VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2012 - 13:12:45 CDT

Hi,
  The STRIDE paper and program documentation outline the cases it handles:
  http://webclu.bio.wzw.tum.de/stride/stride.pdf
  http://webclu.bio.wzw.tum.de/stride/stride.doc
    
There are eight secondary structure codes returned by STRIDE
(one being empty, implying coil), and those are directly assigned
by the VMD STRIDE interface as shown below. You can see that VMD
assigns both the "b" and "B" bridge codes as one, but there is only
a single STRIDE code for turns:
    if (stype == NULL) {
      mol->residueList[uniq_resid]->sstruct = SS_COIL;
      continue;
    }
    switch ((int)(stype - sstypes_start)) {
      case 0: // H
        mol->residueList[uniq_resid]->sstruct = SS_HELIX_ALPHA;
        break;
      case 1: // G
        mol->residueList[uniq_resid]->sstruct = SS_HELIX_3_10;
        break;
      case 2: // I
        mol->residueList[uniq_resid]->sstruct = SS_HELIX_PI;
        break;
      case 3: // E
        mol->residueList[uniq_resid]->sstruct = SS_BETA;
        break;
      case 4: // B
      case 5: // b
        mol->residueList[uniq_resid]->sstruct = SS_BRIDGE;
        break;
      case 6: // T
        mol->residueList[uniq_resid]->sstruct = SS_TURN;
        break;

If you are curious, the complete STRIDE interface in VMD is shown here:
  http://www.ks.uiuc.edu/Research/vmd/doxygen/Stride_8C-source.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 17, 2012 at 12:33:52PM +0530, Neelanjana Sengupta wrote:
> Dear VMD experts,
>
> It appears that Stride as implemented in VMD cannot distinguish between
> type-I (alpha) and type-II (beta) turns. They both are clubbed as "turns".
> Can someone please confirm if this is correct?
>
> Thanks,
> Neelanjana 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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