[phenixbb] Residual B values after refinement

[Pavel Afonine]

Hi All,

Anan sent me files off list and they look fine. So I conclude it is 
likely a glitch in PDB validation.
If you can then just ignore it. If it becomes a roadblock then I 
recommend getting in touch with PDB staff and report the issue. As far 
as I know most programs these days output total ADPs (unless instructed 
otherwise).

Pavel

On 2/6/18 16:20, Edward A. Berry wrote:
> I get the same "error" during validation of a TLS-refined structure, 
> and again during the deposition, however it doesn't seem to interfere 
> with the deposition. I haven't actually pushed the SUBMIT button yet 
> (I'm waiting to submit several at the same time to get consecutive 
> ID's), but all the sections have been completed and show green in the 
> list.  If the annotator brings this up, or if the processed entry 
> contains warnings about this, I shall cite Pavel's response that the 
> atomic B's include the isotropic component of the anisou's.
> The message comes in a list of 4 possible problems with the 
> coordinates, and it is not clear if they are stating that this is a 
> problem or warning that it could be. In the latter case it may be 
> directed more at Refmac5 users, for whom I believe an extra step to 
> recombine the ADP's is required. But the residual B's line is 
> highlighted in red, suggesting it thinks this is the problem.
> The validation came up with R and R-free about .02 higher than 
> phenix.refine reported. If this is because it assumes the B's are 
> residual and adds the ANISOU component again in calculating Fc, and if 
> the difference disappears when this is cleared up, that would be nice!
> Ed
>
> On 02/06/2018 08:26 AM, ANAN YUENYAO wrote:
>> Dear All,
>>
>> I have encountered some error during the PDB validation process after 
>> refinement with PHENIX (1.13). After uploading the coordinates and 
>> structure factor file, in the header 'Basic coordinate validity', it 
>> says that the data contains residual B values. Could anyone please 
>> explain the reason behind this error message. Is it going to be 
>> problematic for the future PDB deposition?
>> P.S. I have already performed TLS and group B-factor refinement.
>>
>> Thank you in advance!
>>
>> Anan
>>
>>
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