CCP4 SFALL program
gerard at rigel.bmc.uu.se
Mon Jan 23 15:30:12 EST 1995
In article <D.LOVE.95Jan23141958 at dlpx1.dl.ac.uk>, d.love at dl.ac.uk (Dave Love) writes:
|> As I understand it you don't need to worry. For what it's worth, the
|> `standard' atom names used are
|> 'C ','CA ','CA2 ','CB ','CB2 ','CG ','CG1 ',
|> 'CG2 ','CD ','CD1 ','CD2 ','CE ','CE1 ','CE2 ','CE3 ',
|> 'CZ ','CZ2 ','CZ3 ','CH2 ','N ','ND1 ','ND2 ','NE ',
|> 'NE1 ','NE2 ','NZ ','NH1 ','NH2 ','O ','OG ','OG1 ',
|> 'OD1 ','OD2 ','OE1 ','OE2 ','OE ','OH ','OW ','SD ',
|> 'SG ','SG2 '
|> I don't know whose standard this is. I will try to get the
|> documentation improved.
|> --Dave (I'm not the Secretary)
Dave Love also wrote:
|> Netnews isn't the best place to get `authoritative' answers concerning
|> CCP4 since none of the developers is guaranteed to read it (and as far
|> as I know no-one who might count as a developer and/or is a
|> crystallographer actually will).
WARNING: the following is a non-authorative comment from someone
who doesn't count either as a developer or a crystallographer:
I think it's plain old PDB atom names, with one important
exception: the atom names are four characters, of which
the *first two* (right justified) are used for the symbol
of the chemical. Therefore, ' CA ' is an alpha-carbon
atom, whereas 'CA ' would be a calcium atom ! In the
same vein, ' NE ' is an epsilon-nitrogen, but 'NE ' would
be a neon atom, etc ad infinitum.
As for SFALL, I haven't checked the source, but I assume
it checks the first two characters of every atom name
to deduce the chemical type. If you have anything out
of the ordinary, include a FORM(factor) line to tell
the program for which chemicals it should look up
form factors, e.g.:
FORM C H N O S P CA
if you would have a Ca and a PO4 in your structure.
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