The only command in the program Gather_map is PUNCH. Most of the details were covered in the previous section. Here we will concentrate on an example. Let's calculate ncs averaged 2Fo-Fc maps for the monoclinic form of Hen Egg White Lysozyme as described in the ``Examples" chapter of the TNT Users' Guide. This crystal has two molecules in the asymmetric unit, and each molecule is composed of two domains. We will calculate an averaged map for each domain. The starting point is a ``gathered" coordinate file.
Since the coordinate file contains all the atoms in the asymmetric unit are required to directly calculate the 2Fo-Fc Fourier coefficients we must first ``scatter" the model, and then calculate normal 2Fo-Fc coefficients. Gather_map will take these coefficients, the ``gathered" coordinates, the ncs transformations (here assumed to be in the file gathered.ncs, and the usual crystallographic information (cell constants, etc.) and produce the map. The script looks like this. (Usually one would enter the TNT control file but I have included the crystallographic informaiton directly to make its presence more obvious.
$tntbin/gather_map << $eof CELL 28 62.9 60.5 90 90.8 90 INCLUDE $tntsymmetry/p21.dat RESOLUTION 2.2 INCLUDE pdb1lym.seq CLUSTER N RESIDUE 1 - 91 CHAINS A B CLUSTER C RESIDUE 92 - OXY CHAINS 1 B INCLUDE gathered.cor INCLUDE gathered.ncs FILE MAP01 2fo-fc.pak FORMAT PACKED FILE MAP02 2fo-fc.pak FORMAT PACKED PUNCH 2fo-fc_n.dsn6 DSN6 CLUSTER N OVERSAMPLE 4 PUNCH 2fo-fc_c.dsn6 DSN6 CLUSTER C OVERSAMPLE 4 $eof if ($status >< 0) exit 1
In this example the layout of the two maps are identical. Each covers all the atoms present in gathered.cor. Each averaged map is only vaild over the atoms in the chain with the name of its cluster, i.e. the map in 2fo-fc_n.dsn6 is only valid for atoms in the N chain prototype.