FYI: here's my reminder on GitHub:
https://github.com/Amber-MD/cpptraj/issues/640. Feel free to add
comments.
-Dan
On Mon, Sep 24, 2018 at 11:46 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 09:00:04 PDT
