Re: [ccp4bb] Wavelength mismatch during PDB deposition

[Santhosh G]

Dear Robbie,

Thank you for the prompt response.

I have verified my PDB file for remark 200 and 3, but I couldn't find the 
wavelength information.

For refinement REFMAC 5.8.0230 was used from CCP4i.

I have tried to convert it into mmCIF using AIMLESS and MOLREP log with 
PDB_extract. Then I have gone through the CIF file, but no wavelength 
information was not observed in the file.



Santhosh



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

Re: [ccp4bb] Wavelength mismatch during PDB deposition

[Robbie Joosten]

Hi Santhosh,

The seems to be the result of a rounded value in the SF file and a truncated 
value in the PDB.  I suppose that the PDB file you are depositing actually does 
have the wavelength (it lives in REMARK 200, but depending on which refinement 
program you used it may also be in REMARK 3, just look in the PDB file for the 
number. You can edit it before resubmitting your PDB file.

Actually, I always run pdb_extract to my final PDB file to add log information 
from data processing and structure solution and then write out the lot in 
mmCIF. The deposition process seems to run much smoother when you upload an 
mmCIF file.

Cheers,
Robbie

 

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Santhosh G
> Sent: Friday, July 13, 2018 09:44
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Wavelength mismatch during PDB deposition
> 
> Dear all,
> 
> I got an issue after submitting my structure to PDB.
> 
> The exact message is as follows...
> 
> 1. Wavelength mismatch (pdb= 0.9794 : sf= 0.9795)!
> 
> Please provide the correct wavelength value used for the structure
> determination.
> 
> The data I have collected at the synchrotron with wavelength-0.97947.
> 
> How PDB extracts wavelength from PDB file, which I have not provided
> during the submission.
> 
> Even though it calculates wavelength, what are situations that lead to the
> discrepancy.
> 
> Please give suggestions.
> 
> 
> Thanks and regards,
> Santhosh
> 
> ##
> ##
> 
> 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

[ccp4bb] Wavelength mismatch during PDB deposition

[Santhosh G]

Dear all,

I got an issue after submitting my structure to PDB. 

The exact message is as follows...

1. Wavelength mismatch (pdb= 0.9794 : sf= 0.9795)!

Please provide the correct wavelength value used for the structure 
determination.

The data I have collected at the synchrotron with wavelength-0.97947.

How PDB extracts wavelength from PDB file, which I have not provided during the 
submission.

Even though it calculates wavelength, what are situations that lead to the 
discrepancy.

Please give suggestions.


Thanks and regards,
Santhosh



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