CCP4 SFALL program

Gerard Kleijwegt 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.

--gerard




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