A general solution to such inquiries is found in Jmol 11.6. Jmol now
allows an extended version of the select command specifically for this
sort of complex selection. The syntax is:
select {someOverallAtomExpression} (some math expression using variable _x)
"_x" here represents "each atom of the atom expression." This allows
for a quite flexible query capability.
For example:
cdrStart = 10
cdrEnd = 15
select {:a} (_x.resno - within("chain", _x)[1].resno >= cdrStart - 1
&& _x.resno - within("chain",_x)[1].resno <= cdrEnd - 1)
selects the 10th through the 15th residues in chain a because
within("chain", _x)[1] gets you the first atom of the chain containing
the atom _x.
You can speed up this search (which isn't very slow anyway) by just
scanning the alpha carbons, then pulling in their entire group.
select {*.ca:a} (_x.resno - within("chain", _x)[1].resno >= cdrStart -
1 && _x.resno - within("chain",_x)[1].resno <= cdrEnd - 1)
select within(group,selected)
You could create a function that does this:
function selectCDR(chainID, r1, r2)
script inline @{"select *.ca and :" + chainID}
select {selected} (_x.resno - within("chain", _x)[1].resno >= r1 - 1
&& _x.resno - within("chain",_x)[1].resno <= r2 - 1)
select within(group,selected)
return {selected}
end function
Here I return the value of the selection, just because perhaps I want
to do something with it:
color @{selectCDR("a",97,115)} red
same as
selectCDR("a",97,115)
color red
Bob Hanson
On Wed, Dec 10, 2008 at 4:15 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:
> Hello Umanga
>
> Jmol will always use the residue numbers that are written in the pdb
> file (not the order in the chain or in the file).
> So, your problem seems to be in the exact data you have in your pdb
> file.
>
> That said, there may be a way for Jmol to find out the length of
> chain A and add it to the actual residue nr. in B. But I would say
> that is a non trustable solution for other models (even for this, see
> below).
>
> More things:
>
> 1. There is some error in the numbering of your first example: it
> cannot go from 98 to 97.
> a look at 1uj3.pdb gives this:
> chain A goes from residues 1 to 214
> chain B goes from residues 301 to 517
> So your offset of 215 is not valid either.
>
> 2. Your commands are OK, but you can use simpler notation for residue
> numbers:
> select :a and (resno > 97 and resno < 106); color red
> is the same as
> select :a and 98-105; color red
> or even
> select 98-105:a; color red
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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