On Mon, Apr 12, 2010 at 7:43 AM, Eric Martz <[email protected]>wrote:
> 1. "cystine" (2 cys residues that are disulfide bonded) appears to be
> undefined as a selection term. This may be an oversight since it was
> defined in Chime. Currently I can select cystine this way:
>
> select cys.sg and connected(cys.sg)
> select within(group, selected)
> define ~cystine selected
>
version=12.0.RC5_dev
# new feature: select CYSTINE
I have no idea why that was removed ages ago. Defined exactly as you
specify.
2. What is the easiest way to select all interchain (or intrachain)
cystines?
couple of ways:
1) use the select() function:
x = select(y;{_S};within(chain, y) and connected(y));select within(group, x)
or, all in one go:
select within(group, @{select(y;{_S};within(chain, y) and connected(y))})
2) use the extended SELECT command:
select {_S} (within("chain",{_S} and connected(_x)))
"_x" here refers to "each atom in the selected set". This second part is a
math expression:
(within("chain",{_S} and connected(_x)))
that is applied for each of the atoms in {_S}.
It says, "from all the _S, select only the atoms _x that are within the
chain of the sulfur atoms that are connected to _x.
Tricky! Should work....
Bob
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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