For the record, occupancy refinement scenario you're looking for is
described here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Cheers,
Pavel
On Thu, Mar 3, 2022 at 7:09 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
*Objet: *[ccp4bb] Ligand occupancy refinement
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After
fixing the protein model and water I fitted the ligand into it.
Currently, I am using Phenix Refine with occupancy refinement for
individual atom
required.
Best
Wim
*De: *"Akanksha Tomar"
*À: *"CCP4BB"
*Envoyé: *Jeudi 3 Mars 2022 15:15:07
*Objet: *[ccp4bb] Ligand occupancy refinement
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing
the pro
ith an occupancy q as
> alternate structures. But nobody does that and it is not really required.
> Best
> Wim
>
> --
> *De: *"Akanksha Tomar"
> *À: *"CCP4BB"
> *Envoyé: *Jeudi 3 Mars 2022 15:15:07
> *Objet: *[ccp4bb] Liga
PS: this does not work for very small atoms, e.g. waters. Here I let the
temperature factor take care of the occupancy as well.
Von: Schreuder, Herman /DE
Gesendet: Donnerstag, 3. März 2022 16:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [ccp4bb] Ligand occupancy refinement
Dear Ankanksha
Auftrag von Jon Cooper
Gesendet: Donnerstag, 3. März 2022 16:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Ligand occupancy refinement
Hello, the ligand needs to be treated as one occupancy group since refining
individual occupancies would be a case of refining too many parameters, unless
Dear Akanksha Tomar,
By default, phenix.refine will assign a single occupancy for the ligand as long
as all atoms have the _same_ occupancy (0https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Hello, the ligand needs to be treated as one occupancy group since refining
individual occupancies would be a case of refining too many parameters, unless
it was a very fragmentary compound!! It is one keyword in refmac, but I can't
remember for phenix, sorry! Ta jc
Sent from ProtonMail mobile
di 3 Mars 2022 15:15:07
Objet: [ccp4bb] Ligand occupancy refinement
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing the protein
model and water I fitted the ligand into it. Currently, I am using Phenix
Refine with occupancy refinement for individual atom
Hello,
What about refining using refmac5 ?
it may yield to different results
Mahmoud Rizk
On 03/03/2022 15:15, Akanksha Tomar wrote:
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing
the protein model and water I fitted the ligand into it. Currently, I
Hi everyone,
I am trying to refine the occupancy of a bound ligand. After fixing the
protein model and water I fitted the ligand into it. Currently, I am using
Phenix Refine with occupancy refinement for individual atoms switched on.
After the refinement, the overall occupancy of the ligand is
Dear users,
Is it advisable to refine the occupancy of
a ligand for a 2.0Ang data by approximately
changing the values of occupancy based on
its b-factor?
After refinement, there were some negative
densities appearing in some parts of the
ligand, like at the centre of a pyrimidine
ring, so I
Dear Kavya
What about using occupancy refinement in refmac?
link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
refinement.
R
On 12 Apr 2013, at 17:12, Kavyashree Manjunath ka...@ssl.serc.iisc.in
wrote:
Dear users,
Is it advisable to refine the occupancy of
a ligand
Respected Sir,
I saw this option in refmac5 - 5.6.0037, (I use
refmac5-5.6.0117), but is this option present in
GUI?
Thanking you
With Regards
Kavya
Dear Kavya
What about using occupancy refinement in refmac?
link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
refinement.
So there is a CCP4 GUI
Just prepare a txt file with the relevant occupancykeywords and use it in the
GUI under 'Refmac keyword file'
Best
R
From my iPhone
On 12 Apr 2013, at 19:50, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote:
Respected Sir,
I saw this option in refmac5 -
Thank you Sir.
With Regards
Kavya
So there is a CCP4 GUI
Just prepare a txt file with the relevant occupancykeywords and use it in
the GUI under 'Refmac keyword file'
Best
R
From my iPhone
On 12 Apr 2013, at 19:50, Kavyashree Manjunath ka...@ssl.serc.iisc.in
wrote:
Respected
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