VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 07 2015 - 22:37:56 CDT

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.Â
> 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.Â
>
> 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 Möller wrote:
>
> Hi,
>
> Â
>
> Iâ**ve seen this output before and itâ**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, itâ**s because
> stride is an external programme which is called by VMD with exec
> and this results in a fork. So stride doesnâ**t have enough memory
> and crash.
>
> Â
>
> Â
>
> Sincerely
>
> Â
>
> Daniel Möller
>
> Â
>
> Â
>
> Â
>
> 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
>
> Â
>
> 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)Â Frishman,D & Argos,P. (1995) Knowledge-based secondary
> structure
> Info)Â 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'); 

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