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

[James Holton]

Certainly Elenaor.  Here are a few:

# typical lysozyme
% refmac_occupancy_setup.com 193l.pdb
occupancy refine
occupancy group id 1 chain A residue 1 alt A
occupancy group id 2 chain A residue 1 alt B
occupancy group id 3 chain A residue 59 alt A
occupancy group id 4 chain A residue 59 alt B
occupancy group id 5 chain A residue 86 alt A
occupancy group id 6 chain A residue 86 alt B
occupancy group id 7 chain A residue 109 alt A
occupancy group id 8 chain A residue 109 alt B
occupancy group alts complete  1 2
occupancy group alts complete  3 4
occupancy group alts complete  5 6
occupancy group alts complete  7 8

#
# another small RT structure

refmac_occupancy_setup.com 1aho.pdb
occupancy refine
occupancy group id 1 chain A residue 9 alt A
occupancy group id 2 chain A residue 9 alt B
occupancy group id 3 chain A residue 12 alt A
occupancy group id 4 chain A residue 12 alt B
occupancy group id 5 chain A residue 24 alt A
occupancy group id 6 chain A residue 24 alt B
occupancy group id 7 chain A residue 63 alt A
occupancy group id 8 chain A residue 63 alt B
occupancy group alts complete  1 2
occupancy group alts complete  3 4
occupancy group alts complete  5 6
occupancy group alts complete  7 8

#
# just the sodium in lysozyme
% egrep "NA|LYS" 2hu3.pdb >! temp.pdb
% refmac_occupancy_setup.com temp.pdb allhet
occupancy refine
occupancy group id 1 residue 1 chain A alt A
occupancy group id 2 residue 1 chain A alt B
occupancy group id 3 residue 33 chain A alt A
occupancy group id 4 residue 33 chain A alt B
occupancy group id 5 residue 97 chain A alt A
occupancy group id 6 residue 97 chain A alt B
occupancy group id 7 residue 9001 chain A
occupancy group id 8 residue 9002 chain A
occupancy group id 9 residue 9003 chain A
occupancy group id 10 residue 9004 chain A
occupancy group id 11 residue 9005 chain A
occupancy group alts complete  5 6
occupancy group alts complete  1 2
occupancy group alts complete  3 4
occupancy group alts incomplete 7
occupancy group alts incomplete 8
occupancy group alts incomplete 9
occupancy group alts incomplete 10
occupancy group alts incomplete 11

#--
Where, for this last one I demonstrate how you can select for various 
things by making a scratch PDB file that contains only the atoms you 
want to occupancy-refine.


Hope this helps!

Cheers,

-James Holton
MAD Scientist


On 6/7/2021 11:16 AM, Eleanor Dodson wrote:
James - could you send me a few examples to add to the documentation? 
Lockdown means I cant easily access my own examples - all trapped on 
the lab desktop..

Eleanor

On Mon, 7 Jun 2021 at 17:18, James Holton > wrote:


I wrote a script for auto-generating occupancy refinement
relationships
for refmac. It is perhaps not as sophisticated as what phenix does
internally, but it gets common things right, like if you have a
2-headed
side chains or partial-occupancy metals.

https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com


It is a csh/awk shell script. You run it with the name of your
input pdb
file on the command line and it dumps the refmac keywords to a file
called refmac_opts_occ.txt and to the terminal.  If you want every
"hetatm" atom to be refined put "allhet" as a second command-line
argument.

You can then perhaps copy-and-paste this to the relevant GUI window.

-James Holton
MAD Scientist

On 6/7/2021 3:35 AM, Marina Gárdonyi wrote:
> Hi,
>
> I didn't know that I can also enter keywords without a file!
That is a
> good note, thank you!!
>
> Best regards,
> Marina
>
> Zitat von Jon Cooper mailto:jon.b.coo...@protonmail.com>>:
>
>> 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.
>>
>> Sent from ProtonMail mobile
>>
>>  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 

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

[Eleanor Dodson]

James - could you send me a few examples to add to the documentation?
Lockdown means I cant easily access my own examples - all trapped on the
lab desktop..
Eleanor

On Mon, 7 Jun 2021 at 17:18, James Holton  wrote:

> I wrote a script for auto-generating occupancy refinement relationships
> for refmac. It is perhaps not as sophisticated as what phenix does
> internally, but it gets common things right, like if you have a 2-headed
> side chains or partial-occupancy metals.
>
> https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com
>
> It is a csh/awk shell script. You run it with the name of your input pdb
> file on the command line and it dumps the refmac keywords to a file
> called refmac_opts_occ.txt and to the terminal.  If you want every
> "hetatm" atom to be refined put "allhet" as a second command-line argument.
>
> You can then perhaps copy-and-paste this to the relevant GUI window.
>
> -James Holton
> MAD Scientist
>
> On 6/7/2021 3:35 AM, Marina Gárdonyi wrote:
> > Hi,
> >
> > I didn't know that I can also enter keywords without a file! That is a
> > good note, thank you!!
> >
> > Best regards,
> > Marina
> >
> > Zitat von 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.
> >>
> >> Sent from ProtonMail mobile
> >>
> >>  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:
> >>> 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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Re: [ccp4bb] How can I refine the occupancy with Refmac?

[James Holton]

I wrote a script for auto-generating occupancy refinement relationships 
for refmac. It is perhaps not as sophisticated as what phenix does 
internally, but it gets common things right, like if you have a 2-headed 
side chains or partial-occupancy metals.


https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com

It is a csh/awk shell script. You run it with the name of your input pdb 
file on the command line and it dumps the refmac keywords to a file 
called refmac_opts_occ.txt and to the terminal.  If you want every 
"hetatm" atom to be refined put "allhet" as a second command-line argument.


You can then perhaps copy-and-paste this to the relevant GUI window.

-James Holton
MAD Scientist

On 6/7/2021 3:35 AM, Marina Gárdonyi wrote:

Hi,

I didn't know that I can also enter keywords without a file! That is a 
good note, thank you!!


Best regards,
Marina

Zitat von 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.


Sent from ProtonMail mobile

 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/

 



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

[Eleanor Dodson]

In GUI2 the Advanced box allows you to do that
eg RESO 10 3 say if you wanted to restrict resolution..
Eleanor

On Mon, 7 Jun 2021 at 11:35, Marina Gárdonyi <
marina@pharmazie.uni-marburg.de> wrote:

> Hi,
>
> I didn't know that I can also enter keywords without a file! That is a
> good note, thank you!!
>
> Best regards,
> Marina
>
> Zitat von 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.
> >
> > Sent from ProtonMail mobile
> >
> >  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:
> >> 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/
>
>
>
> --
> 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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Re: [ccp4bb] How can I refine the occupancy with Refmac?

[Marina Gárdonyi]

Hi,

I didn't know that I can also enter keywords without a file! That is a  
good note, thank you!!


Best regards,
Marina

Zitat von 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.


Sent from ProtonMail mobile

 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/



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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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--
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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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.

Sent from ProtonMail mobile

 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:
> 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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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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