VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Apr 08 2013 - 05:45:35 CDT

Hey Chris,

Thanks for the report! I am CC'ing the list, since this is interesting.

Indeed, there was a bug. Now qwrap should work with your data, but it probably still won't do what you want: since you have set 0 for the protein and 1 for everything else (or the other way around), that defines two big wrapping groups, neither of which ends up being wrapped. What I think you want to do is eg. set beta = residue for all solvent and beta = 0 for the protein - that way the protein stays in one piece but the rest is wrapped residue-wise.

Now, if you save a PDB file with those large beta values, the beta field will overflow, that's not great. A better option is to set beta = (residue % 2) for all solvent, and beta = 2 for the protein. That is an extra couple lines of Tcl. Here they are, for the benefit of the list readers:

set res [[atomselect top "not protein"] get residue]
set beta [list]
foreach r $res { lappend beta [expr $r % 2] }
[atomselect top "not protein"] set beta $beta
[atomselect top "protein"] set beta 2

Hang on in the frozen tundras - spring is just around the corner!
Jerome

----- Original Message -----
>
> Hey Jérôme,
> Chris from the Pomès lab over here in the frozen tundras of Canada. I
> tried using the qwrap code you posted on vmd-l the other day. The
> "compound res" option appears to work great, but I can't seem to get
> the "beta" field option running. I suspect it could be something to
> do with my input psf/pdb. Could you try running your qwrap with my
> psf/pdb's attached and see if the problem is reproducible?
>
>
> I get:
>
> vmd > load /home/ceing/qwrap/qwrap.so
> vmd > qwrap first 0 last -1 compound beta
> Wrapping frame 0
> qwrap: error getting coordinates (wrong data size)
>
>
> It should still work with only 1 frame, right?
> Thanks!
> -Chris Ing