Re: [ccp4bb] Imosflm help twinned crystal data

[Jon Cooper]

That's one you made earlier ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 04/07/2024 20:13, CCP4BB wrote:

> Hi
>
> The best advice I can give if you're new to iMosflm is to work through this 
> tutorial, and feel free to ask questions.
>
> https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/documentation/tutorial.html
>
> Note that I don't work on the project any more so I have to concentrate on 
> the day job - but I can help if you're willing to be a little patient...
>
> Harry
> --
> Dr Harry Powell
>
> On 4 Jul 2024, at 18:42, Marco 
>  wrote:
>
>> Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
>> data, since the autoprocessed data from XDS at the synchotron is not giving 
>> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
>> think the crystal might be twinned however and thus might be making 
>> structural solution difficult for a beginner crystallographer like me. 
>> However an expert in my lab was able to solve the structure with the data 
>> and told me to use imosflm to reprocess the data. They want me to figure 
>> this out on my own with that hint. Is there any tips or resources you can 
>> recommend to help me process my twinned data?
>>
>> Thank you
>>
>> Happy 4th of July!
>>
>> 
>>
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Re: [ccp4bb] Imosflm help twinned crystal data

[Jon Cooper]

Oh dear, that sounds like Blue Peter science. I regret though that I haven't 
used mosflm in earnest for a while myself. I do hope someone can be more 
helpful. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 04/07/2024 18:42, Marco  
wrote:

>  Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
> data, since the autoprocessed data from XDS at the synchotron is not giving 
> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
> think the crystal might be twinned however and thus might be making 
> structural solution difficult for a beginner crystallographer like me. 
> However an expert in my lab was able to solve the structure with the data and 
> told me to use imosflm to reprocess the data. They want me to figure this out 
> on my own with that hint. Is there any tips or resources you can recommend to 
> help me process my twinned data?
>  
>  Thank you
>  
>  Happy 4th of July!
>  
>  
>  
>  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 
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>



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Re: [ccp4bb] Imosflm help twinned crystal data

[CCP4BB]

Hi

The best advice I can give if you're new to iMosflm is to work through this 
tutorial, and feel free to ask questions.

https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/documentation/tutorial.html

Note that I don't work on the project any more so I have to concentrate on the 
day job - but I can help if you're willing to be a little patient...

Harry
--
Dr Harry Powell

> On 4 Jul 2024, at 18:42, Marco 
>  wrote:
> 
> Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
> data, since the autoprocessed data from XDS at the synchotron is not giving 
> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
> think the crystal might be twinned however and thus might be making 
> structural solution difficult for a beginner crystallographer like me. 
> However an expert in my lab was able to solve the structure with the data and 
> told me to use imosflm to reprocess the data. They want me to figure this out 
> on my own with that hint. Is there any tips or resources you can recommend to 
> help me process my twinned data? 
> 
> Thank you
> 
> Happy 4th of July!
> 
> 
> 
> 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 
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[ccp4bb] Imosflm help twinned crystal data

[Marco]

Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction data, 
since the autoprocessed data from XDS at the synchotron is not giving me a 
solution. I think the crystal has decent resolution around 2.5-2.6A. I think 
the crystal might be twinned however and thus might be making structural 
solution difficult for a beginner crystallographer like me. However an expert 
in my lab was able to solve the structure with the data and told me to use 
imosflm to reprocess the data. They want me to figure this out on my own with 
that hint. Is there any tips or resources you can recommend to help me process 
my twinned data? 

Thank you

Happy 4th of July!



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[ccp4bb] Curvature of protein backbone

[Jessica Besaw]

Hello friends,

What is the best way to determine the curvature of a protein backbone, both
for alpha helices and beta sheets?

Is there, by chance, a simple software that can compute this?

Any suggestions are greatly appreciated.

Cheers!

Jessica



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Re: [ccp4bb] Tools for identifying possible contaminants

[Deborah Harrus]

Dear Kyle, Clemens, and all,

We use a similar approach at PDB to look for common assemblies, but 
using the center of mass. The item is not yet public though, but if you 
send me the values (that can be calculated using gemmi: 
https://gemmi.readthedocs.io/en/latest/mol.html#model) I can have a 
quick scan though released entries.


Kind regards,

Deborah


On 04/07/2024 10:25, Clemens Vonrhein wrote:

Dear Kyle,

I often like lookint at the crystal.idx file [1] for PDB structures
with very similar cell dimensions ... and then doing some quick MR to
see if one of those sticks out. Easy to fully automate if you have a
local copy of the PDB archive, but something like that (bash)

   cell="30 40 50 90 90 90" # your cell
   maxd=2   # max deviation (A and degree)
   [ ! -f crystal.idx ] && wget -q 
https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
   awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
 i=split(cell,c)
   }
   /CRYST1/{
 for(i=1;i<=6;i++) {
   d=c[i]-$(i+2);if(d<0)d=-d
   if(d>maxd)next
 }
 print
   }' crystal.idx

would give you a first listing ...

Cheers

Clemens

[1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx


On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:

Dear all,

We have a unit cell that is too small for our expected protein and suspect we 
have crystalised a contaminant.

Does anyone have any recommendations on which tools we could use to identify 
the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't suggest 
anything reasonable.

Kind regards,
Kyle



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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Eleanor Dodson]

I Am thinking about this problem re a set of four carbohydrate binding
proteins - all isomorphous but with different Ligands and weird solvent
features..
first task was to get all sets with same indexing convention!
(SoacegroupP65) That can be done at the data processing stage by giving one
as the reference set.
Then I wanted all the models to be on the same origin and symmetry to make
comparisons easier. You can do molecular replacement fir each then use the
task “match model to reference” but it is easier to just start refinement
with the basic first model then correct and refine the new one as the maps
indicate..
maybe it is enough then to just look at all naps in COOT together but I
want to do an Fobs1 - Fobs2 difference map..
There is a ccp4i2 task to compare datasets using scaleit to match them.
That gives useful analysis of differences and then If you have calculated
phases for your best model then you can do such a difference nap. It
certainly shows up features which I expect to be different
However there seems to be a bug in the cmapcoeff version for this.. The old
*fft* script in ccp4i works OK with that input.
Eleanor

On Sat, 15 Jun 2024 at 13:53, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Comparing maps sounds justi. A like the sort of thing the Uppsala suite
> did. Maybe you can find an old binary for mapman or mapman2(?) or compile
> it from Martin Winn's github page. The closest I can find is EDSTATS which
> I think is in the old ccp4 gui.
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>
>  Original Message 
>
> On 14/06/2024 20:58, Matt Mcleod wrote:
>
> I should clarify.  I am mostly concerned about the electron density map.
>
> I want to make sure that I can most closely compare the maps from two
> different quality structures, rather than the datasets themselves via CC1/2
> or other metrics.  This is more so for interpreting structural changes.
>
> For example, if there is sparse density for some particular thing
> indicating partial occupancy, how can I compare those two maps.  So for
> low-resolution datasets, maybe there is less density but is that because of
> data quality or because in that dataset there is a lower occupancy through
> some meaningful structural change (compared to higher resolution/better
> data)?
>
> On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of
>> the same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is
>> alright, but the data quality in the lower resolution bins are also not the
>> same.  Is there a way to "inject" noise into the data such that the bins
>> are more similar?
>>
>> These datasets cannot be recollected at higher resolution since they are
>> collected at increasingly high pressure, and the resolution change is
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
>
> --
> *Matthew Jordan McLeod, PhD*
> *Post-Doctoral Fellow - Cornell University*
>
>
>
>
> --
>
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Re: [ccp4bb] Tools for identifying possible contaminants

[Eleanor Dodson]

In fact I believe that is what the SIMBAD script does - searches the PDB
archive first for cell dimensions, and only then checks possible MR
matches..

On Thu, 4 Jul 2024 at 10:26, Clemens Vonrhein <
daef624adb06-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Kyle,
>
> I often like lookint at the crystal.idx file [1] for PDB structures
> with very similar cell dimensions ... and then doing some quick MR to
> see if one of those sticks out. Easy to fully automate if you have a
> local copy of the PDB archive, but something like that (bash)
>
>   cell="30 40 50 90 90 90" # your cell
>   maxd=2   # max deviation (A and degree)
>   [ ! -f crystal.idx ] && wget -q
> https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
>   awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
> i=split(cell,c)
>   }
>   /CRYST1/{
> for(i=1;i<=6;i++) {
>   d=c[i]-$(i+2);if(d<0)d=-d
>   if(d>maxd)next
> }
> print
>   }' crystal.idx
>
> would give you a first listing ...
>
> Cheers
>
> Clemens
>
> [1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
>
>
> On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:
> > Dear all,
> >
> > We have a unit cell that is too small for our expected protein and
> suspect we have crystalised a contaminant.
> >
> > Does anyone have any recommendations on which tools we could use to
> identify the possible contaminant? I've tried SIMAD on ccp4cloud and it
> doesn't suggest anything reasonable.
> >
> > Kind regards,
> > Kyle
> >
> > 
> >
> > 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/
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>
> 
>
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Re: [ccp4bb] Tools for identifying possible contaminants

[Clemens Vonrhein]

Dear Kyle,

I often like lookint at the crystal.idx file [1] for PDB structures
with very similar cell dimensions ... and then doing some quick MR to
see if one of those sticks out. Easy to fully automate if you have a
local copy of the PDB archive, but something like that (bash)

  cell="30 40 50 90 90 90" # your cell
  maxd=2   # max deviation (A and degree)
  [ ! -f crystal.idx ] && wget -q 
https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
  awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
i=split(cell,c)
  }
  /CRYST1/{
for(i=1;i<=6;i++) {
  d=c[i]-$(i+2);if(d<0)d=-d
  if(d>maxd)next
}
print
  }' crystal.idx

would give you a first listing ...

Cheers

Clemens

[1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx


On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:
> Dear all,
> 
> We have a unit cell that is too small for our expected protein and suspect we 
> have crystalised a contaminant.
> 
> Does anyone have any recommendations on which tools we could use to identify 
> the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't 
> suggest anything reasonable.
> 
> Kind regards,
> Kyle
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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