[Bioperl-l] Suggestion about Bio::Structure::SecStr::DSSP::Res

[Zhiqiang Ye]

hi, Torsten Seemann,

2006/3/6, Torsten Seemann <torsten.seemann at infotech.monash.edu.au>:
> The Bio::Structure::SecStr::DSSP::Res module is for reading and parsing
> a DSSP output file.
> It does not run dsspcmbi for you, therefore any "-ssa" option for the
> constructor of that module is not meaningful.

I know this. Sorry about my poor expression.
For example:   1crn.pdb, which contains the lines like this:

SSBOND   1 CYS      3    CYS     40                                     1CRN  60
SSBOND   2 CYS      4    CYS     32                                     1CRN  61
SSBOND   3 CYS     16    CYS     26                                     1CRN  62

run this:
dsspcmbi 1crn.pdb 1crn.dssp

then use this script:

my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>"/tmp/1crn.dssp");
print $dssp_obj->resAA(3);
print "\n";

The result is 'a', not 'C'  (You can see the pdb file, the 3rd residue is CYS)

btw: $dssp_obj->getSeq()   runs wrong, so does $dssp_obj->getSeq(' ')

If you remove the 3 lines of SSBOND from the pdb file, then run
dsspcmbi 1crn.pdb  1crn.dssp
$dssp_obj->resAA(3) is 'C'.

but if you run like this:  dsspcmbi -ssa 1crn.pdb 1crn.dssp.
$dssp_obj->resAA(3) is 'a' again.

That is to say,
1. if the pdb file has SSBOND definded explicitly, dsspcmbi will
change CYS's residue character from 'C' to 'a' 'b' or whatever
lowercase

2. if the pdb file don't have SSBOND definded explictly, dsspcmbi with
'-ssa' will calculate the ssbond it self and then chang CYS's residue
character from 'C' to 'a' 'b' or whatever lower case

3. if the pdb file don't have SSBOND definded explictly, and dsspcmbi
without '-ssa' will treat all CYS as 'C'.  No modification.

That's why I think this module would need some modification. :)


Best Regards,
--
Zhiqiang Ye