VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Wed Apr 29 2020 - 09:42:43 CDT

Hi there,

I have a Windows 10 machine that has a space in its username. Stride
runs fine there.
I've seen that error message before where the file just has no hydrogen bonds.

Mortimer

On Wed, Apr 29, 2020 at 10:39 AM <mfeiglab_at_gmail.com> wrote:
>
> Thank you John. I will see how to change the Windows TMP/TEMP environment
> variable.
>
> The output in the VMD console looks like this:
> ----------------------------------------------------------------------------
> ---------------------
> Only one input file is allowed
>
> Action: secondary structure assignment
> Usage: stride [Options] InputFile [ > file ]
> Options:
> -fFile Output file
> -mFile MolScript file
> -o Report secondary structure summary Only
> -h Report Hydrogen bonds
> -rId1Id2.. Read only chains Id1, Id2 ...
> -cId1Id2.. Process only Chains Id1, Id2 ...
> -q[File] Generate SeQuence file in FASTA format and die
>
> Options are position and case insensitive
> ERROR) Unable to find Stride output file: C:\Users\Michael
> Feig\AppData\Local\Temp\3
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
> ----------------------------------------------------------------------------
> ---------------------
> The input file is from a location without space, i.e.
> C:\cygwin64\home\meikelf\C1906_j.pdb
> And I think the error message is slightly different when the input file also
> has a space.
>
> Thank you.
>
> Michael.
>
> -----Original Message-----
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Wednesday, April 29, 2020 2:16 AM
> To: mfeiglab_at_gmail.com
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: STRIDE issues on Windows
>
> Can you send the VMD console error messages you see when it tries (and
> fails) to run STRIDE on your machine?
>
> VMD calls the tempnam() system call to generate legal temporary files for
> input/output. Assuming those are not wrong in some surprising way, this
> should hopefully be a relatively simple thing to track down and fix with
> additional quotation marks around filename strings sent into the system()
> call that actually launches STRIDE.
>
> Best,
> John
>
> On Mon, Apr 27, 2020 at 01:51:01PM -0400, mfeiglab_at_gmail.com wrote:
> > Based on previous posts there is a reasonably well documented issue
> with
> > VMD not able to
> >
> > run STRIDE on Windows 10 (probably older versions as well) when a file
> > name/directory
> >
> > contains a space.
> >
> >
> >
> > In particular, the issue comes up when the Windows user name (and
> > therefore the home
> >
> > directory) contains a space.
> >
> >
> >
> > There are ways to read input PDB files from locations where there is no
> > space in the file name,
> >
> > but it seems impossible to get around the name of the Temp directory as
> it
> > resides within
> >
> > the User home directory (C:\Users\...\AppData\Local\Temp\ ...).
> >
> >
> >
> > I tried to change the location of the temporary directory but so far no
> > success. Perhaps the VMD
> >
> > variables are not effective and STRIDE gets the location from Windows
> > instead.
> >
> >
> >
> > One obvious solution is to change the Windows user name (and user
> > directory) but there seems to be
> >
> > a high chance of breaking other things, especially with other installed
> > programs and I am not quite
> >
> > ready yet to go down this road.
> >
> >
> >
> > Any other ideas for how to get around this?
> >
> >
> >
> > The system is Windows 10, VMD 1.9.3.
> >
> >
>
> --
> 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/
>