way to use something similar like FVAR in a pdb
> >> file?
> >>
> >>
> >>
> >>
> >> Dr. Matthias Barone
> >>
> >> AG Kuehne, Rational Drug Design
> >>
> >> Leibniz-Forschungsinstitut für Molekulare Pharmakolo
rmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
From: bogba...@yahoo.co.uk
Sent: Thursday, February 6, 2020 5:01:14 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelx
rsday, February 6, 2020 5:01:14 PM
> To: Barone, Matthias
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
>
>
> Hello, hope I can help.
>
>
> OK, so here is the disp table...
>
> SFAC C H CL N O
>
> DISP $C 0.005
ert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
From: bogba...@yahoo.co.uk
Sent: Thursday, February 6, 2020 5:01:14 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Hello, hope I can help
94793-284
From: bogbasic@yahoo.co.uk
Sent: Thursday, February 6, 2020 5:01:14 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Hello, hope I can help.
OK, so here is the disp table...
SFAC C H CL N O
10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
From: bogba...@yahoo.co.uk
Sent: Thursday, February 6, 2020 5:01:14 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Hello, hope I can help.
OK, so
uesday, February 4, 2020 9:24:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Dear Jon,
in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like.
The scattering factor is derived from the number next to the name. The name is
ehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
> --
> *From:* CCP4 bulletin board on behalf of Tim
> Gruene
Thanks, sorry, shelx is wonderful! I was thinking back to shelxpro days when your hetero-atoms could acquire the wrong scattering factors if they were not positioned right in the pdb file. The classic, which I saw several times, was calcium (CA) being treated as an alpha-carbon (CA), and I think
Dear Jon,
in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like.
The scattering factor is derived from the number next to the name. The name is
just that, and identifier.
Best,
Tim
On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
14:25 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Hi Matthias,
did you use correct model parameterization and optimal refinement strategy for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisot
7:14:25 PM
To: Barone, Matthias
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl
Hi Matthias,
did you use correct model parameterization and optimal refinement strategy for
the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs
Hi Matthias,
did you use correct model parameterization and optimal refinement strategy
for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this
resolution);
- Add solvent (water, crystallization
Hello, sorry if this is a really obvious question, but have you used the ANIS option? I remember it is good at cleaning-up difference density around halogen atoms that sort of resolution.Jon CooperOn 3 Feb 2020 11:08, "Barone, Matthias" wrote:
Dear ccp4 community
Im having some problems
Maybe the figures were just contoured odd...but my recollection of a good
0.8 A map appearance is differentwhich might be consistent with the
high Rf...a look at the high res data or images/stats might help?
Best, br
On Mon, Feb 3, 2020, 14:58 George Sheldrick
wrote:
> Dear Matthias,
>
>
>
Dear Matthias,
That is very strange. First please repeat the shelxl refinement with the
occupancy of the offending chlorine(s) in the .ins file changed from 11
(i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If
that does not help I would be happy to look at it in
The maps look beautiful, but maybe the high resolution data is refining
poorly.
Not sure how to do this with phenix or SHELX but REFMAC gives you a plot of
and v resolution. You sometimes see wild divergence in some
resolution shells.
Looking at Rfactors v resolution can also highlight such
17 matches
Mail list logo
