Hi Dan,
Thanks for your rapid response. I can understand why the program functions
as you mentioned. I suppose that if I wanted it to run as I described, I
could just strip the unnecessary atoms from my system, thus sparing
everyone the headache of altering the source code. Thanks!
Take care,
Sam
On Tue, Apr 7, 2015 at 1:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Apr 7, 2015 at 11:52 AM, Samuel Bowerman <sbowerma.hawk.iit.edu>
> wrote:
> > Is this a known bug or is this a deliberate action taken by the command?
>
> It's not a bug - the map size spans from the minimum atom to the
> maximum atom, regardless of what is selected in between. While this
> can be useful in the sense that it gives a better idea of the relative
> sequence distance between two indices, it is as you mentioned quite
> wasteful for certain cases, where having each index in the map
> correspond directly to the atom mask would be more compact. Honestly I
> hardly ever use the map option so I never really think about it; I've
> recently focused on adding features to 'nativecontacts' like
> generating a PDB of important contacts with B-factors set to relative
> contact strength (available in cpptraj from the upcoming AmberTools 15
> release). However, it's a feature I may add via a future update (time
> permitting).
>
> Thanks for bringing it to my attention.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Apr 07 2015 - 13:30:05 PDT
