Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

[Hekstra, Doeke Romke]

Hi Murpholino,

You could go the route of comparing refined models, as described by Dr. Yorke. 
As Dr. Dodson describes, isomorphous difference maps are another way to compare 
datasets. A benefit is that they do not require separate refinement of models 
for both states, which can render the comparison susceptible to differences in 
modeling choices. Isomorphous difference maps have been used for comparison of 
crystallographic datasets for decades.

Using CCP4’s utilities provides one way of doing so. Depending on your comfort 
with python and need to understand exactly what you are doing, you may also 
appreciate the following non-CCP4 options (apologies; this includes some 
self-promotion):


  1.  Use of PHENIX’s isomorphous difference map routine—it’s easy to use but 
could be better documented.
  2.  Use of reciprocalspaceship (rs), which is based on modern python. See 
here for an example: 
https://rs-station.github.io/reciprocalspaceship/examples/6_timeresolvedPYP.html
 (this was developed by Jack Greisman and Kevin Dalton, initially within my 
research group).

In cases where the unit cells are similar but not quite the same, it may be 
helpful to try MatchMaps, developed by Dennis Brookner in my group: 
https://rs-station.github.io/matchmaps/quickstart.html. Matchmaps, rs, and its 
add-on rs-booster, are open-source and you and everyone else are welcome to 
adapt the code for your  own purposes.

Hope this helps,
Doeke

From: CCP4 bulletin board  On Behalf Of Murpholino 
Peligro
Sent: Monday, April 8, 2024 9:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to compare the same protein crystallized in different 
conditions?

Hi...
Let's say I want to compare the same protein crystallized in different 
conditions. Same space group, almost same resolution. The global RMSD will be 
pretty small (around 0.3 Angstroms). There will be some changes in rotamers in 
some residues and some extra waters here and there... Besides local rsmd and 
contact maps (or differences in contact maps)... is there anything else to get 
a decent view of these small changes?
Thanks a lot.





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Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

[Eleanor Dodson]

I like to use difference maps between Fa and Fb ..
It is a bit tricky now to set them up..but they do highlight changes.

Obviously
1) you need to have the same spacegroup and cell, and the same indexing
convention.
(Easy to check this in the data processing task when importing the second
data set. - give the first data set as a reference)

2) Dont be tempted to run molecular replacement on the second structure -
just start refinemen from structure 1) - it is MUCH simpler if both
examples are on the same origin..


Now maybe you go back to the old fashioned ccp4i.

Run CAD to put both sets (and associated phases for one of the structures)
into a single mtz
Run SCALEIT to a) put the two data sets on the same scale, and b) look for
a sensible resolution to choose, and to pinpoint any unlikely differences
that could dominate a difference map..
Then I run the old FFT task where you could input these cut offs easily,
but maybe it is possible with the newer program?? No documentation though
that I could find..
The FFT map can then be read into COOT (dont forget to mark it as a
difference map)
And a peak search will highlight large positive and negative regions
Positive where there is something in structure 1) but not in 2)
Negative where there is something in structure 2) but not in 1)

Easy-peasy??? well - it really is informative!
Eleanor



On Tue, 9 Apr 2024 at 08:33, Briony Yorke  wrote:

> Hi Murpholino,
>
>
>
> Helen Ginn is developing software to characterise changes in protein
> structures (especially informative when the changes are small but
> significant)– there is a web app and a download here:
>
>
>
> https://rope.hginn.co.uk
>
>
>
> I recommend watching the youtube tutorial.
>
>
>
> *From: *CCP4 bulletin board  on behalf of
> Murpholino Peligro 
> *Date: *Tuesday, 9 April 2024 at 02:39
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[ccp4bb] How to compare the same protein crystallized in
> different conditions?
>
> *Caution External Email:* Do not click any links or open any attachments
> unless you trust the sender and know that the content is safe.
>
> Hi...
>
> Let's say I want to compare the same protein crystallized in different
> conditions. Same space group, almost same resolution. The global RMSD will
> be pretty small (around 0.3 Angstroms). There will be some changes in
> rotamers in some residues and some extra waters here and there... Besides
> local rsmd and contact maps (or differences in contact maps)... is there
> anything else to get a decent view of these small changes?
>
> Thanks a lot.
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
>
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>



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Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

[Briony Yorke]

Hi Murpholino,

Helen Ginn is developing software to characterise changes in protein structures 
(especially informative when the changes are small but significant)– there is a 
web app and a download here:

https://rope.hginn.co.uk

I recommend watching the youtube tutorial.

From: CCP4 bulletin board  on behalf of Murpholino 
Peligro 
Date: Tuesday, 9 April 2024 at 02:39
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] How to compare the same protein crystallized in different 
conditions?

Caution External Email: Do not click any links or open any attachments unless 
you trust the sender and know that the content is safe.
Hi...
Let's say I want to compare the same protein crystallized in different 
conditions. Same space group, almost same resolution. The global RMSD will be 
pretty small (around 0.3 Angstroms). There will be some changes in rotamers in 
some residues and some extra waters here and there... Besides local rsmd and 
contact maps (or differences in contact maps)... is there anything else to get 
a decent view of these small changes?
Thanks a lot.





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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

[Robbie Joosten]

Make sure everything is built. Sometimes it is the crystallisation agents that 
sit at surprising places: 
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2923

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Murpholino Peligro
> Sent: Tuesday, April 9, 2024 03:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] How to compare the same protein crystallized in different
> conditions?
> 
> Hi...
> Let's say I want to compare the same protein crystallized in different
> conditions. Same space group, almost same resolution. The global RMSD will
> be pretty small (around 0.3 Angstroms). There will be some changes in
> rotamers in some residues and some extra waters here and there... Besides
> local rsmd and contact maps (or differences in contact maps)... is there
> anything else to get a decent view of these small changes?
> 
> 
> Thanks a lot.
> 
> 
> 
> 
> 
> 
> 
> 
> 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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[ccp4bb] How to compare the same protein crystallized in different conditions?

[Murpholino Peligro]

Hi...
Let's say I want to compare the same protein crystallized in different
conditions. Same space group, almost same resolution. The global RMSD will
be pretty small (around 0.3 Angstroms). There will be some changes in
rotamers in some residues and some extra waters here and there... Besides
local rsmd and contact maps (or differences in contact maps)... is there
anything else to get a decent view of these small changes?

Thanks a lot.



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