VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu May 07 2015 - 21:53:44 CDT

Sorry guys for interrupt this closed thread.

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.

Regards,
Kevin

On 7 May, 2015, at 20:48, Matic Kisovec <Matic.Kisovec_at_ki.si
<javascript:_e(%7B%7D,'cvml','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 <Matic.Kisovec_at_ki.si
<javascript:_e(%7B%7D,'cvml','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,
>
>
>
> I’ve seen this output before and it’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, it’s because stride is an external programme which is
> called by VMD with exec and this results in a fork. So stride doesn’t have
> enough memory and crash.
>
>
>
>
>
> Sincerely
>
>
>
> Daniel Möller
>
>
>
>
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu
> <javascript:_e(%7B%7D,'cvml','owner-vmd-l_at_ks.uiuc.edu');> [
> mailto:owner-vmd-l_at_ks.uiuc.edu
> <javascript:_e(%7B%7D,'cvml','owner-vmd-l_at_ks.uiuc.edu');>] *Im Auftrag
> von *Matic Kisovec
> *Gesendet:* Mittwoch, 6. Mai 2015 13:29
> *An:* vmd-l_at_ks.uiuc.edu
> <javascript:_e(%7B%7D,'cvml','vmd-l_at_ks.uiuc.edu');>
> *Betreff:* vmd-l: Problem with assignation of secondary structure in VMD
>
>
>
> 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) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) 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>