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Task #2320

documentation of gmx rmsf

Added by Johannes Wagner over 2 years ago. Updated over 2 years ago.

Status:
Closed
Priority:
Low
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-
Category:
documentation
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simple
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Description

the documentation says:

With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file with the coordinates, of the structure file, or of a .pdb file when -q is specified. 
Option -ox writes the B-factors to a file with the average coordinates.

I find this to be a confusing and unclear sentence. Does -oq write the B-factors to the coordinates supplied with -s ? I think the sentence should go like this:

With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file with the coordinates of the structure file supplied with -s. 
Option -ox writes the B-factors to a file with the average coordinates. Option -q writes the B-factor into the supplied  .pdb file. 

And what happens if the -q .pdb doesn't match the topology of the .tpr?

Associated revisions

Revision 24db1d08 (diff)
Added by Erik Lindahl over 2 years ago

Clarified gmx rmsf documentation

Made it clearer what input files coordinates
are taken from when writing B-factors.

Fixes #2320.

Change-Id: Ic47cbb7d9b1036c9e87a77b244dde3cd3da5df36

History

#1 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #2320.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~Ic47cbb7d9b1036c9e87a77b244dde3cd3da5df36
Gerrit URL: https://gerrit.gromacs.org/7440

#2 Updated by Erik Lindahl over 2 years ago

  • Status changed from New to Fix uploaded

#3 Updated by Mark Abraham over 2 years ago

  • Status changed from Fix uploaded to Closed

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