[gmx-users] Re: A problem with do_dssp command
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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