[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: refmac and cns quirks
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
> Well, I have a monomer so no chain identifier is needed. When I run
> through refmac, it automatically names it chain X. Other refinement
> progs like SHELXL and CNS don't do this. This isn't that important,
> though I would like to switch it off.
> A different problem is that CNS shifts my heavy atoms, say HG by one
> column to the right and that causes the HG atom to not be recognized by
> refmac and shelxl. So I have to shift it back again one space the left
> for them to be parsed properly. Anyone familiar with this?
Very familiar- The old convention of atom name in columns 13-16
with the element right-justified in 13-14 is being abandoned
in favor of element symbol right-justified in 77-78, for reasons outlined
at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html .
During the transitions things are not easy. I keep a copy of
ccp4 "pdbset" from version 3.3, which stuck consistently to the old
convention, and the command "Element FE HG" fixes these
elements in the cns file so sfall etc will understand them, while
completely ignoring what some previous run of pdbset may have put
in columns 77-78. Of course I have to be sure I have no epsilon-flourine
atom named FE, as it will surely be converted to iron.
PS- from the above URL- Note HG11 can be a hydrogen:
* Columns 77 - 78 contain the atom's element symbol (as given in the
periodic table), right-justified. This is especially needed because
in some cases it has not been possible to follow the convention that
columns 13 - 14 of the atom name contain the element symbol.
The most common cases are:
- In large het groups it sometimes is not possible to follow the
convention of having the first two characters be the chemical symbol
and still use atom names that are meaningful to users. A example is
nicotinamide adenine dinucleotide, atom names begin with an A or N,
depending on which portion of the molecule they appear in, e.g.,
AC6 or NC6, AN1 or NN1.
- Hydrogen naming sometimes conflicts with IUPAC conventions. For example,
a hydrogen named HG11 in columns 13 - 16 is differentiated from a mercury
atom by the element symbol in columns 77 - 78. Columns 13 - 16 present a
unique name for each atom.
> On Wed, 2003-03-26 at 18:37, Jan Dohnalek wrote:
>>I am afraid you have to explain a bit more what
>>you want to do.
>>>*** For details on how to be removed from this list visit the ***
>>>*** CCP4 home page http://www.ccp4.ac.uk ***
>>>does anyone know how to tell refmac not to put in a chain X when there
>>>is only a single protein chain being refined?
>>York Structural Biology Laboratory
>>Department of Chemistry
>>Phone: +44 1904 328270 Fax: +44 1904 328266
>>(Institute of Macromolecular Chemistry, Academy of Sciences
>>of the Czech Republic, Prague, Czech Republic)
Edward A. Berry, MailStop 3-250
Lawrence Berkeley National Laboratory
1 Cyclotron Road, Berkeley, CA 94720
Jfax +1-510-588-4829 (you send fax, I receive email)
LBNL Emergency status number: 800-445-5830 - Call after "The Big One"
to see if the lab slid off into the bay.