[phenixbb] Problems about AutoSol: too many HA sites identified.

[Tom Terwilliger]

Hi Kaibo,

It is normal to find more sites than are in the sequence, both due to
multiple conformations of SeMet side chains and due to identifying other
anomalous scatterers as Se.  It is fine for you to edit these sites for
refinement based on chemical plausibility.   You can also use the
difference in f" values for different scatterers to give clues as to the
identity of any particular scatterer.  This can be done in phenix.refine.

All the best,
Tom T


On Mon, Jul 9, 2018 at 3:32 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Kaibo,
>
> 2. The 2Fo-Fc map and AutoBuild solution looked fine, but the Fo-Fc map is
>> kinda noisy with positive peaks showing up within the main-chain density
>> which causes troubles for refinement.
>>
>
> what contouring level you use to see Fo-Fc map? Note, usual "3 sigma" is
> not universally optimal but depends on solvent content. Do you still see
> lots of artifacts at say 0.35 or 0.4e/A**3 (mean solvent density) ?
>
> Pavel
>
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Hello,

I tried to use AutoSol to solve a SAD date set. The space group is P212121,
with two proteins per ASU each containing one SeMet. However, the Hyss
would always find 4~5 extra sites per ASU besides the two SeMet residues.

So my questions are:
a. Is this normal to have so many more sites identified? Or what might be
the problem?
b. Could I remove those extra Se sites during refinement if the occupancy
is low or doesn't make sense biologically?

Here are some details:
1. Most of the extra sites are around 20% occupancy and not within the
range as alternate SeMet side-chain positions. One of them even overlapped
with the position where should be a ligand phosphate.

2. The 2Fo-Fc map and AutoBuild solution looked fine, but the Fo-Fc map is
kinda noisy with positive peaks showing up within the main-chain density
which causes troubles for refinement.

3. No twining was detected for the dataset. Several space groups have been
tried (including no screw axis) and all of the solutions contained more
sites than there should be.

Please let me know if you encountered similar problems before. Thanks a lot!

Best regards
Kaibo


*Kaibo Zhang*
PULSe, Purdue University
Hockmeyer Hall, Room 321
240 S. Martin Jischke Drive, West Lafayette, IN 47907
Telephone: 765-337-1955
E-mail: zhang644 at purdue.edu




-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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