From: Elizabeth Wait (elizabethewait_at_gmail.com)
Date: Tue Jun 11 2019 - 11:16:04 CDT

Hi,

Thank you for the suggestion, Josh. Unfortunately it did not work for me.
Thank you, John, I will use that when it becomes more available. I have a
workaround in the meantime.
I greatly appreciate you both taking the time to help me.

Best regards,
Elizabeth

On Thu, Jun 6, 2019 at 9:45 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>