[phenixbb] Residual B values after refinement
pafonine at lbl.gov
Wed Feb 7 07:46:21 PST 2018
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
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!
> 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!
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