Preparing your data for TEXTAL^TM

TEXTAL^TM takes, as input, an electron density map and automatically assigns amino acids to the density. Only maps of 2.4 Å resolution or better have been tested. The results have been optimized for 2.8 Å maps. Limiting the resolution to 2.8 Å has been shown to help on the high resolution maps which have been tested. TEXTAL^TM will produce the best results if there is only one molecule in the input map and if the amino acid sequence is provided. However, these are not absolute requirements.

MAPMAN can be used to reformat electron density maps.

MAPMAN Authors : Gerard J. Kleywegt & T. Alwyn Jones, Dept. of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, SWEDEN

After installing MAPMAN, type the following commands from the command line:

mapman
re
m1
<name of input map>
<format of input map> (type ‘?’ to see a format list)
wr
m1
<name for output map>
X-PLOR
quit

How many protein molecules are included in your electron density map?

TEXTAL^TM will perform best if you submit electron density covering only one molecule and if the molecule is centered in the middle of the map so it is not fragmented.

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In some space groups it may be difficult to find one molecule and create a map centered on that one molecule. It may help to create a mask around the molecule and use that to pick bounds for a map, which will contain only one molecule in one piece. The reasons for you to take the time to make a map covering only one molecule are:

• Some of the routines in TEXTAL^TM run exponentially more slowly as the map size increases.
• The sequence alignment near the end of TEXTAL^TM produces unpredictable results when it receives chains for multiple molecules.

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