VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 06 2019 - 22:45:26 CDT

Hi,
  While not an ideal solution in all cases, we have added support for
DSSP variants (e.g. "xdssp" and others with compatible behavior) in
the new developmental versions of VMD. This will become available in
an upcoming test version of VMD in the next couple of weeks, but it's in the
main source code already for those that are curious. Support for DSSP should
soften the blow in cases when STRIDE fails. Going further, we are working
on our own secondary structure determination code for VMD, which while a
long ways off yet, will hopefully solve these kinds of issues
more permanently.

Best,
  John

On Thu, Jun 06, 2019 at 10:33:14PM +0000, Vermaas, Joshua wrote:
> Hi Elizabeth,
>
> Stride is can be fragile, and can give no output on some input structures.
> What I think is going on is that when you did this originally, you loaded
> the pdb, changed your representations (this is when Stride would have been
> called), and *then* loaded the trajectory file. In a visualization state,
> by default all the molecular loading file commands happen first, and then
> the representations are processed second, when stride is called on the
> active frame (usually the last one when loading from a visualization
> state). In this last frame configuration, Stride is apparently bailing
> out, resulting in no secondary structure information being read into VMD
> and the cartoon representation turns into spagetti. What I would try is to
> add these two lines to the end of your visualization state:
>
> animate goto 0
> mol ssrecalc top
>
> The first line changes the active frame to the first one rather than the
> last, and then recalculates the secondary structure at that point, where
> Stride is known to work.
>
> -Josh
>
>
>
>
> On 2019-06-06 15:37:05-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hello, VMD users.
>
> I am somewhat new to VMD (3 weeks). I have a trajectory of 5013 frames
> which I am viewing on an Ubuntu computer.
> When I load the trajectory (xtc) into the molecule, which I load with a
> pdb, I can play the trajectory and everything works fine.
> If I save the visualization state and open it again later, secondary
> structure is not recognized. In New Cartoon, the protein looks like gray
> spaghetti. All of my representations load fine, but even sequence viewer
> does not show any secondary structure.
>
> This is the error I receive:
>
> ERROR) Unable to find Stride output file: /tmp/fileYel4Lr
> ERROR) Stride::read_stride_record: unable to read output file from
> Stride
> ERROR) Call to Stride program failed.
>
> I have made sure that Stride exists and the right path is in my bashrc.
>
> I can open visualization states with my pdb, or pdbs and smaller
> trajectories (such as the files from the tutorial) and secondary
> structure is recognized properly.
>
> I have told vmd to write stride SS files to ~/.vmdtmp/ rather than /tmp
> which should help if the issue is having sufficient memory.
>
> Unfortunately, none of this helped. I have reduced my trajectory and pdb
> to only protein, GTP, and Mg and that works fine, but in some cases I
> may need to consider interactions with solvent and membrane. Would
> anyone be so kind as to offer any suggestions of what I can do?
>
> Thank you,
> Elizabeth
>
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/