VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Nov 15 2011 - 02:38:34 CST

Thanks John,

indeed, the RMSDTT-Plugin works without problems?
But just out of curiosity, is there a way to reset the molecule IDs?

Cheers,
Bjoern

On Friday 11 November 2011 16:48:57 John Stone wrote:
> Hi Bjoern,
> Can you try using the RMSD Trajectory Tool instead of the older RMSD
> plugin? The RMSDTT plugin shouldn't have this problem as far as I know.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 11, 2011 at 12:52:11PM +0100, Bjoern Olausson wrote:
> > Hi,
> >
> > I am loading a bunch of small peptides into VMD an noticed, that the RMSD
> > Tool fails when the Molecule ID is above 999.
> >
> > It bails out with the following message:
> >
> > expected integer but got "1000candidate_02624_13706.pdb"Not valid
> > molecule id 1000candidate_02624_13706.pdb in atomselect's 'molId'
> > expected integer but got "1000candidate_02624_13706.pdb"Not valid
> > molecule id 1000candidate_02624_13706.pdb in atomselect's 'molId'
> >
> > while executing
> >
> > "atomselect $i $sel_text"
> >
> > (procedure "compute_rms" line 14)
> > invoked from within
> >
> > "compute_rms $rmsd_base [concat "(" $rms_sel ") and backbone"]"
> >
> > (in namespace inscope "::RMSDTool" script line 1)
> > invoked from within
> >
> > "::namespace inscope ::RMSDTool { if { $bb_only } { set tot_rms
> > [compute_rms $rmsd_base [concat "(" $rms_sel ") and backbone"]] } else
> > { set tot_rm..."
> >
> > invoked from within
> >
> > ".rmsdtool.top.right.rmsd invoke"
> >
> > ("uplevel" body line 1)
> > invoked from within
> >
> > "uplevel #0 [list $w invoke]"
> >
> > (procedure "tk::ButtonUp" line 22)
> > invoked from within
> >
> > "tk::ButtonUp .rmsdtool.top.right.rmsd"
> >
> > (command bound to event)
> >
> > Is there a way to reset the Molecule ID or another quick workaround?
> >
> > Cheers,
> > Bjoern 

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Institut für Pharmazie
Wolfgang-Langenbeck-Str.4
06120 Halle/Saale
Phone: +49-345-55-25122