IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

special positions

Herman Schreuder hermanschreuder at mmd.com
Mon Feb 19 04:19:54 EST 1996

Dear Axel & X-plor users,

Although special positions are automatically recognized by X-plor,
I found it impossible to do any positional refinement afterwards
(at least with waters), because the special waters always drifted away 
from the twofold and got repelled from their symmetry mate. I therefore
had to adopt the rather awkward procedure of manually positioning the
waters and then fixing their positions. In addition, the file produced
is not formally correct because the special waters have full occupancy,
instead of half, on third etc., which means that one has to manually
correct this if one wants to deposit the coordinates or if one wants to
use some other programs. 

Since the automatic procedure as currently implemented still needs a lot
of manual intervention, one might as well explicitly define the special
positions in the input file and, instead of reassigning a non-special 
status once the molecule has drifted a little away, resetting the
special coordinates to their exact values.

Herman Schreuder

More information about the X-plor mailing list

Send comments to us at archive@iubioarchive.bio.net