VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 08 2015 - 00:09:44 CDT

The pop-up window indicating the STRIDE stopped means that it crashed
for some reason, and this is why VMD isn't getting output from it.
I don't have a particular suggestion for you at this moment, but it might
be useful for me to know more details about your structure such as how large
it is, etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 08, 2015 at 11:50:35AM +0800, Kevin C Chan wrote:
> 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 <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â 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,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Fri, May 08, 2015 at 10:53:44AM +0800, Kevin C Chan wrote:
> >Â Â Sorry guys for interrupt this closed thread.Ä*
> >Â Â But I am getting the same problem - all Cyan for SS colouring and
> Tube for
> >Â Â New Cartoon. So does it mean adding memory can solve the
> colouring problem
> >Â Â but not the Tube problem? How can I solve that then?
> >Â Â Any help will be appreciated.Ä*
> >
> >Â Â Regards,
> >Â Â Kevin
> >Â Â On 7 May, 2015, at 20:48, Matic Kisovec
> <[1][3]Matic.Kisovec_at_ki.si> wrote:
> >
> >Â Â Â Dear Stefan,
> >Â Â Â Fortunately in my case I get the expected representation, for
> example
> >Â Â Â 'NewCartoon'.
> >
> >Â Â Â Thank you for the information anyway!
> >
> >Â Â Â Best regards,
> >Â Â Â Matic
> >
> >Â Â Â On 07. 05. 2015 11:34, Stefan Doerr wrote:
> >
> >Â Â Â Â Also if you are still getting tube representation it might
> be a known
> >Â Â Â Â bug in STRIDE where if your protein moves too far from the
> origin it
> >Â Â Â Â messes up the SS prediction.
> >Â Â Â Â On Thu, May 7, 2015 at 7:41 AM, Matic Kisovec
> <[2][4]Matic.Kisovec_at_ki.si>
> >Â Â Â Â wrote:
> >
> >Â Â Â Â Â Dear Daniel,
> >
> >Â Â Â Â Â thank you for your suggestion. I added some RAM and now
> I don't get
> >Â Â Â Â Â the STRIDE error anymore.
> >Â Â Â Â Â I still get that strange (to me at least) set of numbers
> mentioned
> >Â Â Â Â Â in the first mail but that doesn't seem to cause any
> problems. I
> >Â Â Â Â Â just don't remember seeing them but perhaps they are
> even a part of
> >Â Â Â Â Â normal output.
> >
> >Â Â Â Â Â Thank you for your time and have a nice day,
> >Â Â Â Â Â Matic Kisovec
> >
> >     On 06. 05. 2015 20:13, Daniel MÄ*¶ller wrote:
> >
> >Â Â Â Â Â Â Hi,
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â IÄ***ve seen this output before and itÄ***s caused by
> to less
> >Â Â Â Â Â Â memory. For stride you need at least as much free
> memory as your
> >Â Â Â Â Â Â current VMD with the loaded structure. I think,
> itÄ***s because
> >Â Â Â Â Â Â stride is an external programme which is called by
> VMD with exec
> >Â Â Â Â Â Â and this results in a fork. So stride doesnÄ***t have
> enough memory
> >Â Â Â Â Â Â and crash.
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Sincerely
> >
> >Â Â Â Â Â Â Ä*
> >
> >      Daniel MÄ*¶ller
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Von: [3][5]owner-vmd-l_at_ks.uiuc.edu
> >Â Â Â Â Â Â [[4]mailto:[6]owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
> Matic Kisovec
> >Â Â Â Â Â Â Gesendet: Mittwoch, 6. Mai 2015 13:29
> >Â Â Â Â Â Â An: [5][7]vmd-l_at_ks.uiuc.edu
> >Â Â Â Â Â Â Betreff: vmd-l: Problem with assignation of secondary
> structure in
> >Â Â Â Â Â Â VMD
> >
> >Â Â Â Â Â Â Ä*
> >
> >Â Â Â Â Â Â Dear all,
> >
> >Â Â Â Â Â Â I encounter an issue when I open and GROMACS
> trajectory (.gro +
> >Â Â Â Â Â Â .xtc) and then try to colour aminoacid residues by
> secondary
> >Â Â Â Â Â Â structure. Output is pasted below.
> >Â Â Â Â Â Â The trajectory loads just fine but there is a strange
> output right
> >Â Â Â Â Â Â after the loading finishes (the numbers). Then when I
> select the
> >Â Â Â Â Â Â option to colour the molecule by secondary structure
> I get the
> >Â Â Â Â Â Â three ERROR lines. The entire structure changes
> colour to light
> >Â Â Â Â Â Â grey and if I select 'NewCarton' representation there
> is no
> >Â Â Â Â Â Â secondary elements (just a 'tube').
> >
> >Â Â Â Â Â Â I can reproduce this with two of my trajectory files
> but not
> >Â Â Â Â Â Â others that I tried so far. I suppose it could be an
> issue with my
> >Â Â Â Â Â Â files. The other thing is that the trajectory is
> quite long (43
> >Â Â Â Â Â Â 000 frames).
> >
> >Â Â Â Â Â Â Has anybody else had similar issues? Any idea on how
> to fix this
> >Â Â Â Â Â Â so I can get the SS properly coloured?
> >
> >Â Â Â Â Â Â Thank you all and kind regards,
> >Â Â Â Â Â Â Matic
> >
> >Â Â Â Â Â Â Info) Using plugin xtc for coordinates from file
> xyz.xtc
> >Â Â Â Â Â Â Info) Coordinate I/O rate 1328.7 frames/sec, 115
> MB/sec, 32.2 sec
> >Â Â Â Â Â Â Info) Finished with coordinate file xyz.xtc.
> >Â Â Â Â Â Â 1
> >Â Â Â Â Â Â {{1 0 0 -113.603} {0 1 0 -113.64} {0 0 1 -53.5547} {0
> 0 0 1}} {{1
> >Â Â Â Â Â Â 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.012288 0 0
> 0} {0
> >Â Â Â Â Â Â 0.012288 0 0} {0 0 0.012288 0} {0 0 0 1}} {{1 0 0 0}
> {0 1 0 0} {0
> >Â Â Â Â Â Â 0 1 0} {0 0 0 1}}
> >Â Â Â Â Â Â 0 1
> >Â Â Â Â Â Â 1
> >Â Â Â Â Â Â Info) In any publication of scientific results based
> in part or
> >Â Â Â Â Â Â Info) completely on the use of the program STRIDE,
> please
> >Â Â Â Â Â Â reference:
> >Â Â Â Â Â Â Info)Ä*Â Frishman,D & Argos,P. (1995)
> Knowledge-based secondary
> >Â Â Â Â Â Â structure
> >Â Â Â Â Â Â Info)Ä*Â assignment. Proteins: structure, function
> and genetics,
> >Â Â Â Â Â Â 23, 566-579.
> >Â Â Â Â Â Â ERROR) Unable to find Stride output file:
> /tmp/filegxwJFP
> >Â Â Â Â Â Â ERROR) Stride::read_stride_record: unable to read
> output file from
> >Â Â Â Â Â Â Stride
> >Â Â Â Â Â Â ERROR) Call to Stride program failed.
> >
> >Â Â Â <matic_kisovec.vcf>
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. javascript:_e(%7B%7D,'cvml','[8]Matic.Kisovec_at_ki.si');
> >Â Â 2. javascript:_e(%7B%7D,'cvml','[9]Matic.Kisovec_at_ki.si');
> >Â Â 3. javascript:_e(%7B%7D,'cvml','[10]owner-vmd-l_at_ks.uiuc.edu');
> >Â Â 4. javascript:_e(%7B%7D,'cvml','[11]owner-vmd-l_at_ks.uiuc.edu');
> >Â Â 5. javascript:_e(%7B%7D,'cvml','[12]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
> [13]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> [14]217-244-3349
> [15]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:Matic.Kisovec_at_ki.si
> 4. mailto:Matic.Kisovec_at_ki.si
> 5. mailto:owner-vmd-l_at_ks.uiuc.edu
> 6. mailto:owner-vmd-l_at_ks.uiuc.edu
> 7. mailto:vmd-l_at_ks.uiuc.edu
> 8. mailto:Matic.Kisovec_at_ki.si
> 9. mailto:Matic.Kisovec_at_ki.si
> 10. mailto:owner-vmd-l_at_ks.uiuc.edu
> 11. mailto:owner-vmd-l_at_ks.uiuc.edu
> 12. mailto:vmd-l_at_ks.uiuc.edu
> 13. http://www.ks.uiuc.edu/~johns/
> 14. file:///tmp/tel:217-244-3349
> 15. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/