VMD-L Mailing List

From: J. Rui Rodrigues (jrui_at_ci.uc.pt)
Date: Fri Oct 17 2003 - 11:46:41 CDT

Dear vmd-l,

I am trying to compute a map of intra contacts for my protein (127 aa), using
the contactmap tool provided in VMD 1.8.1. To do this, I have selected the
same molecule as MoleculeA and MoleculeB.

The residue sequence displayed at the vertical axis is OK, but at the
horizontal axis, the sequence is right shifted by one residue. So, instead of
having black squares at residue pairs (1,1), (2,2),...(127,127), the black
squares are at (0?,1), (1,2),...(123,124).
Also, contact distances are missing for the last 3 residues in the horizontal
axis.

I know that this tool should be primarily used with two structures, but is
there any way to use it for a single structure?

Thanks,
Rui Rodrigues 

-- 
J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal