Re: [ccp4bb] How can I refine the occupancy with Refmac?

[Jon Cooper]

Hello, the keywords can be entered in refmac gui (in one of the dropdown 
things), so you don't need a file, as such, but it's useful to keep a record.

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 Original Message 
On 5 Jun 2021, 16:39, Marina Gárdonyi wrote:

> Hello everyone,
>
> I am trying to refine structures with Refmac.
>
> The problem is that nobody from my working group is familiar with this
> programm. They are using Phenix exclusively.
>
> That's why I need your help. I would like to refine the occupancy. I
> know that I need a keyword file for this, but I have no idea how to
> create such a keyword file.
>
> Can someone maybe send me a sample file? I think that would help me. I
> have found essential keywords, but I don't know how to build up such a
> file.
>
> Thank you very much in advance!
>
> Best regards,
> Marina
>
> --
> Marina Gárdonyi
>
> PhD Student, Research Group Professor Dr. Klebe
>
> Department of Pharmaceutical Chemistry
>
> Philipps-University Marburg
>
> Marbacher Weg 6, 35032 Marburg, Germany
>
> Phone: +49 6421 28 21392
>
> E-Mail: marina@pharmazie.uni-marburg.de
>
> http://www.agklebe.de/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] How can I refine the occupancy with Refmac?

[Eleanor Dodson]

here is an extract from the documentation.

is it a help?


i will try to find examples.


eleanor


This keyword defines number of cycles of refinement.
Occupancy refinement (version 5.6.0037) from Tidied up

occupancy group id  chain  ...  residue 
atom  alt 

or

occupancy group id  chain  ...  residue from
 to  atom  alt 

occuppancy group alts complete/incomplete  ... 

occupancy refine ncycle .

Example:

occupancy group id 1 chain A # chain A belongs to occupancy group 1

occupancy group id 1 chain B residues from 200 to 500 # all residues
between residues 200 and 500 of chain A belong to the group with id 1

occupancy group id 2 chain C residue 250 alt A # all atoms of residue 250
of chain C with alt code A belonge to group 2

occupancy group id 2 chain D residue 250 atom OW # atom OW of the residue
250 of chain d belong to the group 3

occupancy group alts complete 1 2 # occupancy group 1 and two are mutually
exclusive. Moreover sum of their occupancise should be equal to 1
(subkeyword complete)

occupancy group alts incomplete 1 3 # sum of occupancies of occupancy group
1 and 3 must be less than 1 (and more than 0 obviously)

occupancy refine ncycle 

occupancy refine # refine occupancies. Refinement of occupancy parameters
will be carried out at every ncycle-th cycle. Defalt is 1, i.e. occupancy
and restrained refinements are carried out one after another at every cycle.

If occupancy refine has not been defined then group definitions will only
be used in making decision about non-bonded contacts. Atoms belonging to
the alternative groups (e.g. group 1 and 2) do not see each other and
therefore there is no non-bonding (vdw or other) interaction between them.
Of course user can use  external restrain

  t

keyword
to enforce bonds between mutually exclusive atoms.




On Sat, 5 Jun 2021 at 16:40, Marina Gárdonyi <
marina@pharmazie.uni-marburg.de> wrote:

> Hello everyone,
>
> I am trying to refine structures with Refmac.
>
> The problem is that nobody from my working group is familiar with this
> programm. They are using Phenix exclusively.
>
> That's why I need your help. I would like to refine the occupancy. I
> know that I need a keyword file for this, but I have no idea how to
> create such a keyword file.
>
> Can someone maybe send me a sample file? I think that would help me. I
> have found essential keywords, but I don't know how to build up such a
> file.
>
> Thank you very much in advance!
>
> Best regards,
> Marina
>
> --
> Marina Gárdonyi
>
> PhD Student, Research Group Professor Dr. Klebe
>
> Department of Pharmaceutical Chemistry
>
> Philipps-University Marburg
>
> Marbacher Weg 6, 35032 Marburg, Germany
>
> Phone: +49 6421 28 21392
>
> E-Mail: marina@pharmazie.uni-marburg.de
>
> http://www.agklebe.de/
>
> 
>
> 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
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] How can I refine the occupancy with Refmac?

[Marina Gárdonyi]

Hello everyone,

I am trying to refine structures with Refmac.

The problem is that nobody from my working group is familiar with this  
programm. They are using Phenix exclusively.


That's why I need your help. I would like to refine the occupancy. I  
know that I need a keyword file for this, but I have no idea how to  
create such a keyword file.


Can someone maybe send me a sample file? I think that would help me. I  
have found essential keywords, but I don't know how to build up such a  
file.


Thank you very much in advance!

Best regards,
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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