Hi,
Unfortunately this is one of the current limitations of the 'nastruct'
code. The ability to load custom bases is something I've wanted to do
for a while but just haven't gotten around to. It's possible to add
directly to the code but not very straightforward. You'll have to make
modifications in four places.
First, you have to add an enumeration for your custom base to
NA_Base::NAType (AxisType.h). Let's call the new base TMP, so the
enumeration will read:
enum NAType { UNKNOWN_BASE, ADE, CYT, GUA, THY, URA, TMP };
Second you'll need to modify 'NA_Base::ID_BaseFromName()' in
AxisType.cpp so the base can be recognized.
Third you have to add a NA_RefAtom array that defines the standard
reference axis for your base. You can use the existing ones as a
guide; they are located at the top of AxisType.cpp. The naming format
I've used for each array is just R_<Name>, so in this case I would
create an array named R_TMP. Each member of the array defines one atom
of the base. The format is:
Xcoord, Ycoord, Zcoord, Hbond type, Rms-fit, Atom name
the 'Rms-fit' component is 1 if the atom should be used for
rms-fitting to fit the base reference axis and 0 otherwise. Don't
forget to end the array with a blank entry (see the current arrays for
an example).
Fourth, you'll have to add your custom base to the switch in
'NA_Base::Setup_Base()' in AxisType.cpp, e.g.
switch (baseType) {
case ADE : REF = R_ADE; break;
case CYT : REF = R_CYT; break;
case GUA : REF = R_GUA; break;
case THY : REF = R_THY; break;
case URA : REF = R_URA; break;
case TMP: REF = R_TMP; break;
case UNKNOWN_BASE:
...
that *should* be it, but I have not tested that this will work. If you
try it and it doesn't work, let me know. Hope this helps,
-Dan
On Sun, Feb 21, 2016 at 4:45 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good evening,
>
> I was hoping to inquire what potential there is to change the matching
> protocol in the resmap command. If I have a non-standard residue which
> does not sufficiently closely map to A, G, T, C, or U, can I define the
> unit otherwise?
>
> In my particular case, I have a guanine with no N7 nitrogen. I cannot
> run nastruct to identify the helix due to the poor matching.
>
> If not, can someone suggest a place in the code to modify to "add" a unit?
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 23 2016 - 08:00:05 PST
