Hi,
Sorry for the delay in replying.
On Thu, Sep 20, 2018 at 12:19 PM Sourav Purohit <sour000.gmail.com> wrote:
> > > The output contact map is a 93 X 93 matrix.
> > > As two masks are specified should we not get a 60 X 33 matrix as the
> > output?
The current behavior is the intended one, but that's not to say it is
the best. I originally wrote it that way to make the data set logic
simpler; what happens write now is that the final dimensions of the
contact map matrix are min(mask1, mask2) by max(mask1, mask2). This
makes the indexing easier, but for non-overlapping mask1 and mask2 it
creates a lot of empty entries. I'll open up a GitHub issue to remind
me to try and simplify output when mask1 and mask2 don't overlap.
-Dan
>
> Hello,
> I am using AmberTools18.
> Thanks
>
> On Thu, Sep 20, 2018 at 3:01 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > What version of cpptraj are you using?
> >
> > -Dan
> > On Mon, Sep 17, 2018 at 4:54 PM Sourav Purohit <sour000.gmail.com> wrote:
> > >
> > > Hello all,
> > >
> > > I am simulating a protein-DNA complex.
> > > I used the folllowing command to calculate the residue-wise contact map
> > of
> > > the contacts between the protein and the DNA :
> > >
> > > trajin 1-combined.trj
> > > nativecontacts :1-60 :61-93 byresidue map mapout 1-contact-map.dat
> > >
> > > residue id 1-60 correspond to DNA, while 61-93 correspond to protein.
> > >
> > > Is the command line correct or is something needed to be added to this.
> > >
> > > Does this command also calculate the intra-mask contacts?
> > >
> > > Thanks in advance for your help and suggestions.
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Received on Mon Sep 24 2018 - 09:00:03 PDT
