VMD-L Mailing List

From: mfeiglab_at_gmail.com
Date: Wed Apr 29 2020 - 10:45:52 CDT

I can confirm that changing the variables TMP and TEMP fixes the problem!

One has to be careful though to find a location that is outside the user directory but still user writable.

Thank you everybody!

-----Original Message-----
From: Mortimer Hemmit <mortimer.hemmit_at_gmail.com>
Sent: Wednesday, April 29, 2020 11:34 AM
To: mfeiglab_at_gmail.com
Cc: John Stone <johns_at_ks.uiuc.edu>; VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: STRIDE issues on Windows

In terms of the workaround for setting your temp:

Temporary workaround;

Each time, before you open VMD:

Open a command prompt window. Type
set TMP=[the folder you want temp to be] set TEMP=[the folder you want temp to be]

Now spawn VMD from within that command prompt. Type [path to wherever VMD is located, probably "C:\Program Files (x86)\University of Illinois\VMD\vmd.exe"]

Now you should be able to do your stuff.

More permanent workaround (Note: be careful with this):

Go Control Panel -> System and Security -> System In the sidebar on the left, click on "Advanced System Settings", then "Environment Variables" on the bottom.
Edit TMP and TEMP there.

Hope this helps,
Mortimer

On Wed, Apr 29, 2020 at 11:15 AM Mortimer Hemmit <mortimer.hemmit_at_gmail.com> wrote:
>
> 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/
> > >