 AM
To: Dr. Kay Diederichs
Cc: phenixbb at phenix-online.org
Subject: [EXTERNAL] Re: [phenixbb] red blobs (Andrea Smith)

Hi Kay,

I tried the mask optimization and there is no change in how the final map looks like.

Should I just make peace with it?

Best,
Andrea

On Thursday, March 14, 2024 23:11 CET, Kay Diederichs <kay.diederichs at uni-konstanz.de> wrote:

Hi Andrea,

in your case, phenix.refine seems to fill bulk solvent into volumes that
are not actually filled by solvent.
It might help to optimize the mask, see
https://phenix-online.org/documentation/reference/refinement.html#bulk-solvent-correction-and-anisotropic-scaling
"6. Mask parameters".

Best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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