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:
>
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
individua
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] Ligand oc
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,
The
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
it was a
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&A=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 atoms sw
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
am
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 0.7
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"
> wrote:
>
>> Respected Sir,
>>
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" wrote:
> Respected Sir,
>
> I saw this option in refmac5 - 5.6.0037, (I use
> refm
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
> refinem
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
wrote:
> Dear users,
>
> Is it advisable to refine the occupancy of
> a ligand for a 2.0Ang data by
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 expec
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