Residual B values after refinement
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
Hi Anan, could you please send me files relevant to the refinement run that resulting in PDB file in question? Specifically: - input/output models; - log file; - *.eff file. Thanks, Pavel On 2/6/18 05:26, 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.
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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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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participants (3)
-
ANAN YUENYAO -
Edward A. Berry -
Pavel Afonine