The easiest thing to do is to make a PDB file that contains ONLY the
residues you are interested in and set all the residue numbers to "1".
Use this PDB file to calculate the "MODE ATMMAP" and the "MODE ATMMAP
RESMOD" maps with SFALL. Then OVERLAPMAP (in "correlate residue" mode)
will give you a CC and RSR for "resiude 1", which is your
region-of-interest.
-James Holton
MAD Scientist
[email protected] wrote:
Hi James:
Actually I did OVERLAPMAP calculation in this way. I first flagged the map
grid points by using the provided pdb information, which serves as
"mapin3" for the OVERLAPMAP calculation. However, the calculated CCs or
RSRs are either based on each individual atom, residue or map section, but
it didn't calculate a single CC or RSR by integrating over the whole
region encomprassed by a group of residues as I wanted.
Maybe there is something I didn't discovered in OVERLAPMAP to do this? I
appreicate if you could point out which key word I need to use. This will
save me lots of time in coding on the map:-(
Thanks a lot!
Best Regards, Hailiang
OVERLAPMAP will do this, but you need to calculate a "label map" with
SFALL first and provide that to OVERLAPMAP as "mapin3", as MW and others
have pointed out already.
RTFM:
http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3
http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod
-James Holton
MAD Scientist
Hailiang Zhang wrote:
Dear Eleanor:
Yes, this is something I want to do (RSR and CC). But I just want to do
the calculation based on a group of residues or atoms, and it seems
OVERLAPMAP doesn't do it, so I think I have to find other ways.
Hailiang
mapdump does this if you select the right flags. But as Ian says you
will get a LOT of numbers. You dont say why you want this information,
but if it is to find the electron density at an atom site overlapmap
will do that if you ask for "real space rfactor"
eleanor
Hailiang Zhang wrote:
Hi,
I wanted to convert a binary ccp4 map file to a readable format so
that
I
can retrieve the electron density at each real space grid point. Just
tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not
readable, and I didn't find any documentataion about how to read them.
Could somebody give me any hint? Thanks a lot!
Best Regards, Hailiang
