From: Axel Kohlmeyer (
Date: Wed Jan 07 2009 - 10:44:18 CST

On Wed, 7 Jan 2009, Nadja Lederer wrote:

dear nadja,

NL> I didn't find much information as far as the measure rmsf-command
NL> ("measure rmsf <selection> first <firstfr> last <lastfr> step <nr>")
NL> is concerned..

please feel free to send in an improved version of the documentation
in the user's guide. it is _very_ difficult for developers to identify
what kind of information has to be given to make it easily
understandable to users, particularly less experienced ones.
for a developer the flags are understadably "obvious".

the best way to handle this would be to have people that were struggling
with the documentation, rewrite it and then have a developer review it
and include it for the next release. unfortunately, rarely anybody is
willing to do this and thus documentation frequently has quite cryptic
paragraphs and pieces that are tersely documented or even not documented
at all.

NL> so far it's clear that the rmsf-value is computed for every atom in
NL> selection over frame area firstfr till lastfr. now, do I guess
NL> right, if I say, reference position is firstfr? and what about the

no. the reference is the average of the positions in the frame
range given. measure rmsf internally calls measure avpos first.

NL> step argument? does it mean that the command computes the rmsf
NL> within the given frame area only considering every second or third
NL> (or whatever nr is given in the step argument) frame?

yes. the first/last/step terminology is used in several places
in VMD and always means the same (as far as i remember, that is).


NL> regards,
NL> nl

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.