On Wed, Jul 27, 2011, Anjan Dwaraknath wrote:
>
> 1) I want to know what are the right parameters to use in wc_helix to get
> A-RNA structure
Sorry: I don't know the answer here.
>
> 2) When I use the wc_helix function for RNA,
> I am not getting the right basepairs in the output PDB file.
This is a long-standing bug in the wc_helix code; I guess no one had tried
this with RNA. Here is a patch, which is probably easiest to just apply by
hand:
--- wc_helix.nab.orig
+++ wc_helix.nab
.. -55,7 +55,7 .. molecule wc_helix(
else sres = getresidue( srname, sreslib_use );
setreslibkind( areslib_use, anatype );
- arname = loup[ substr( seq, 1, 1 ) ];
+ arname = loup[ substr( aseq, 1, 1 ) ];
if( anatype == "dna") arname = "D" + loup[ substr( aseq, 1, 1 ) ];
if( opts =~ "a3" )
ares = getresidue( arname + "3", areslib_use );
.. -77,7 +77,7 .. molecule wc_helix(
if( snatype == "dna" ) srname = "D" + loup[ substr( seq, i, 1
)
setreslibkind( sreslib_use, snatype );
sres = getresidue( srname, sreslib_use );
- arname = loup[ substr( seq, i, 1 ) ];
+ arname = loup[ substr( aseq, i, 1 ) ];
if( anatype == "dna" ) arname = "D" + loup[ substr( aseq, i, 1
)
setreslibkind( areslib_use, anatype );
ares = getresidue( arname, areslib_use );
.. -112,7 +112,7 .. molecule wc_helix(
sres = getresidue( srname + "3", sreslib_use );
else
sres = getresidue( srname, sreslib_use );
- arname = loup[ substr( seq, i, 1 ) ];
+ arname = loup[ substr( aseq, i, 1 ) ];
if( anatype == "dna" ) arname = "D" + loup[ substr( aseq, i, 1
)
setreslibkind( areslib_use, anatype );
if( opts =~ "a5" )
Thanks for the report.
....dac
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Received on Fri Jul 29 2011 - 08:00:03 PDT
