VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu May 07 2015 - 22:50:35 CDT

Thanks for the reply.

It says:
ERROR) Unable to find Stride output file:
C:\Users\CCHAN2~1\AppData\Local\Temp\3

ERROR) Stride::read_stride_record: unable to read output file from Stride
ERROR) Call to Stride program failed.

And it gives me a pop-out window saying stride_WIN32.exe has stopped
working.

Regards,
Kevin

On Fri, May 8, 2015 at 11:37 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> STRIDE is picky about atom naming, it may also be caused by atom names
> it doesn't like, or some similar issue. What output does STRIDE emit in
> the VMD console when it runs?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, May 08, 2015 at 10:53:44AM +0800, Kevin C Chan wrote:
> > Sorry guys for interrupt this closed thread.Ā
> > But I am getting the same problem - all Cyan for SS colouring and
> Tube for
> > New Cartoon. So does it mean adding memory can solve the colouring
> problem
> > but not the Tube problem? How can I solve that then?
> > Any help will be appreciated.Ā
> >
> > Regards,
> > Kevin
> > On 7 May, 2015, at 20:48, Matic Kisovec <[1]Matic.Kisovec_at_ki.si>
> wrote:
> >
> > Dear Stefan,
> > Fortunately in my case I get the expected representation, for
> example
> > 'NewCartoon'.
> >
> > Thank you for the information anyway!
> >
> > Best regards,
> > Matic
> >
> > On 07. 05. 2015 11:34, Stefan Doerr wrote:
> >
> > Also if you are still getting tube representation it might be a
> known
> > bug in STRIDE where if your protein moves too far from the origin
> it
> > messes up the SS prediction.
> > On Thu, May 7, 2015 at 7:41 AM, Matic Kisovec <[2]
> Matic.Kisovec_at_ki.si>
> > wrote:
> >
> > Dear Daniel,
> >
> > thank you for your suggestion. I added some RAM and now I don't
> get
> > the STRIDE error anymore.
> > I still get that strange (to me at least) set of numbers
> mentioned
> > in the first mail but that doesn't seem to cause any problems. I
> > just don't remember seeing them but perhaps they are even a
> part of
> > normal output.
> >
> > Thank you for your time and have a nice day,
> > Matic Kisovec
> >
> > On 06. 05. 2015 20:13, Daniel Mƶller wrote:
> >
> > Hi,
> >
> > Ā
> >
> > Iā**ve seen this output before and itā**s caused by to less
> > memory. For stride you need at least as much free memory as
> your
> > current VMD with the loaded structure. I think, itā**s because
> > stride is an external programme which is called by VMD with
> exec
> > and this results in a fork. So stride doesnā**t have enough
> memory
> > and crash.
> >
> > Ā
> >
> > Ā
> >
> > Sincerely
> >
> > Ā
> >
> > Daniel Mƶller
> >
> > Ā
> >
> > Ā
> >
> > Ā
> >
> > Von: [3]owner-vmd-l_at_ks.uiuc.edu
> > [[4]mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Matic
> Kisovec
> > Gesendet: Mittwoch, 6. Mai 2015 13:29
> > An: [5]vmd-l_at_ks.uiuc.edu
> > Betreff: vmd-l: Problem with assignation of secondary
> structure in
> > VMD
> >
> > Ā
> >
> > Dear all,
> >
> > I encounter an issue when I open and GROMACS trajectory (.gro
> +
> > .xtc) and then try to colour aminoacid residues by secondary
> > structure. Output is pasted below.
> > The trajectory loads just fine but there is a strange output
> right
> > after the loading finishes (the numbers). Then when I select
> the
> > option to colour the molecule by secondary structure I get the
> > three ERROR lines. The entire structure changes colour to
> light
> > grey and if I select 'NewCarton' representation there is no
> > secondary elements (just a 'tube').
> >
> > I can reproduce this with two of my trajectory files but not
> > others that I tried so far. I suppose it could be an issue
> with my
> > files. The other thing is that the trajectory is quite long
> (43
> > 000 frames).
> >
> > Has anybody else had similar issues? Any idea on how to fix
> this
> > so I can get the SS properly coloured?
> >
> > Thank you all and kind regards,
> > Matic
> >
> > Info) Using plugin xtc for coordinates from file xyz.xtc
> > Info) Coordinate I/O rate 1328.7 frames/sec, 115 MB/sec, 32.2
> sec
> > Info) Finished with coordinate file xyz.xtc.
> > 1
> > {{1 0 0 -113.603} {0 1 0 -113.64} {0 0 1 -53.5547} {0 0 0 1}}
> {{1
> > 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.012288 0 0 0} {0
> > 0.012288 0 0} {0 0 0.012288 0} {0 0 0 1}} {{1 0 0 0} {0 1 0
> 0} {0
> > 0 1 0} {0 0 0 1}}
> > 0 1
> > 1
> > Info) In any publication of scientific results based in part
> or
> > Info) completely on the use of the program STRIDE, please
> > reference:
> > Info)Ā Frishman,D & Argos,P. (1995) Knowledge-based secondary
> > structure
> > Info)Ā assignment. Proteins: structure, function and
> genetics,
> > 23, 566-579.
> > ERROR) Unable to find Stride output file: /tmp/filegxwJFP
> > ERROR) Stride::read_stride_record: unable to read output file
> from
> > Stride
> > ERROR) Call to Stride program failed.
> >
> > <matic_kisovec.vcf>
> >
> > References
> >
> > Visible links
> > 1. javascript:_e(%7B%7D,'cvml','Matic.Kisovec_at_ki.si');
> > 2. javascript:_e(%7B%7D,'cvml','Matic.Kisovec_at_ki.si');
> > 3. javascript:_e(%7B%7D,'cvml','owner-vmd-l_at_ks.uiuc.edu');
> > 4. javascript:_e(%7B%7D,'cvml','owner-vmd-l_at_ks.uiuc.edu');
> > 5. javascript:_e(%7B%7D,'cvml','vmd-l_at_ks.uiuc.edu');
>
> --
> 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/
>