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 <jmhol...@lbl.gov
<mailto:jmhol...@lbl.gov>> 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
<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 <jon.b.coo...@protonmail.com
<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 Pharmaceutical Chemistry
>>>
>>> Philipps-University Marburg
>>>
>>> Marbacher Weg 6, 35032 Marburg, Germany
>>>
>>> Phone: +49 6421 28 21392
>>>
>>> E-Mail: marina....@pharmazie.uni-marburg.de
<mailto:marina....@pharmazie.uni-marburg.de>
>>>
>>> http://www.agklebe.de/ <http://www.agklebe.de/>
>>>
>>>
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