Re: [ccp4bb] mixture

2024-03-05 Thread Eleanor Dodson 
This is best done by calculating  the structure factors for the part you
want to fix. (make sure the occupancies are set yo 0.8)
The REFMAC hklout will contain F SIGF etc plus FCALC PHIcalc for that bit
Define this file as your input hkl
Then refine the 20% structure (occs=0.2) with input
LABI FP=F SIGFP=SIGf  FPARTi=FCALC_80% PHIPARTi-PHIC
THis will refine the 20% part and add on the structure factors from the 80%
without any refinement of that..
Eleanor


On Tue, 5 Mar 2024 at 13:32, Martin Malý  wrote:

> Dear Marius,
>
> could the 'refinement exclude' keyword for refmac5 help?
> refinement exclude all from [residue] [chain] to [residue] [chain]
>
> Best regards,
> Martin
>
> On Tue, 2024-03-05 at 14:06 +0100, Ilme Schlichting wrote:
>
> Dear Marius,
>
> Thomas discussed this issue in great detail in the supplement of our
> recent publication
> https://www.nature.com/articles/s41586-024-07032-9
>
> Good luck,
>
> Ilme
>
> On 28/02/2024 17:43, Marius Schmidt wrote:
>
> Dear All,
> can someone quickly update me with a
> way to refine a mixture of structures in
> refmac or phenix.
> For example, the mixture consists of
> 80 % structure 1 and 20 % structure 2.
> It is important that structure 1 is kept
> fixed (is not refined) and only structure
> 2 is varied.
>
> Best
> Marius
>
>
> Marius Schmidt, Dr. rer. Nat. (habil.)
> Professor
> University of Wisconsin-Milwaukee
> Kenwood Interdisciplinary Research Complex
> Physics Department, Room 3087
> 3135 North Maryland Avenue
> Milwaukee, Wi 53211
> phone (office): 1-414-229-4338
> phone (lab): 414-229-3946
> email: smar...@uwm.edu
> https://uwm.edu/physics/people/schmidt-marius/
> 
> https://sites.uwm.edu/smarius/ 
> https://www.bioxfel.org/ 
> Nature News and Views:
> https://www.nature.com/articles/d41586-023-00504-4
> 
>
>
> 
>
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Re: [ccp4bb] mixture

2024-03-05 Thread Martin Malý 
Dear Marius,

could the 'refinement exclude' keyword for refmac5 help?
refinement exclude all from [residue] [chain] to [residue] [chain]

Best regards,
Martin

On Tue, 2024-03-05 at 14:06 +0100, Ilme Schlichting wrote:
> Dear Marius,
> 
> Thomas discussed this issue in great detail in the supplement of our 
> recent publication
> https://www.nature.com/articles/s41586-024-07032-9
> 
> Good luck,
> 
> Ilme
> 
> On 28/02/2024 17:43, Marius Schmidt wrote:
> > Dear All,
> > can someone quickly update me with a
> > way to refine a mixture of structures in
> > refmac or phenix.
> > For example, the mixture consists of
> > 80 % structure 1 and 20 % structure 2.
> > It is important that structure 1 is kept
> > fixed (is not refined) and only structure
> > 2 is varied.
> > 
> > Best
> > Marius
> > 
> > 
> > Marius Schmidt, Dr. rer. Nat. (habil.)
> > Professor
> > University of Wisconsin-Milwaukee
> > Kenwood Interdisciplinary Research Complex
> > Physics Department, Room 3087
> > 3135 North Maryland Avenue
> > Milwaukee, Wi 53211
> > phone (office): 1-414-229-4338
> > phone (lab): 414-229-3946
> > email: smar...@uwm.edu
> > https://uwm.edu/physics/people/schmidt-marius/ 
> > 
> > https://sites.uwm.edu/smarius/ 
> > https://www.bioxfel.org/ 
> > Nature News and Views: 
> > https://www.nature.com/articles/d41586-023-00504-4 
> > 
> > 
> > 
> > ---
> > -
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> > 
> > 
> 




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Re: [ccp4bb] mixture

2024-03-05 Thread Ilme Schlichting 

Dear Marius,

Thomas discussed this issue in great detail in the supplement of our 
recent publication

https://www.nature.com/articles/s41586-024-07032-9

Good luck,

Ilme

On 28/02/2024 17:43, Marius Schmidt wrote:

Dear All,
can someone quickly update me with a
way to refine a mixture of structures in
refmac or phenix.
For example, the mixture consists of
80 % structure 1 and 20 % structure 2.
It is important that structure 1 is kept
fixed (is not refined) and only structure
2 is varied.

Best
Marius


Marius Schmidt, Dr. rer. Nat. (habil.)
Professor
University of Wisconsin-Milwaukee
Kenwood Interdisciplinary Research Complex
Physics Department, Room 3087
3135 North Maryland Avenue
Milwaukee, Wi 53211
phone (office): 1-414-229-4338
phone (lab): 414-229-3946
email: smar...@uwm.edu
https://uwm.edu/physics/people/schmidt-marius/ 


https://sites.uwm.edu/smarius/ 
https://www.bioxfel.org/ 
Nature News and Views: 
https://www.nature.com/articles/d41586-023-00504-4 






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--
Ilme Schlichting

Max-Planck Institute for Medical Research
Department of Biomolecular Mechanisms
Jahn-Str. 29, D-69120 Heidelberg, Germany

fon : +49 6221 486 500; fax: +49 6221 486 585
e-mail direct: ilme.schlicht...@mpimf-heidelberg.mpg.de
e-mail secretary: sekretariat-...@mpimf-heidelberg.mpg.de
(please cc. communications concerning scheduling)



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Re: [ccp4bb] mixture

2024-03-04 Thread Tim Gruene 
Dear Marius,

it looks like you didn't receive an answer, yet. It would be easy in
SHELXL. You may convert the PDB file to the starting instruction
filewith PDB2INS.

Fixing any parameter is done by adding 10 to it, i.e. you can simply
run awk on the ins-file to fix x,y,z and Uiso for structure 1, and
leave structure 2 to be refined. Actually you would want to add 20 to
Uiso and -20 to Uiso for structure 2 in order to refine the fraction of
1:2.

Best,
Tim

On Wed, 28 Feb 2024 16:43:14 + Marius Schmidt 
wrote:

> Dear All,
> can someone quickly update me with a
> way to refine a mixture of structures in
> refmac or phenix.
> For example, the mixture consists of
> 80 % structure 1 and 20 % structure 2.
> It is important that structure 1 is kept
> fixed (is not refined) and only structure
> 2 is varied.
> 
> Best
> Marius
> 
> 
> Marius Schmidt, Dr. rer. Nat. (habil.)
> Professor
> University of Wisconsin-Milwaukee
> Kenwood Interdisciplinary Research Complex
> Physics Department, Room 3087
> 3135 North Maryland Avenue
> Milwaukee, Wi 53211
> phone (office): 1-414-229-4338
> phone (lab): 414-229-3946
> email: smar...@uwm.edu
> https://uwm.edu/physics/people/schmidt-marius/
> https://sites.uwm.edu/smarius/
> https://www.bioxfel.org/
> Nature News and Views:
> https://www.nature.com/articles/d41586-023-00504-4
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpR0vQOyi6A6.pgp
Description: OpenPGP digital signature

[ccp4bb] mixture

2024-02-28 Thread Marius Schmidt 
Dear All,
can someone quickly update me with a
way to refine a mixture of structures in
refmac or phenix.
For example, the mixture consists of
80 % structure 1 and 20 % structure 2.
It is important that structure 1 is kept
fixed (is not refined) and only structure
2 is varied.

Best
Marius


Marius Schmidt, Dr. rer. Nat. (habil.)
Professor
University of Wisconsin-Milwaukee
Kenwood Interdisciplinary Research Complex
Physics Department, Room 3087
3135 North Maryland Avenue
Milwaukee, Wi 53211
phone (office): 1-414-229-4338
phone (lab): 414-229-3946
email: smar...@uwm.edu
https://uwm.edu/physics/people/schmidt-marius/
https://sites.uwm.edu/smarius/
https://www.bioxfel.org/
Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4




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