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Bug #891

do_dssp no longer complies with dssp input

Added by Erik Marklund over 7 years ago. Updated over 7 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Since last year the dssp program has different in-/output and e.g. no longer recognizes -na, which is used by do_dssp. Preferrably do_dssp should test what kind of input dssp takes before invoking dssp. Here's the new help text from dssp:

DSSP options:
-h [ --help ] Display help message
-i [ --input ] arg Input file
-o [ --output ] arg Output file, use 'stdout' to output to screen
-v [ --verbose ] Verbose output
-d [ --debug ] arg Debug level (for even more verbose output)

Examples:

To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

dssp.exe -i 1crn.pdb -o 1crn.dssp

Associated revisions

Revision 30d128af (diff)
Added by Erik Marklund over 7 years ago

Added support for dssp2.X with the -ver option

Fixes #891

Change-Id: If274058aa776f64b04cb6f5a3c8303f8c567ef97

History

#1 Updated by Erik Marklund over 7 years ago

This was apparently discussed on the user list with a quick fix (below). Still, automatic detection or manual selection of dssp version would be nice.

http://lists.gromacs.org/pipermail/gmx-users/2011-August/063606.html

#2 Updated by Erik Marklund over 7 years ago

Here's a suggestion that means minimal effort for programmers. If a sevond environment variable, DSSP2, is set to the full name of the new dssp executable, then the new syntax is used. Alternatively, a command-line option could turn on the new syntax. The thing is that the old dssp is not downloadable from the dssp website, so in one way or another gromacs should learn to handle the new version.

#3 Updated by Erik Marklund over 7 years ago

  • Assignee changed from David van der Spoel to Erik Marklund

#4 Updated by Roland Schulz over 7 years ago

  • Target version set to 4.6

#5 Updated by Erik Marklund over 7 years ago

  • Status changed from New to Closed

I consider this bug closed.

#6 Updated by Erik Marklund over 7 years ago

  • % Done changed from 0 to 100

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