Hi All,
I’m preparing a structure for deposition on the PDB; everything is ready but I got a red alert in the Refinement statistic page.
The error is relative to refinement of Shell 8 and it says “Resolution is lower than overall refined resolution”. This values are respectively 45.53 and 45.51 A for Shell 8 and the overall structure (you can find a screen attached for ease).
I checked both on PHENIX refinement page and into the PDB file and those values still differ.
I also checked the 1st round of refinement to see if they were changed somehow throughout the whole refinement procedure but they were not, and PHENIX never gave any alert about that.
Since the extremely tiny difference in the actual numbers, I’m supposing it’s a noise (or rounding) related thing due to the low resolution they represent maybe?
I already contacted the PDB and I got this answer:
“Thank you for your message. Though the difference in values are small, your refinement shells should not extend beyond your overall refinement range. You may wish to check your refinement details and determine which is correct and adjust those values accordingly. It may be an underlying rounding error somewhere in the process - as long as the values are consistent with each other, this level of discrepancy should not make much difference.”
I also made a couple of trials doing refinements but this time setting the low resolution limit myself:
- Low resolution limit set to 45.53 instead of the automatic one 45.51 A: problem remained the same.
- Low resolution limit set to 45.48 A: Overall low resolution limit is 44.777 and for shell 8 becomes 44.7951 A, so different numbers but still same problem.
I’m unsure of what to do as I don’t know which value is actually the correct one, would anyone have any suggestion?
Alternatively, would there be a tweak I could make to the options of final refinement to adjust these value so not to have such a error during the deposition?
How do I get help during and after deposition?
If you have any questions about deposition, you can log in to your deposition session and use the Communication page to communicate with wwPDB annotation staff. The Communication page is available toward the bottom of the left menu in the Deposition Tool.
Hi Alessandro,
I do not know if you already solved your problem.
But I have some suggestion for this case and your future depositions.
The problem is how different program packages deal with unit cell parameters and low or high resolution limits. To avoid this problem I do one extra step during conversion of my data from *.sca format to *.mtz format.
I am using ccp4 package. So, after converting *.sca into *.mtz (Import Merged Data) I am using Sftools and delete reflections based on resolution Low limit and high resolution. I had several cases when data processed with low resolution 30.00 after conversion got 52.33 or other random numbers. And the same with the high resolution, processed to 1.5Å data after conversion got 1.498Å resolution. This extra step prevents all possible problems with data resolution limits between processed data (*.sca) and converted data (*.mtz).
Hope this helps.
George.
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