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Good afternoon, Dr. Lu
I've noticed an issue with long chain identifiers in the section with dot-brackets.
Example:
Entry - 1VY6
fragment from DSSR output header:
no. of DNA/RNA chains: 12 [AA=1498,AV=13,AW=2,AX=76,BA=2819,BB=120,CA=1503,CV=12,CW=2,CX=76,DA=2800,DB=120]fragments from dbn section:
>1vy6-1-A #1 nts=1498 [chain] RNA*
>1vy6-1-A #2 nts=13 [chain] RNA
>1vy6-1-A #3 nts=2 [chain] RNA
>1vy6-1-A #4 nts=76 [chain] RNA
>1vy6-1-B #5 nts=2819 [chain] RNA*
>1vy6-1-B #6 nts=120 [chain] RNA
>1vy6-1-C #7 nts=1503 [chain] RNA*
>1vy6-1-C #8 nts=12 [chain] RNA
>1vy6-1-C #9 nts=2 [chain] RNA
>1vy6-1-C #10 nts=76 [chain] RNA
>1vy6-1-D #11 nts=2800 [chain] RNA*
>1vy6-1-D #12 nts=120 [chain] RNA
I cannot recover one-to-one correspondence from these lines. I mean, of course in the given case i am able to find correspondence not from identifiers but from lengths, but this is just a lucky example.
Could you fix this, please?
Best regards,
Eugene
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Hi Eugene,
Thanks for reporting this inconsistency in dbn output with chain names longer than 1-char. The current setting reports only the first letter, which can cause problems, as you see here.
Would changing the current
>1vy6-1-A #1 nts=1498 [chain] RNA*
>1vy6-1-A #2 nts=13 [chain] RNA
>1vy6-1-A #3 nts=2 [chain] RNA
>1vy6-1-A #4 nts=76 [chain] RNA
to
>1vy6-1-AA #1 nts=1498 [chain] RNA*
>1vy6-1-AV #2 nts=13 [chain] RNA
>1vy6-1-AW #3 nts=2 [chain] RNA
>1vy6-1-AX #4 nts=76 [chain] RNA
fits the bill? Please confirm.
I will release an updated DSSR soon.
Xiang-Jun
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Hi Eugene,
DSSR has been updated to v1.4.9-2016jan25 which should have fixed the inconsistency in chain names for the dbn section, as tested on 1vy6 (http://www.rcsb.org/pdb/explore/explore.do?structureId=1vy6).
Please check the new DSSR release (still shown as v1.4.8-2016jan16 on the download page -- I'll update the release note later). Please report back how it goes.
Best regards,
Xiang-Jun
Xiang-Jun
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Good afternoon, Dr. Lu
Sorry for late reply.
This fix should be great.
Just in case:
In pdb entries I saw chain identifiers up to 4 chars (I do not know if it can be longer or not, but 4 is the largest I have seen).
Does the last update of DSSR take it into consideration?
Best regards,
Eugene
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Hi Eugene,
Yes, 4-char chain names should have been taken care of by DSSR. As far as I know, in mmCIF formatted structures, chain names can have up to 4 characters.
Please do not hesitate to report back any bug/inconveniency you may find in DSSR.
Best regards,
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University