From: Matic Kisovec (Matic.Kisovec_at_ki.si)
Date: Wed May 06 2015 - 06:29:20 CDT

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.