Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[Harry Powell]

Apropos Phil’s last point - 

> 
> 4.  On the model front, go find an AlphaFold model, they have worked for me 
> multiple times in molecular replacement so far.

If there is no extant Alphafold model, it may be worthwhile creating your own 
via colabfold (duckduckgo it like I did…). Only takes a short time...

best wishes

Harry

> On 2 Aug 2023, at 20:20, Phil Jeffrey  wrote:
> 
> 1.  Completeness is primarily an issue with using the right point group and 
> crystal system, not the actual space group (e.g. in primitive point group mmm 
> the space groups P222, P2221, P21212, P212121 should all have essentially the 
> same completeness).
> 2.  If "refinalize" in CrysAlisPro doesn't let you choose the right point 
> group and system, then you should process the data with another program.  
> XDS, MOSFLM, DIALS, autoPROC etc might work, and I have to believe they'd be 
> better at scaling your data.
> 3.  If you can export the unscaled data from CrysAlisPro you might be able to 
> feed it into POINTLESS and AIMLESS for scaling
> 
> 4.  On the model front, go find an AlphaFold model, they have worked for me 
> multiple times in molecular replacement so far.
> 
> Phil Jeffrey
> Princeton
> 
> 
> 
> On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote:
>> Hello,
>> So I'm trying to get the data processed that I gathered from XRD for the 
>> protein BsAlaDH. Unfortunately from the method that I know of on CrysAlisPro 
>> I cannot select the recommended space group for the protein. This results in 
>> the data not being complete. Still I can get good unit cells and the 
>> degrees. Another problem is that this protein has no structure published on 
>> PDB. And the homolog proteins do not have high similarities. By that way I 
>> cannot really find a suitable space group. Can someone give me a hand on 
>> this issue.
>> Thank you.
>> 
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> 
> 
> 
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Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[Phil Jeffrey]

1.  Completeness is primarily an issue with using the right point group 
and crystal system, not the actual space group (e.g. in primitive point 
group mmm the space groups P222, P2221, P21212, P212121 should all have 
essentially the same completeness).
2.  If "refinalize" in CrysAlisPro doesn't let you choose the right 
point group and system, then you should process the data with another 
program.  XDS, MOSFLM, DIALS, autoPROC etc might work, and I have to 
believe they'd be better at scaling your data.
3.  If you can export the unscaled data from CrysAlisPro you might be 
able to feed it into POINTLESS and AIMLESS for scaling


4.  On the model front, go find an AlphaFold model, they have worked for 
me multiple times in molecular replacement so far.


Phil Jeffrey
Princeton



On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote:

Hello,
So I'm trying to get the data processed that I gathered from XRD for the 
protein BsAlaDH. Unfortunately from the method that I know of on 
CrysAlisPro I cannot select the recommended space group for the protein. 
This results in the data not being complete. Still I can get good unit 
cells and the degrees. Another problem is that this protein has no 
structure published on PDB. And the homolog proteins do not have high 
similarities. By that way I cannot really find a suitable space group. 
Can someone give me a hand on this issue.

Thank you.




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[ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[CENGIZ KAAN FERAH]

Hello,
So I'm trying to get the data processed that I gathered from XRD for the
protein BsAlaDH. Unfortunately from the method that I know of on
CrysAlisPro I cannot select the recommended space group for the protein.
This results in the data not being complete. Still I can get good unit
cells and the degrees. Another problem is that this protein has no
structure published on PDB. And the homolog proteins do not have high
similarities. By that way I cannot really find a suitable space group. Can
someone give me a hand on this issue.
Thank you.



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