VMD-L Mailing List

From: mfeiglab_at_gmail.com
Date: Wed Apr 29 2020 - 10:08:18 CDT

Thanks, Mortimer.

All is fine on my Linux workstation at work but this (new) Windows 10 laptop could never show Cartoon representations due to failing STRIDE no matter what PDB I look at.

Things also worked fine on an older laptop where I had a user name without a space and the error message from STRIDE makes sense if there is a space character that is not quoted properly. There was a discussion about this some time ago with one solution being a change of the user name and - more importantly - the user directory name, but that is not quite as straightforward as it seems.

It didn't bother me as much before but now this laptop is all I have to work on things while staying home.

I don't think it has to do with missing hydrogens in my case as the PDB files have hydrogens, they are well-behaved proteins, and I look at those and similar files all the time, except on Linux.

But I would be curious to find out what else may be different in your setup.
So far I have not yet succeeded in getting windows to use a different TEMP directory.

-----Original Message-----
From: Mortimer Hemmit <mortimer.hemmit_at_gmail.com>
Sent: Wednesday, April 29, 2020 10:43 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

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/
>