Re: [ccp4bb] Ligand occupancy refinement

[Pavel Afonine]

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:

> 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
>
>
>
>  Original Message 
> On 3 Mar 2022, 14:15, Akanksha Tomar < akankshat...@gmail.com> 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 using
> Phenix Refine with occupancy refinement for individual atoms switched on.
> After the refinement, the overall occupancy of the ligand is 0.7 and the
> RSCC value is 0.86. The resolution of the structure is 2.1 Å.
>
> Now the problem is that the program has assigned different occupancies to
> different atoms of the ligand. For some cases, it has assigned 0
> occupancies to atoms for which there is a clear positive peak.
>
> Why it has been done so and is it acceptable?
>
> Any help would be greatly appreciated.
>
> Thank you.
>
> --
> Best Regards,
> Akanksha Tomar
> Pre-Doctoral Fellow,
> C\o Dr. Arockiasamy Arulandu,
> Membrane Protein Biology Group,
> International Center for Genetic Engineering and Biotechnology,
> New Delhi, India
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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/

Re: [ccp4bb] Ligand occupancy refinement

[Steven Herron]

Dear Akanksha,

When you re-do the occupancy refinement, don't include a b-factor 
refinement along with the occupancy refinement.  Do them separately. Do 
one, then do the other, and then repeat until convergence.


If your B-factor values are either high or low, the computer will try to 
adjust using occupancy.  If your occupancy values are either high or 
low, then the computer will try to adjust using B-factors. In the end 
you want the best occupancy and b-factor estimates you can get by making 
sure the refinement programs don't get trapped.


Once you have a good estimate, I suggest that you try a few different 
initial occupancy values to make sure you are not trapped in a local 
minimum.  If you start off with a high occupancy, it should move back 
down during the refinement.  If you start off with a low occupancy, then 
it should back up during the refinement. B-Factors should do the same 
thing.


With a large ligand, I suspect that some of the waters will also have 
alternate orientations.  You also might look at the amino acids that 
bind to the ligand to see if there is any alternate conformations.



Best
Steven Herron



On 3/3/2022 8:51 AM, Akanksha Tomar wrote:

Thank you for the suggestions
I will try again by setting the occupancy of the entire ligand to the 
single average occupancy and re-do the refinement with Buster, Phenix 
refine and Remac5 with full positional and B-factor refinement and 
check the B-factor of the neighbouring residues.
The ligand is a 30 atom containing molecule binding at a shallow 
solvent-exposed site.




On Thu, 3 Mar 2022 at 20:38, Wim Burmeister  wrote:

Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are
strongly correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy
and then to include it into a full positional and B-factor
refinement. You can check whether the result is coherent by
comparing the B-factors of the ligand and of the atoms, which are
in contact with it. If this is not the case, you may want to
adjust the occupancy manually. As ther are also solvent atoms at
the ligand positions, when it is not bound, there is another
source of inaccuracy and theoretically you would have to model the
site with the solvent and an occupancy 1-q and the ligand with 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 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 switched on. After the refinement, the overall
occupancy of the ligand is 0.7 and the RSCC value is 0.86. The
resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different
occupancies to different atoms of the ligand. For some cases, it
has assigned 0 occupancies to atoms for which there is a clear
positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

-- 
Best Regards,

Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>



-- 
*Wim Burmeister*

Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

<https://www.google.com/maps/search/71+avenue+des+Martyrs?entry=gmail=g>
/ CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Mobile:  +33 (0) 7 50 49 19 91
website

<http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/>





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
<https:

Re: [ccp4bb] Ligand occupancy refinement

[mesters]

Hi Akanksha,

years ago I tried to refine, using refmac, an inhibitor only with 
partial occupancy bound to HIV-1 PR and was not that happy (probably a 
biased view) with the outcome.
In a next step I included water molecules with partial occupancies that 
normally occupy the binding site in the absence of inhibitor but was not 
happy at all because especially the water molecules, despite partial 
occupancies and total occupancy of both water and inhibitor equal to 1, 
shifted to positions deviating from the positions observed in the 
uninhibited structure. For a refinement involving the inhibitor only I 
can understand some drift of the inhibitor which is related to the 
position/density of the partial waters that were not included in the 
model..


In a next step I then compared NCS, Refmac and SHELXL refinement with 
partial occupancy for inhibitor + waters in the binding site and spend 
weeks optimizing the parameters in the different programs.


End of story, SHELX - based on a visual inspection of the final ED maps 
- came closest to what I considered acceptable but again, maybe a biased 
view (did not test Buster tough!):


What I learned from this "partial occupancy" odyssee:
1) Different programs handled this type of "constellation" differently
2) Including partial waters did make a difference altough it was/is not 
common practice
3) Inhibitor occupancy and position drifted somewhat comparing with or 
without waters


As already pointed out, you can not have different occupancies for the 
different atoms of the ligand. At 2.1 Å resolution, test several fixed 
occupancies - start at 0.5 and increase by 0.1 - and compare/inspect the 
different ED maps along witht the R/Rfree etc. and pick the occupancy 
that makes most sense


Good luck,

Jeroen




Am 03.03.22 um 16:08 schrieb Wim Burmeister:

Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are 
strongly correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy and 
then to include it into a full positional and B-factor refinement. You 
can check whether the result is coherent by comparing the B-factors of 
the ligand and of the atoms, which are in contact with it. If this is 
not the case, you may want to adjust the occupancy manually. As there 
are also solvent atoms at the ligand positions, when it is not bound, 
there is another source of inaccuracy and theoretically you would have 
to model the site with the solvent and an occupancy 1-q and the ligand 
with 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 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 
switched on. After the refinement, the overall occupancy of the ligand 
is 0.7 and the RSCC value is 0.86. The resolution of the structure is 
2.1 Å.


Now the problem is that the program has assigned different occupancies 
to different atoms of the ligand. For some cases, it has assigned 0 
occupancies to atoms for which there is a clear positive peak.


Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>




--
*Wim Burmeister*
Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Mobile:   +33 (0) 7 50 49 19 91
website 
<http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/> 






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>




--
signature.html *Dr. /math. et dis. nat./ Jeroen R. Mesters
*Deputy, Lecturer, Program Coordinator Infection Biology 
<https://www.uni-luebeck.de/en/university-education/degree-programmes/infection-biology.html>
Visiting Professorship (South Bohemian University 
<https://www.jcu.

Re: [ccp4bb] Ligand occupancy refinement

[Akanksha Tomar]

Thank you for the suggestions
I will try again by setting the occupancy of the entire ligand to the
single average occupancy and re-do the refinement with Buster, Phenix
refine and Remac5 with full positional and B-factor refinement and check
the B-factor of the neighbouring residues.
The ligand is a 30 atom containing molecule binding at a shallow
solvent-exposed site.



On Thu, 3 Mar 2022 at 20:38, Wim Burmeister  wrote:

> Hello,
> at 2.1 A resolution, atomic temperature factors and occupancy are strongly
> correlated. So you have to be very careful with the results.
> So the best is just to set the inhibitor to the average occupancy and then
> to include it into a full positional and B-factor refinement. You can check
> whether the result is coherent by comparing the B-factors of the ligand and
> of the atoms, which are in contact with it. If this is not the case, you
> may want to adjust the occupancy manually. As ther are also solvent atoms
> at the ligand positions, when it is not bound, there is another source of
> inaccuracy and theoretically you would have to model the site with the
> solvent and an occupancy 1-q and the ligand with 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 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 switched on.
> After the refinement, the overall occupancy of the ligand is 0.7 and the
> RSCC value is 0.86. The resolution of the structure is 2.1 Å.
>
> Now the problem is that the program has assigned different occupancies to
> different atoms of the ligand. For some cases, it has assigned 0
> occupancies to atoms for which there is a clear positive peak.
>
> Why it has been done so and is it acceptable?
>
> Any help would be greatly appreciated.
>
> Thank you.
>
> --
> Best Regards,
> Akanksha Tomar
> Pre-Doctoral Fellow,
> C\o Dr. Arockiasamy Arulandu,
> Membrane Protein Biology Group,
> International Center for Genetic Engineering and Biotechnology,
> New Delhi, India
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
> *Wim Burmeister*
> Professor
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs
> <https://www.google.com/maps/search/71+avenue+des+Martyrs?entry=gmail=g>
> / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Mobile:   +33 (0) 7 50 49 19 91
> website
> <http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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/

[ccp4bb] AW: [ccp4bb] Ligand occupancy refinement

[Schreuder, Herman /DE]

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 ligand is either present, or it is not present. It cannot be that some 
atoms are present and others not. For ligands, I always use a single group 
occupancy using the program Buster from global phasing. In my hands, this 
always works. There is a correlation between occupancy and B-factors, but if 
you use a single occupancy for a large number of atoms, this correlation is not 
longer a problem. Also, modern maximum likelihood refinement programs do a good 
job in separating the contributions of occupancy and B-factors.

Best,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Jon Cooper
Gesendet: Donnerstag, 3. März 2022 16:09
An: CCP4BB@JISCMAIL.AC.UK<mailto: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 very fragmentary compound!! It is one keyword in refmac, but I can't 
remember for phenix, sorry! Ta jc


Sent from ProtonMail mobile



 Original Message 
On 3 Mar 2022, 14:15, Akanksha Tomar < 
akankshat...@gmail.com<mailto:akankshat...@gmail.com>> 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 using Phenix 
Refine with occupancy refinement for individual atoms switched on. After the 
refinement, the overall occupancy of the ligand is 0.7 and the RSCC value is 
0.86. The resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different occupancies to 
different atoms of the ligand. For some cases, it has assigned 0 occupancies to 
atoms for which there is a clear positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>



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/

[ccp4bb] AW: [ccp4bb] Ligand occupancy refinement

[Schreuder, Herman /DE]

Dear Ankanksha,

The ligand is either present, or it is not present. It cannot be that some 
atoms are present and others not. For ligands, I always use a single group 
occupancy using the program Buster from global phasing. In my hands, this 
always works. There is a correlation between occupancy and B-factors, but if 
you use a single occupancy for a large number of atoms, this correlation is not 
longer a problem. Also, modern maximum likelihood refinement programs do a good 
job in separating the contributions of occupancy and B-factors.

Best,
Herman

Von: CCP4 bulletin board  Im 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 very fragmentary compound!! It is one keyword in refmac, but I can't 
remember for phenix, sorry! Ta jc


Sent from ProtonMail mobile



 Original Message 
On 3 Mar 2022, 14:15, Akanksha Tomar < 
akankshat...@gmail.com<mailto:akankshat...@gmail.com>> 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 using Phenix 
Refine with occupancy refinement for individual atoms switched on. After the 
refinement, the overall occupancy of the ligand is 0.7 and the RSCC value is 
0.86. The resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different occupancies to 
different atoms of the ligand. For some cases, it has assigned 0 occupancies to 
atoms for which there is a clear positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>



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/

Re: [ccp4bb] Ligand occupancy refinement

[Weiergräber , Oliver H .]

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





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht,
Prof. Dr. Frauke Melchior





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/

Re: [ccp4bb] Ligand occupancy refinement

[Jon Cooper]

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

 Original Message 
On 3 Mar 2022, 14:15, 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 using 
> Phenix Refine with occupancy refinement for individual atoms switched on. 
> After the refinement, the overall occupancy of the ligand is 0.7 and the RSCC 
> value is 0.86. The resolution of the structure is 2.1 Å.
>
> Now the problem is that the program has assigned different occupancies to 
> different atoms of the ligand. For some cases, it has assigned 0 occupancies 
> to atoms for which there is a clear positive peak.
>
> Why it has been done so and is it acceptable?
>
> Any help would be greatly appreciated.
>
> Thank you.
>
> --
>
> Best Regards,
> Akanksha Tomar
> Pre-Doctoral Fellow,
> C\o Dr. Arockiasamy Arulandu,
> Membrane Protein Biology Group,
> International Center for Genetic Engineering and Biotechnology,
> New Delhi, India
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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/

Re: [ccp4bb] Ligand occupancy refinement

[Wim Burmeister]

Hello, 
at 2.1 A resolution, atomic temperature factors and occupancy are strongly 
correlated. So you have to be very careful with the results. 
So the best is just to set the inhibitor to the average occupancy and then to 
include it into a full positional and B-factor refinement. You can check 
whether the result is coherent by comparing the B-factors of the ligand and of 
the atoms, which are in contact with it. If this is not the case, you may want 
to adjust the occupancy manually. As there are also solvent atoms at the ligand 
positions, when it is not bound, there is another source of inaccuracy and 
theoretically you would have to model the site with the solvent and an 
occupancy 1-q and the ligand with 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 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 switched on. After the 
refinement, the overall occupancy of the ligand is 0.7 and the RSCC value is 
0.86. The resolution of the structure is 2.1 Å. 

Now the problem is that the program has assigned different occupancies to 
different atoms of the ligand. For some cases, it has assigned 0 occupancies to 
atoms for which there is a clear positive peak. 

Why it has been done so and is it acceptable? 

Any help would be greatly appreciated. 

Thank you. 

-- 
Best Regards, 
Akanksha Tomar 
Pre-Doctoral Fellow, 
C\o Dr. Arockiasamy Arulandu, 
Membrane Protein Biology Group, 
International Center for Genetic Engineering and Biotechnology, 
New Delhi, India 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ] 




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/

Re: [ccp4bb] Ligand occupancy refinement

[Mahmoud RIZK]

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 using Phenix Refine with occupancy refinement for individual atoms 
switched on. After the refinement, the overall occupancy of the ligand 
is 0.7 and the RSCC value is 0.86. The resolution of the structure is 
2.1 Å.


Now the problem is that the program has assigned different occupancies 
to different atoms of the ligand. For some cases, it has assigned 0 
occupancies to atoms for which there is a clear positive peak.


Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 







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/

[ccp4bb] Ligand occupancy refinement

[Akanksha Tomar]

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 and the
RSCC value is 0.86. The resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different occupancies to
different atoms of the ligand. For some cases, it has assigned 0
occupancies to atoms for which there is a clear positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

-- 
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



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/

[ccp4bb] ligand occupancy

[Monica Mittal]

Dear all

I have a protein which is dimer having one ligand binding site in each
monomer. I refined the crystal structure with ligand in both sites finally.
I refined will full occupancy of 1 for ligands (same in both). But now i
want to see is there any difference in the occupancy of both ligands in
ligand binding sites of monomer A and B. Is there any way i can get any
information about the occupancy of ligands in two monomers like one is
binding more tightly than another so that i can get an idea about their
differential binding contacts also.

Thank you very much in advance.

Regards
Monica

Re: [ccp4bb] ligand occupancy

[George Kontopidis]

Hi Monica,

 

Calculate the mean B-factor of all atoms that making interactions with each 
ligand in monomer A and B.

Use those means values as  B-factors for each ligand respectively.

Adjust manually the occupancies, in order  the B-factors for each ligand  to 
stay after refinement close to the above values.

 

In order to calculate occupancies more precisely,  it would help to have the 
un-liganded structure and thus the  location of  the water molecules in each 
binding site.

If you have the above information you could refine water molecules and ligands 
simultaneously in the binding site and get accurate refined occupancies. 

 

George

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Monica 
Mittal
Sent: Friday, April 18, 2014 1:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand occupancy

 

Dear all

 

I have a protein which is dimer having one ligand binding site in each monomer. 
I refined the crystal structure with ligand in both sites finally. I refined 
will full occupancy of 1 for ligands (same in both). But now i want to see is 
there any difference in the occupancy of both ligands in ligand binding sites 
of monomer A and B. Is there any way i can get any information about the 
occupancy of ligands in two monomers like one is binding more tightly than 
another so that i can get an idea about their differential binding contacts 
also. 

 

Thank you very much in advance.

 

Regards

Monica 

Re: [ccp4bb] ligand occupancy

[Boaz Shaanan]

Hi Monica,

You can refine the ligand occupancy in refmac as explained here:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

or in phenix, whichever program you're using.

 Cheers,

 Boaz




Boaz Shaanan, Ph.D.

Dept. of Life Sciences 
Ben-Gurion University of the Negev 
Beer-Sheva 84105 
Israel 
 
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220Skype: boaz.shaanan 
Fax: 972-8-647-2992 or 972-8-646-1710










From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Monica Mittal [monica.mitta...@gmail.com]
Sent: Friday, April 18, 2014 1:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand occupancy




Dear all


I have a protein which is dimer having one ligand binding site in each monomer. I refined the crystal structure with ligand in both sites finally. I refined will full occupancy of 1 for ligands (same in both). But now i want to see is there any difference
 in the occupancy of both ligands in ligand binding sites of monomer A and B. Is there any way i can get any information about the occupancy of ligands in two monomers like one is binding more tightly than another so that i can get an idea about their differential
 binding contacts also.


Thank you very much in advance.


Regards
Monica

[ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

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 expected that the problem is with
the occupancy. (the crystal was obtained by
co-crystallisation method).
Kindly provide some suggestions.

Thanking you
With Regards
Kavya


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

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 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 expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.
 
 Thanking you
 With Regards
 Kavya
 
 
 -- 
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

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.

 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 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 expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.

 Thanking you
 With Regards
 Kavya


 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.


 Roberto A. Steiner
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London
 roberto.stei...@kcl.ac.uk

 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL
 London

 Phone 0044 20 78488216
 Fax0044 20 78486435



 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.





-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

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 - 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.
 
 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 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 expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.
 
 Thanking you
 With Regards
 Kavya
 
 
 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 
 
 Roberto A. Steiner
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London
 roberto.stei...@kcl.ac.uk
 
 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL
 London
 
 Phone 0044 20 78488216
 Fax0044 20 78486435
 
 
 
 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 
 
 
 
 
 -- 
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

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 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.

 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 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 expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.

 Thanking you
 With Regards
 Kavya


 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.


 Roberto A. Steiner
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London
 roberto.stei...@kcl.ac.uk

 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL
 London

 Phone 0044 20 78488216
 Fax0044 20 78486435



 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.





 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.


 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.





-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.