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Comments (6)

cbaakman avatar cbaakman commented on August 25, 2024

What's the output of your compiled mkdssp, when used on a mmCIF file?

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touwwouter avatar touwwouter commented on August 25, 2024

On cmbi23

$ mkdssp /mnt/cmbi4/mmCIF/1crn.cif.gz
DSSP could not be created due to an error:
empty protein, or no valid complete residues

On cmbi4, using the exact same file:

$ mkdssp /data/mmCIF/1crn.cif.gz
==== Secondary Structure Definition by the program DSSP, CMBI version by M.L. Hekkelman/2010-10-21 ==== DATE=2014-10-02        .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
HEADER    PLANT SEED PROTEIN, PLANT PROTEIN       1981-07-28 1CRN                                                              .
COMPND    CRAMBIN                                                                                                              .
SOURCE    Crambe hispanica subsp. abyssinica                                                                                   .
AUTHOR    Hendrickson, W.A.; Teeter, M.M.                                                                                      .
   46  1  3  3  0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
  3007.3   ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)                                                                         .
   27 58.7   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS IN     PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
    3  6.5   TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES                              .
...

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touwwouter avatar touwwouter commented on August 25, 2024

This seems to work for an unzipped file, but not for a gzipped-file...

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cbaakman avatar cbaakman commented on August 25, 2024

2.2.3 works on cmbi4 and my local machine. This problem could be compiler-related.

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cbaakman avatar cbaakman commented on August 25, 2024

Defining USE_COMPRESSION in structure.h fixes the problem. Now we have to find out why USE_COMPRESSION isn't defined automatically on cmbi23.

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touwwouter avatar touwwouter commented on August 25, 2024

No, a compiler flag should be used instead. Closing this issue, discuss further at #39

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