[ccp4bb] postdoctoral Fellow Position

[krish]

Dear All,

We have an immediate opening for a talented, highly motivated postdoctoral
fellow in my laboratory at the Ohio State University located in Columbus,
Ohio. The research in our laboratory is mainly focused on understanding the
role of cytoskeletal proteins in cell adhesion dynamics. We use
multifaceted approach involving X-ray Crystallography, cryo-EM and cell
biology to understand the mechanisms that dictate cell adhesion processes
in health and disease.


We are looking for a postdoctoral candidate who is highly interested and
motivated in the structure-function studies of macromolecular assemblies
involved in cell adhesion. We expect that the successful candidate have
demonstrated skills in structural biology (either cryo-EM or X-ray
crystallography) and is willing to expand his/her skill set based on the
demands of the project.


Review of applications will begin immediately and will continue until the
position is filled. Interested applicants should send their CV along with a
cover letter briefly describing their research accomplishments, current
research interests and contact information for three references directly to
krishna.chinthalap...@osumc.edu.



Thank you.



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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[John Berrisford]

Hopefully you all have the link to the survey (below as plain text)
https://bit.ly/2FFmHFG

CCP4BB subscribers feedback was really helpful in designing the PDBe-KB 
protein pages. We are hoping for a similar response for help in designing 
the ligand pages.


Thanks

John


On 4 April 2019 16:12:19 Jon Agirre  wrote:
Thank you all for your help with this - it looks like John's link was being 
wiped out from the e-mail by an ad-blocking extension (?). So if you can't 
find the link, make sure you try deactivating whatever ad-blocker your 
browser is using :)



On Thu, 4 Apr 2019 at 15:56, Jon Agirre  wrote:

No link to the survey :(


On Thu, 4 Apr 2019 at 15:55, John Berrisford  wrote:


Dear All,



We are in the process of redesigning the ligand pages of PDBe and we would 
be grateful if you could fill out a short survey to help us understand what 
information about small molecules / ligands you would find useful. The 
survey is available at https://bit.ly/2FFmHFG




Recently, we have introduced protein-specific aggregated views on the 
structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in 
Europe Knowledge Base (PDBe-KB). We highlight the available information 
related to structures of specific proteins, including structural and 
functional annotations, domains, ligand-binding sites and interfaces. In 
the next step we would like to present a similar aggregated view from a 
small molecule / ligand perspective.




Thank you for your time,



John Berrisford



--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529



http://www.pdbe.org

http://www.facebook.com/proteindatabank

http://twitter.com/PDBeurope






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--

Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252

Twitter: @glycojones




--

Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252

Twitter: @glycojones





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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[Jon Agirre]

Thank you all for your help with this - it looks like John's link was being
wiped out from the e-mail by an ad-blocking extension (?). So if you can't
find the link, make sure you try deactivating whatever ad-blocker your
browser is using :)

On Thu, 4 Apr 2019 at 15:56, Jon Agirre  wrote:

> No link to the survey :(
>
> On Thu, 4 Apr 2019 at 15:55, John Berrisford  wrote:
>
>> Dear All,
>>
>>
>>
>> We are in the process of redesigning the ligand pages of PDBe and we
>> would be grateful if you could fill out a short survey to help us
>> understand what information about small molecules / ligands you would find
>> useful. The survey is available at https://bit.ly/2FFmHFG
>>
>>
>>
>> Recently, we have introduced protein-specific aggregated views on the
>> structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
>> Europe Knowledge Base (PDBe-KB). We highlight the available information
>> related to structures of specific proteins, including structural and
>> functional annotations, domains, ligand-binding sites and interfaces. In
>> the next step we would like to present a similar aggregated view from a
>> small molecule / ligand perspective.
>>
>>
>>
>> Thank you for your time,
>>
>>
>>
>> John Berrisford
>>
>>
>>
>> --
>>
>> John Berrisford
>>
>> PDBe
>>
>> European Bioinformatics Institute (EMBL-EBI)
>>
>> European Molecular Biology Laboratory
>>
>> Wellcome Trust Genome Campus
>>
>> Hinxton
>>
>> Cambridge CB10 1SD UK
>>
>> Tel: +44 1223 492529
>>
>>
>>
>> http://www.pdbe.org
>>
>> http://www.facebook.com/proteindatabank
>>
>> http://twitter.com/PDBeurope
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[Jon Agirre]

No link to the survey :(

On Thu, 4 Apr 2019 at 15:55, John Berrisford  wrote:

> Dear All,
>
>
>
> We are in the process of redesigning the ligand pages of PDBe and we would
> be grateful if you could fill out a short survey to help us understand what
> information about small molecules / ligands you would find useful. The
> survey is available at https://bit.ly/2FFmHFG
>
>
>
> Recently, we have introduced protein-specific aggregated views on the
> structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
> Europe Knowledge Base (PDBe-KB). We highlight the available information
> related to structures of specific proteins, including structural and
> functional annotations, domains, ligand-binding sites and interfaces. In
> the next step we would like to present a similar aggregated view from a
> small molecule / ligand perspective.
>
>
>
> Thank you for your time,
>
>
>
> John Berrisford
>
>
>
> --
>
> John Berrisford
>
> PDBe
>
> European Bioinformatics Institute (EMBL-EBI)
>
> European Molecular Biology Laboratory
>
> Wellcome Trust Genome Campus
>
> Hinxton
>
> Cambridge CB10 1SD UK
>
> Tel: +44 1223 492529
>
>
>
> http://www.pdbe.org
>
> http://www.facebook.com/proteindatabank
>
> http://twitter.com/PDBeurope
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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[ccp4bb] PDBe-KB ligand centric pages survey

[John Berrisford]

Dear All,

 

We are in the process of redesigning the ligand pages of PDBe and we would
be grateful if you could fill out a short survey to help us understand what
information about small molecules / ligands you would find useful. The
survey is available at https://bit.ly/2FFmHFG

 

Recently, we have introduced protein-specific aggregated views on the
structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
Europe Knowledge Base (PDBe-KB). We highlight the available information
related to structures of specific proteins, including structural and
functional annotations, domains, ligand-binding sites and interfaces. In the
next step we would like to present a similar aggregated view from a small
molecule / ligand perspective.

 

Thank you for your time,

 

John Berrisford

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Clemens Vonrhein]

Dear all,

And if you want to process with XDS: autoPROC [1] will try to detect
and exclude ice-rings automatically - if present [2].

If you know that you have ice-rings you can force it [3] to exclude
all known ice-rings ranges - but this might not be the best solution
if you have "just" diffuse ice-rings (where the special treatment of
background within DIALS might be better). Something to test and
compare maybe?

Cheers

Clemens

[1] https://www.globalphasing.com/autoproc/
https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
[2] https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
[3] 
https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically

On Thu, Apr 04, 2019 at 10:51:19AM +, melanie.voll...@diamond.ac.uk wrote:
> Dear Sam,
> 
> 
> to continue from James Parkhurst's email...
> 
> 
> You can do more analysis regarding ice rings using Auspex 
> (https://www.auspex.de/) if you already have some integrated file.
> 
> Regarding re-integrating images, what did you use the first time round? I 
> think if you use DIALS it got some clever implementation in it that is better 
> in estimating the errors of reflections in proximity to ice rings. Hence you 
> should get better Rfactors without having to remove the effected resolution 
> range and the data it covers 
> (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
> 
> 
> HTH
> 
> 
> M
> 
> 
> 
> From: CCP4 bulletin board  on behalf of 
> herman.schreu...@sanofi.com 
> Sent: 04 April 2019 10:26:09
> To: ccp4bb
> Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
> 
> 
> Dear Sam,
> 
> 
> 
> I would remove the ice ring and reprocess the data. Ice rings may wreak havoc 
> with scaling so at minimum you have to redo the scaling.
> 
> 
> 
> Best,
> 
> Herman
> 
> 
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam 
> Tang
> Gesendet: Donnerstag, 4. April 2019 11:01
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
> 
> 
> 
> 
> Dear Eleanor and Eric
> 
> 
> 
> Thanks for your replies.
> 
> 
> 
> Yes indeed when we looked at the plots e.g. R factor vs resln there was a 
> sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the 
> image. Thus our first thought was to remove the ic ring. (either reprocess or 
> can we bypass this resolution range during refinement?)
> 
> 
> 
> The protein is 50 kDa, two molecule in the ASU, seemingly no obvious density 
> was unassigned. We got ~3 total observations, ~15000 unique observations. 
> NCS restraints was applied.
> 
> 
> 
> Best regards
> 
> Sam
> 
> 
> 
> 
> 
> 
> 
> On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
> mailto:montemayor.e...@gmail.com>> wrote:
> 
> That’s a rather large gap between Rwork and Rfree.  I suspect you have 
> mis-assigned your space group and as a result have a large number of copies 
> in your asymmetric unit.  Any structure can be solved in P1, but that does 
> not mean the true space group is indeed P1. If you use P1 when it’s not 
> actually P1, you will have an unnecessarily overparamerized model, hence the 
> large gap between Rwork and Rfree.
> 
> 
> 
> Questions:
> 
> 1- how many copies in your asymmetric unit in P1?
> 
> 2- how many atoms in your model vs number of unique reflections?
> 
> 3- if more than one copy per asymmetric unit, are you imposing NCS restraints 
> during refinement?
> 
> 
> 
> -Eric
> 
> 
> 
> 
> 
> 
> 
> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang 
> mailto:samtys0...@gmail.com>> wrote:
> 
> Hi everyone again
> 
> 
> 
> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However after 
> refinement the Rfree stuck at 33%-35% with Rwork around 26%. The structure 
> was solved by MR and current model seems to fit density well. In Refmac log I 
> found that at the resolution corresponding to high R there may be a 
> solvent/ice ring. Since imosflm should be able to exclude ice rings, I am not 
> 100% sure whether it's the cause to high R. But if this is actually the case, 
> is there a way I can exclude certain resolution bins during Refmac (and is it 
> an appropriate way to do so?)
> 
> 
> 
> PS - the data is not affected by twining or pseudosymmetry as checked by 
> Xtriage.
> 
> 
> 
> Many thanks!
> 
> 
> 
> Sam
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> To unsubscribe 

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Eleanor Dodson]

Can you use sftools to get two ranges eg:  select reso   >3.85   and > 3.75

Eleanor

On Thu, 4 Apr 2019 at 11:39, Frank von Delft 
wrote:

> You can use sftools to set a shell of reflections to MNF - then Refmac
> will fill those in with DFc, and that'll presumably be much better than
> having very wrong reflections.
>
> Whether that will fix your Rfactor is a different story.
>
> phx
>
>
> On 04/04/2019 11:05, Eleanor Dodson wrote:
>
> You cant exclude one resolution ring in REFMAC - there would be ways to
> fudge the exclusion from your current file, but much safer to use a data
> integration tool
>
> On Thu, 4 Apr 2019 at 10:27,  wrote:
>
>> Dear Sam,
>>
>>
>>
>> I would remove the ice ring and reprocess the data. Ice rings may wreak
>> havoc with scaling so at minimum you have to redo the scaling.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Sam Tang
>> *Gesendet:* Donnerstag, 4. April 2019 11:01
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>>
>>
>>
>>
>> Dear Eleanor and Eric
>>
>>
>>
>> Thanks for your replies.
>>
>>
>>
>> Yes indeed when we looked at the plots e.g. R factor vs resln there was a
>> sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
>> the image. Thus our first thought was to remove the ic ring. (either
>> reprocess or can we bypass this resolution range during refinement?)
>>
>>
>>
>> The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
>> density was unassigned. We got ~3 total observations, ~15000 unique
>> observations. NCS restraints was applied.
>>
>>
>>
>> Best regards
>>
>> Sam
>>
>>
>>
>>
>>
>>
>>
>> On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
>> wrote:
>>
>> That’s a rather large gap between Rwork and Rfree.  I suspect you have
>> mis-assigned your space group and as a result have a large number of copies
>> in your asymmetric unit.  Any structure can be solved in P1, but that does
>> not mean the true space group is indeed P1. If you use P1 when it’s not
>> actually P1, you will have an unnecessarily overparamerized model, hence
>> the large gap between Rwork and Rfree.
>>
>>
>>
>> Questions:
>>
>> 1- how many copies in your asymmetric unit in P1?
>>
>> 2- how many atoms in your model vs number of unique reflections?
>>
>> 3- if more than one copy per asymmetric unit, are you imposing NCS
>> restraints during refinement?
>>
>>
>>
>> -Eric
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang  wrote:
>>
>> Hi everyone again
>>
>>
>>
>> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
>> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
>> structure was solved by MR and current model seems to fit density well. In
>> Refmac log I found that at the resolution corresponding to high R there may
>> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
>> am not 100% sure whether it's the cause to high R. But if this is actually
>> the case, is there a way I can exclude certain resolution bins during
>> Refmac (and is it an appropriate way to do so?)
>>
>>
>>
>> PS - the data is not affected by twining or pseudosymmetry as checked by
>> Xtriage.
>>
>>
>>
>> Many thanks!
>>
>>
>>
>> Sam
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[melanie.voll...@diamond.ac.uk]

Dear Sam,


to continue from James Parkhurst's email...


You can do more analysis regarding ice rings using Auspex 
(https://www.auspex.de/) if you already have some integrated file.

Regarding re-integrating images, what did you use the first time round? I think 
if you use DIALS it got some clever implementation in it that is better in 
estimating the errors of reflections in proximity to ice rings. Hence you 
should get better Rfactors without having to remove the effected resolution 
range and the data it covers 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).


HTH


M



From: CCP4 bulletin board  on behalf of 
herman.schreu...@sanofi.com 
Sent: 04 April 2019 10:26:09
To: ccp4bb
Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring


Dear Sam,



I would remove the ice ring and reprocess the data. Ice rings may wreak havoc 
with scaling so at minimum you have to redo the scaling.



Best,

Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang
Gesendet: Donnerstag, 4. April 2019 11:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring




Dear Eleanor and Eric



Thanks for your replies.



Yes indeed when we looked at the plots e.g. R factor vs resln there was a sharp 
peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the image. 
Thus our first thought was to remove the ic ring. (either reprocess or can we 
bypass this resolution range during refinement?)



The protein is 50 kDa, two molecule in the ASU, seemingly no obvious density 
was unassigned. We got ~3 total observations, ~15000 unique observations. 
NCS restraints was applied.



Best regards

Sam







On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
mailto:montemayor.e...@gmail.com>> wrote:

That’s a rather large gap between Rwork and Rfree.  I suspect you have 
mis-assigned your space group and as a result have a large number of copies in 
your asymmetric unit.  Any structure can be solved in P1, but that does not 
mean the true space group is indeed P1. If you use P1 when it’s not actually 
P1, you will have an unnecessarily overparamerized model, hence the large gap 
between Rwork and Rfree.



Questions:

1- how many copies in your asymmetric unit in P1?

2- how many atoms in your model vs number of unique reflections?

3- if more than one copy per asymmetric unit, are you imposing NCS restraints 
during refinement?



-Eric







On Wed, Apr 3, 2019 at 1:41 PM Sam Tang 
mailto:samtys0...@gmail.com>> wrote:

Hi everyone again



Hmmm I think we have solved a structure in P1 space, to 2.5 A. However after 
refinement the Rfree stuck at 33%-35% with Rwork around 26%. The structure was 
solved by MR and current model seems to fit density well. In Refmac log I found 
that at the resolution corresponding to high R there may be a solvent/ice ring. 
Since imosflm should be able to exclude ice rings, I am not 100% sure whether 
it's the cause to high R. But if this is actually the case, is there a way I 
can exclude certain resolution bins during Refmac (and is it an appropriate way 
to do so?)



PS - the data is not affected by twining or pseudosymmetry as checked by 
Xtriage.



Many thanks!



Sam





To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[james.parkhu...@diamond.ac.uk]

Dear Sam,


Cutting out reflections obviously means you lose information. If you are using 
dials to process your data, then an alternative would be to try the ice ring 
background modelling algorithm which may give you better results.


Taking the output of dials.integrate you can do this as follows:


dials.model_background integrated_experiments.json


dials.integrate refined.pickle integrated_experiments.json \

  background.algorithm=gmodel \

  background.gmodel.model=background.pickle


Then scale as normal.


You can also use auspex to look at your scaled intensities to see if the ice 
rings are causing systematic errors.


Best wishes

James



From: CCP4 bulletin board  on behalf of Frank von Delft 

Sent: 04 April 2019 11:39:19
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

You can use sftools to set a shell of reflections to MNF - then Refmac will 
fill those in with DFc, and that'll presumably be much better than having very 
wrong reflections.

Whether that will fix your Rfactor is a different story.

phx


On 04/04/2019 11:05, Eleanor Dodson wrote:
You cant exclude one resolution ring in REFMAC - there would be ways to fudge 
the exclusion from your current file, but much safer to use a data integration 
tool

On Thu, 4 Apr 2019 at 10:27, 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sam,

I would remove the ice ring and reprocess the data. Ice rings may wreak havoc 
with scaling so at minimum you have to redo the scaling.

Best,
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam 
Tang
Gesendet: Donnerstag, 4. April 2019 11:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring


Dear Eleanor and Eric

Thanks for your replies.

Yes indeed when we looked at the plots e.g. R factor vs resln there was a sharp 
peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the image. 
Thus our first thought was to remove the ic ring. (either reprocess or can we 
bypass this resolution range during refinement?)

The protein is 50 kDa, two molecule in the ASU, seemingly no obvious density 
was unassigned. We got ~3 total observations, ~15000 unique observations. 
NCS restraints was applied.

Best regards
Sam



On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
mailto:montemayor.e...@gmail.com>> wrote:
That’s a rather large gap between Rwork and Rfree.  I suspect you have 
mis-assigned your space group and as a result have a large number of copies in 
your asymmetric unit.  Any structure can be solved in P1, but that does not 
mean the true space group is indeed P1. If you use P1 when it’s not actually 
P1, you will have an unnecessarily overparamerized model, hence the large gap 
between Rwork and Rfree.

Questions:
1- how many copies in your asymmetric unit in P1?
2- how many atoms in your model vs number of unique reflections?
3- if more than one copy per asymmetric unit, are you imposing NCS restraints 
during refinement?

-Eric



On Wed, Apr 3, 2019 at 1:41 PM Sam Tang 
mailto:samtys0...@gmail.com>> wrote:
Hi everyone again

Hmmm I think we have solved a structure in P1 space, to 2.5 A. However after 
refinement the Rfree stuck at 33%-35% with Rwork around 26%. The structure was 
solved by MR and current model seems to fit density well. In Refmac log I found 
that at the resolution corresponding to high R there may be a solvent/ice ring. 
Since imosflm should be able to exclude ice rings, I am not 100% sure whether 
it's the cause to high R. But if this is actually the case, is there a way I 
can exclude certain resolution bins during Refmac (and is it an appropriate way 
to do so?)

PS - the data is not affected by twining or pseudosymmetry as checked by 
Xtriage.

Many thanks!

Sam



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Frank von Delft]

You can use sftools to set a shell of reflections to MNF - then Refmac 
will fill those in with DFc, and that'll presumably be much better than 
having very wrong reflections.


Whether that will fix your Rfactor is a different story.

phx


On 04/04/2019 11:05, Eleanor Dodson wrote:
You cant exclude one resolution ring in REFMAC - there would be ways 
to fudge the exclusion from your current file, but much safer to use a 
data integration tool


On Thu, 4 Apr 2019 at 10:27, > wrote:


Dear Sam,

I would remove the ice ring and reprocess the data. Ice rings may
wreak havoc with scaling so at minimum you have to redo the scaling.

Best,

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
] *Im Auftrag von *Sam Tang
*Gesendet:* Donnerstag, 4. April 2019 11:01
*An:* CCP4BB@JISCMAIL.AC.UK 
*Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring


Dear Eleanor and Eric

Thanks for your replies.

Yes indeed when we looked at the plots e.g. R factor vs resln
there was a sharp peak near 3.6 - 3.8 A which is where we visibly
saw an ice ring on the image. Thus our first thought was to remove
the ic ring. (either reprocess or can we bypass this resolution
range during refinement?)

The protein is 50 kDa, two molecule in the ASU, seemingly no
obvious density was unassigned. We got ~3 total observations,
~15000 unique observations. NCS restraints was applied.

Best regards

Sam

On Thu, 4 Apr 2019 at 08:57, Eric Montemayor
mailto:montemayor.e...@gmail.com>> wrote:

That’s a rather large gap between Rwork and Rfree.  I suspect
you have mis-assigned your space group and as a result have a
large number of copies in your asymmetric unit.  Any structure
can be solved in P1, but that does not mean the true space
group is indeed P1. If you use P1 when it’s not actually P1,
you will have an unnecessarily overparamerized model, hence
the large gap between Rwork and Rfree.

Questions:

1- how many copies in your asymmetric unit in P1?

2- how many atoms in your model vs number of unique reflections?

3- if more than one copy per asymmetric unit, are you imposing
NCS restraints during refinement?

-Eric

On Wed, Apr 3, 2019 at 1:41 PM Sam Tang mailto:samtys0...@gmail.com>> wrote:

Hi everyone again

Hmmm I think we have solved a structure in P1 space, to
2.5 A. However after refinement the Rfree stuck at 33%-35%
with Rwork around 26%. The structure was solved by MR and
current model seems to fit density well. In Refmac log I
found that at the resolution corresponding to high R there
may be a solvent/ice ring. Since imosflm should be able to
exclude ice rings, I am not 100% sure whether it's the
cause to high R. But if this is actually the case, is
there a way I can exclude certain resolution bins during
Refmac (and is it an appropriate way to do so?)

PS - the data is not affected by twining or pseudosymmetry
as checked by Xtriage.

Many thanks!

Sam




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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Christian Roth]

I would also check carefully the other potential ice rings resolution
ranges.  I doubt there is just the one you can identify easily.


On Thu, Apr 4, 2019 at 12:07 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You cant exclude one resolution ring in REFMAC - there would be ways to
> fudge the exclusion from your current file, but much safer to use a data
> integration tool
>
> On Thu, 4 Apr 2019 at 10:27,  wrote:
>
>> Dear Sam,
>>
>>
>>
>> I would remove the ice ring and reprocess the data. Ice rings may wreak
>> havoc with scaling so at minimum you have to redo the scaling.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Sam Tang
>> *Gesendet:* Donnerstag, 4. April 2019 11:01
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>>
>>
>>
>>
>> Dear Eleanor and Eric
>>
>>
>>
>> Thanks for your replies.
>>
>>
>>
>> Yes indeed when we looked at the plots e.g. R factor vs resln there was a
>> sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
>> the image. Thus our first thought was to remove the ic ring. (either
>> reprocess or can we bypass this resolution range during refinement?)
>>
>>
>>
>> The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
>> density was unassigned. We got ~3 total observations, ~15000 unique
>> observations. NCS restraints was applied.
>>
>>
>>
>> Best regards
>>
>> Sam
>>
>>
>>
>>
>>
>>
>>
>> On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
>> wrote:
>>
>> That’s a rather large gap between Rwork and Rfree.  I suspect you have
>> mis-assigned your space group and as a result have a large number of copies
>> in your asymmetric unit.  Any structure can be solved in P1, but that does
>> not mean the true space group is indeed P1. If you use P1 when it’s not
>> actually P1, you will have an unnecessarily overparamerized model, hence
>> the large gap between Rwork and Rfree.
>>
>>
>>
>> Questions:
>>
>> 1- how many copies in your asymmetric unit in P1?
>>
>> 2- how many atoms in your model vs number of unique reflections?
>>
>> 3- if more than one copy per asymmetric unit, are you imposing NCS
>> restraints during refinement?
>>
>>
>>
>> -Eric
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang  wrote:
>>
>> Hi everyone again
>>
>>
>>
>> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
>> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
>> structure was solved by MR and current model seems to fit density well. In
>> Refmac log I found that at the resolution corresponding to high R there may
>> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
>> am not 100% sure whether it's the cause to high R. But if this is actually
>> the case, is there a way I can exclude certain resolution bins during
>> Refmac (and is it an appropriate way to do so?)
>>
>>
>>
>> PS - the data is not affected by twining or pseudosymmetry as checked by
>> Xtriage.
>>
>>
>>
>> Many thanks!
>>
>>
>>
>> Sam
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Eleanor Dodson]

You cant exclude one resolution ring in REFMAC - there would be ways to
fudge the exclusion from your current file, but much safer to use a data
integration tool

On Thu, 4 Apr 2019 at 10:27,  wrote:

> Dear Sam,
>
>
>
> I would remove the ice ring and reprocess the data. Ice rings may wreak
> havoc with scaling so at minimum you have to redo the scaling.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Sam Tang
> *Gesendet:* Donnerstag, 4. April 2019 11:01
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>
>
>
>
> Dear Eleanor and Eric
>
>
>
> Thanks for your replies.
>
>
>
> Yes indeed when we looked at the plots e.g. R factor vs resln there was a
> sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
> the image. Thus our first thought was to remove the ic ring. (either
> reprocess or can we bypass this resolution range during refinement?)
>
>
>
> The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
> density was unassigned. We got ~3 total observations, ~15000 unique
> observations. NCS restraints was applied.
>
>
>
> Best regards
>
> Sam
>
>
>
>
>
>
>
> On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
> wrote:
>
> That’s a rather large gap between Rwork and Rfree.  I suspect you have
> mis-assigned your space group and as a result have a large number of copies
> in your asymmetric unit.  Any structure can be solved in P1, but that does
> not mean the true space group is indeed P1. If you use P1 when it’s not
> actually P1, you will have an unnecessarily overparamerized model, hence
> the large gap between Rwork and Rfree.
>
>
>
> Questions:
>
> 1- how many copies in your asymmetric unit in P1?
>
> 2- how many atoms in your model vs number of unique reflections?
>
> 3- if more than one copy per asymmetric unit, are you imposing NCS
> restraints during refinement?
>
>
>
> -Eric
>
>
>
>
>
>
>
> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang  wrote:
>
> Hi everyone again
>
>
>
> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
> structure was solved by MR and current model seems to fit density well. In
> Refmac log I found that at the resolution corresponding to high R there may
> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
> am not 100% sure whether it's the cause to high R. But if this is actually
> the case, is there a way I can exclude certain resolution bins during
> Refmac (and is it an appropriate way to do so?)
>
>
>
> PS - the data is not affected by twining or pseudosymmetry as checked by
> Xtriage.
>
>
>
> Many thanks!
>
>
>
> Sam
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Post-doctoral position in structural studies on the malarial actomyosin motor

[Inari Kursula]

Dear colleagues,

I would be grateful if you could bring the following ad for a post-doctoral 
position in my lab to the attention of suitable candidates.

Kind regards,
Inari Kursula

***

Post-doctoral position in the group of Inari Kursula at the Faculty of 
Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 
Finland

We have an opening for an enthusiastic post-doctoral fellow to study the 
molecular mechanisms governing actin polymerization, ATP hydrolysis, phosphate 
release, and filament stability in malaria parasite actins. The successful 
candidate has a keen interest to understand cytoskeletal proteins and cell 
motility in depth. A strong background in protein biochemistry and X-ray 
crystallography is required. Expertise in cryo-EM sample preparation and 
structure determination will be highly valued. In addition, a high level of own 
initiative and the ability to work in a team and supervise younger scientists 
are necessary.

The Faculty of Biochemistry and Molecular Medicine (FBMM; 
https://www.oulu.fi/fbmm/) is a dynamic and international working place, where 
the working language is English. Protein science is one of the focal areas of 
the Faculty. FBMM provides cutting-edge research facilities for molecular 
biology, protein biochemistry, X-ray crystallography, and light and electron 
microscopy. In addition, we have generous access to several large-scale 
facilities for structural biology (MX/SAXS/cryo-EM).

Funding is initially available for 2.5 years, but there may be possibilities 
for an extension. The starting date should be as soon as possible. Applications 
and informal enquiries should be sent by e-mail to inari.kurs...@oulu.fi. 
Applications should contain (i) a cover letter detailing your specific interest 
in this project and your key skills and expertise, (ii) a CV including a list 
of publications, and (iii) contact information (e-mail) for 3 referees. 
Applications should preferably be sent by 30.4.2019, but screening of 
candidates will continue until a suitable one has been identified.

For more information on our work, please visit our website: 
http://cc.oulu.fi/~inkursul/lab

Some recent publications directly relevant for the topic:

Kumpula EP, Lopez AJ, Tajedin L, Han H & Kursula I (2018) Atomic view into 
Plasmodium actin polymerization, ATP hydrolysis, and phosphate release. 
bioRxiv: 467423, https://doi.org/10.1101/467423.

Kumpula EP, Pires IP, Lasiwa D, Piirainen H, Bergmann U, Vahokoski J & Kursula 
I (2017) Apicomplexan actin polymerization depends on nucleation. Sci Rep 7: 
12137.

Pospich S, Kumpula EP, von der Ecken J, Vahokoski J, Kursula I & Raunser S 
(2017) Near-atomic structure of jasplakinolide-stabilized malaria parasite 
F-actin reveals the structural basis of filament instability. Proc Natl Acad 
Sci 114: 10636-10641.

Green JL, Wall RJ, Vahokoski J, Yusuf NA, Ridzuan MAM, Stanway RR, Stock J, 
Knuepfer E, Brady D, Martin SR, Howell SA, Pires IP, Moon RW, Molloy JE, 
Kursula I, Tewari R & Holder AA (2017) Compositional and expression analyses of 
the glideosome during the Plasmodium life cycle reveal an additional myosin 
light chain required for maximum motility. J Biol Chem 292: 17857-17875.

For a full list of publications from our group, see: 
http://cc.oulu.fi/~inkursul/lab/Molecular_mechanisms_of_actin-based_motility/publications.html
 

***

--
Prof. Inari Kursula

Department of Biomedicine
University of Bergen
Jonas Lies vei 91
5009 Bergen
Norway

Faculty of Biochemistry and Molecular Medicine
University of Oulu
Aapistie 7
90220 Oulu
Finland

European XFEL GmbH
Holzkoppel 4
22869 Schenefeld
Germany

http://cc.oulu.fi/~inkursul/lab
inari.kurs...@uib.no, inari.kurs...@oulu.fi, inari.kurs...@xfel.eu
Tel. +47 5558 6846, +49 40 8998 6862
--


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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Herman . Schreuder]

Dear Sam,

I would remove the ice ring and reprocess the data. Ice rings may wreak havoc 
with scaling so at minimum you have to redo the scaling.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang
Gesendet: Donnerstag, 4. April 2019 11:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring


Dear Eleanor and Eric

Thanks for your replies.

Yes indeed when we looked at the plots e.g. R factor vs resln there was a sharp 
peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the image. 
Thus our first thought was to remove the ic ring. (either reprocess or can we 
bypass this resolution range during refinement?)

The protein is 50 kDa, two molecule in the ASU, seemingly no obvious density 
was unassigned. We got ~3 total observations, ~15000 unique observations. 
NCS restraints was applied.

Best regards
Sam



On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
mailto:montemayor.e...@gmail.com>> wrote:
That’s a rather large gap between Rwork and Rfree.  I suspect you have 
mis-assigned your space group and as a result have a large number of copies in 
your asymmetric unit.  Any structure can be solved in P1, but that does not 
mean the true space group is indeed P1. If you use P1 when it’s not actually 
P1, you will have an unnecessarily overparamerized model, hence the large gap 
between Rwork and Rfree.

Questions:
1- how many copies in your asymmetric unit in P1?
2- how many atoms in your model vs number of unique reflections?
3- if more than one copy per asymmetric unit, are you imposing NCS restraints 
during refinement?

-Eric



On Wed, Apr 3, 2019 at 1:41 PM Sam Tang 
mailto:samtys0...@gmail.com>> wrote:
Hi everyone again

Hmmm I think we have solved a structure in P1 space, to 2.5 A. However after 
refinement the Rfree stuck at 33%-35% with Rwork around 26%. The structure was 
solved by MR and current model seems to fit density well. In Refmac log I found 
that at the resolution corresponding to high R there may be a solvent/ice ring. 
Since imosflm should be able to exclude ice rings, I am not 100% sure whether 
it's the cause to high R. But if this is actually the case, is there a way I 
can exclude certain resolution bins during Refmac (and is it an appropriate way 
to do so?)

PS - the data is not affected by twining or pseudosymmetry as checked by 
Xtriage.

Many thanks!

Sam



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[ccp4bb] 1st French Congress on Integrative Structural Biology - 7-10 October 2019, Toulouse

[maveyrau]

Dear colleagues,

The first French congress on Integrative Structural Biology, jointly organized 
by the Association Française de Cristallographie and the Société Française de 
Biophysique, will take place in Toulouse from 7 to 11 October 2019. We invite 
you to visit its website (http://bsi-2019.ipbs.fr/ ) 
where registrations are now open. Please circulate this announcement. We hope 
to see you in Toulouse where autumn is often sunny.

With kind regards,

The organizing and scientific committees


Laurent Maveyraud
PICT, Plateforme Intégrée de Criblage de Toulouse
Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
Département Biologie Structurale et Biophysique
http://cribligand.ipbs.fr, http://www.ipbs.fr
205 route de Narbonne 31077 TOULOUSE Cedex FRANCE
Tél: +33 (0)561 175 435  Mob.: +33 (0)646 042 111
---


1st French Congress on Integrative Structural Biology: please check 
http://bsi-2019.ipbs.fr 





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Re: [ccp4bb] High Rfree - ice ring

[Sam Tang]

Dear Eleanor and Eric

Thanks for your replies.

Yes indeed when we looked at the plots e.g. R factor vs resln there was a
sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
the image. Thus our first thought was to remove the ic ring. (either
reprocess or can we bypass this resolution range during refinement?)

The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
density was unassigned. We got ~3 total observations, ~15000 unique
observations. NCS restraints was applied.

Best regards
Sam



On Thu, 4 Apr 2019 at 08:57, Eric Montemayor 
wrote:

> That’s a rather large gap between Rwork and Rfree.  I suspect you have
> mis-assigned your space group and as a result have a large number of copies
> in your asymmetric unit.  Any structure can be solved in P1, but that does
> not mean the true space group is indeed P1. If you use P1 when it’s not
> actually P1, you will have an unnecessarily overparamerized model, hence
> the large gap between Rwork and Rfree.
>
> Questions:
> 1- how many copies in your asymmetric unit in P1?
> 2- how many atoms in your model vs number of unique reflections?
> 3- if more than one copy per asymmetric unit, are you imposing NCS
> restraints during refinement?
>
> -Eric
>
>
>
> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang  wrote:
>
>> Hi everyone again
>>
>> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
>> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
>> structure was solved by MR and current model seems to fit density well. In
>> Refmac log I found that at the resolution corresponding to high R there may
>> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
>> am not 100% sure whether it's the cause to high R. But if this is actually
>> the case, is there a way I can exclude certain resolution bins during
>> Refmac (and is it an appropriate way to do so?)
>>
>> PS - the data is not affected by twining or pseudosymmetry as checked by
>> Xtriage.
>>
>> Many thanks!
>>
>> Sam
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>



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[ccp4bb] 2y PostDoc position @ University of Groningen

[Albert Guskov]

Dear all,
I have an immediate opening for the 2y industry sponsored PostDoc position
in Structural Biology. The project is about membrane-embedded /
membrane-associated enzymes.
The essential skills: membrane protein expression (bacterial and or yeast)
and purification (IMAC + SEC), excellent level of English (both oral and
written);
Desirable skills: crystallisation / structure determination or experience
in single-particle Cryo-EM.
Salary according to the collective labour agreement (cao) of Dutch
Universities: level 10.4. Applicants from outside The Netherlands might be
eligible for 30% tax deduction.
Please send your CV+motivation letter+1-2 recommendations (including one
from your PhD supervisor) by 30th of April, 23:59 CET to the following
e-mail:
a.guskov at rug.nl with the header 'application for a PostDoc position'
Please note, only shortlisted candidates will be notified.
With kind regards,

Albert Guskov (Dr) |Assistant Professor | Biomolecular X-ray
Crystallography |University of Groningen
Nijenborgh 7, Groningen 9747 AG, The Netherlands Tel: +31 50 363-4391
|Secretary:
+31 50 363-4378 |E-mail: a.gus...@rug.nl|



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Re: [ccp4bb] Current "best" software for computing volumes of active sites

[Martyn Winn - UKRI STFC]

Hi,

At the request of Gerard, I have rescued the USF packages into github 
https://github.com/martynwinn/Uppsala-Software-Factory

So far, I have done nothing with this, so no guarantees that the code still 
compiles or that the old binaries still work.

Nevertheless, it does contain a cavity.lib file for voidoo (in fact, 4 
variants). Perhaps that helps.

cheers
Martyn

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fred 
Vellieux
Sent: 04 April 2019 07:24
To: ccp4bb
Subject: [ccp4bb] Current "best" software for computing volumes of active sites

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.

I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.

I am running Linux.

Thanks for the advice,

Fred. Vellieux



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Re: [ccp4bb] pseudo internal symmetry

[Daniele de Sanctis]

Hi again,

thanks for your replies. Based on the suggestions and since the difference
between the two "conformations" is limited to few residues, the data
statistics do not show any problem, there is no problem with the refinement
and the maps clearly show the two conformations we will keep it like this.

Cheers

Daniele

On Wed, Apr 3, 2019 at 10:36 AM Daniele de Sanctis 
wrote:

> Hi all,
>
> we have a structure with a pseudo internal symmetry along a 2-fold axis
> that sits on a 2-fold crystallographic axis. For refinement purposes we
> have modeled the parts that differ with 50% occupancy, but before
> depositing the structure we wanted to make sure that this is the best way
> to deal with it and it is in agreement with PDB standards.
>
> Did anyone deal with similar cases in the past?
>
> Cheers
>
> Daniele
>
>
> --
>
> ἀρετή
> ---
> Daniele de Sanctis
> Structural Biology Group
> ESRF - The European Synchrotron
> Grenoble, France
> Tel 33 (0)4 76 88 2869
>
> http://www.esrf.eu/id29
>


-- 
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869



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Re: [ccp4bb] Current "best" software for computing volumes of active sites

[Gianluca SANTONI]

You can have a look at Caver.
I find it quite easy to use and it worked for me on some weirdly shaped 
cavities.


Gianluca Santoni, serial crystallographer

ESRF structural biology group
71 avenue des Martyrs
38027 Grenoble cedex (France)

On 04/04/2019 08:24, Fred Vellieux wrote:

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.


I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.


I am running Linux.

Thanks for the advice,

Fred. Vellieux



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Re: [ccp4bb] Current "best" software for computing volumes of active sites

[Christian Roth]

Well, I don't know if that is the newest appropriate piece of software, but
pdbsum does automatic calculation of clefts using MOLE I think. It does
provide jmol and rasmol scripts and volume and surface calculations.

Cheers
Christian

On Thu, Apr 4, 2019 at 8:24 AM Fred Vellieux 
wrote:

> Hi CCP4BBers,
>
> With software constantly changing, new versions arriving to us and new
> software reaching the intended audience, I am looking for the most
> appropriate piece(s) of software to compute the volume of active site
> "cavities" in related 3D structures.
>
> I have tried to use Voidoo however I do not know where to download an
> initial (and fairly comprehensive) cavity.lib file which I'd modify if
> need be. The links on the USF web site appear to be broken.
>
> I am running Linux.
>
> Thanks for the advice,
>
> Fred. Vellieux
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Current "best" software for computing volumes of active sites

[Fred Vellieux]

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.


I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.


I am running Linux.

Thanks for the advice,

Fred. Vellieux



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