> That parially solved my problem let me give u in pictures what i have in > mind. > > Image 1.jpg: is a full pdb structure of 1asz.pdb OK
> Image 2.jpg: result obtained when "restrict within > (648,within(5.0,648:s))" > command is run The search specification that you gave is not correct. You want: restrict within(group, within(5.0, 648:s)) The command that you gave: restrict within(648, within(5.0, 648:s)) Is restricting to within 648 rasmol units of any atom that is within 5.0 angstroms of any atom in group #648 of chain 's' A rasmol unit is 1/250 Angstrom. The following are equivalent: restrict within(648, within(5.0, 648:s)) OR restrict within(2.59, within(5.0, 648:s)) OR select 648:s select within(5.0, selected) select within(2.59, selected) restrict selected RasMol units are a disaster ... people writing scripts should always use decimal numbers to specify angstroms. (I realize that in this case you were trying to specify a group number) > 2.jpg shows the complete residues of some of them within 5 ang of 648:s. > > Image 3.jpg: result obtained by running "restrict > 614:s,615:s,616:s,621:s,646:s,647:s,648:s" command which is actually what > i > need. > > I need to display complete residues within 5 ang of 648:s whithout me > knowing whats around. 648:s. I am sorry that my previous message was not clear. You are trying to select groups. You need to use the word 'group' in the within clause of the query specification. > I want to display the complete residue even if a single atom of a residue > falls in the restriction radius. Correct. select within(group, <set-specification>) will select all the atoms in any group that is referenced by the <set-specification> So restrict within(group, within(5.0, 648:s)) can be rewritten as: #select all atoms in group 648 chain s select 648:s #anything within 5.0 angstroms of any of those atoms select within(5.0, selected) #any atom that is in the same group as any selected atom select within(group, selected) #only show those atoms restrict selected Miguel ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
