[gmx-users] Re: A problem with do_dssp command

Justin Lemkul jalemkul at vt.edu
Thu May 9 01:03:35 CEST 2013

On 5/8/13 6:59 PM, zugunder wrote:
> But don't you know where I could find the default settings used in xpm to eps
> conversion (without di flag)?

The default values simply indicate that each element occupies 1 pixel, such that 
you have some matrix that is N residues by some tens of thousands (maybe) of 
frames, hence why everything is so stretched.  Probably any default settings are 
hard-coded in xpm2ps, but I've never bothered looking for them.

> I used the m2p from the example and tried to change some parameters to take
> a look what happens, but I can't see any image at all now :-(

Increasing y-size and decrease x-size is appropriate for most DSSP output .xpm 
files, since in general there are many more frames than there are residues in 
the protein.  The difference is typically orders of magnitude.  The example 
online has a nicely annotated description of the parameters.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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