VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Wed Apr 29 2020 - 10:15:45 CDT

I found something different.

Upon further investigation, it turns out that on my computer with
spaces, VMD/STRIDE (I'm not sure which program) is using a DOS short
name for the folder to remove the spaces. The first 6 letters plus ~1,
like Mortimer Hemmit -> MORTIM~1.

When I intentionally create an error, I get

ERROR) Unable to find Stride output file: C:\Users\MORTIM~1\AppData\Local\Temp\3
ERROR) Stride::read_stride_record: unable to read output file from Stride
ERROR) Call to Stride program failed.

Your error message doesn't use this short name.

Mortimer

On Wed, Apr 29, 2020 at 10:42 AM Mortimer Hemmit
<mortimer.hemmit_at_gmail.com> wrote:
>
> 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/
> >