VMD-L Mailing List

From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Fri Feb 13 2015 - 09:17:54 CST

Dear Stefan,

Thank you for informing the VMD community of this issue. For those of us working with small proteins, would a temporary fix be to remove the translational motion (using an r.m.s alignment, for example) before calling STRIDE?

Thank you,

Brittany

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Stefan Doerr [stefdoerr_at_gmail.com]
Sent: Monday, February 09, 2015 11:53 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: VMD secondary structure Stride bug

Hi all. I sent this message to vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu> but since I didn't receive a response I am posting it here.
There is a bug in the secondary structure calculation in VMD. Stride is not designed for use on MD coordinates (or really large proteins) which can reach high positive or negative coordinate values.
The reason is that by default it reads PDB files which have a limited number of columns for the coordinates.

Even better, in a nice example of bad coding, in p_atom.c it replaces the first value of the coordinate fields with empty char, making coordinates under -99.999 A, like -100.000 look positive, just so that it can split the coordinate string on whitespace.

    strcpy(Tmp,Buffer);
    Buffer[38] = ' ';
    SplitString(Tmp+30,Field,1);
    r->Coord[NA][0] = atof(Field[0]);

    strcpy(Tmp,Buffer);
    Buffer[46] = ' ';
    SplitString(Tmp+38,Field,1);
    r->Coord[NA][1] = atof(Field[0]);

    strcpy(Tmp,Buffer);
    Buffer[54] = ' ';
    SplitString(Tmp+46,Field,1);
    r->Coord[NA][2] = atof(Field[0]);

This leads to wrong secondary structure in all molecules which move more than 100A from the origin. I saw that VMD is writing the coordinates out for each frame into a PDB and feeding it to STRIDE. So the problem definitely exists in VMD and I've seen it happen in various cases.

I have made my own version of Stride which can be compiled into a C project like VMD, which accepts atom coordinates directly in a C matrix instead of reading them from a PDB to avoid truncations and also fixes multiple memory leaks in the code. I could provide you the code, however it would require a bit of work to make it work in VMD since I only implemented it for a single chain and I haven't looked up how to access all the atom information it needs from the VMD source code.

Best greetings,
Stefan