[Jmol-developers] disappearing isosurfaces in multi-frame load

[Timothy D. <mol...@ma...>]

hi again,

I'm trying to pull together the final piece of a new software tool  
for visualizing enzyme active sites, and I've run into some problems  
on the Jmol side.  can anyone please tell me what I'm doing wrong?

I am trying to load multiple files; this works fine.  I am coloring  
certain regions according to external data files, using the new  
propertyAtomField and propertyDataField features, and this seems to  
work great, too.

I'm having trouble with surfaces here though. I have three files,  
loaded using 'load files':

load files "1S1T.pdb" "1S1U.pdb" "1S1V.pdb"

I want a surface associated with a region of each model.  so this is  
what  I'm trying:

model 1.1
define ligand1 (hetero and not (solvent,[CA])) and model=1.1
define bsregion1 model=1.1 and (protein and within(12.0,ligand1))
isosurface surfapbs1 select(bsregion1) model 1.1 solvent 0.8


the above works fine.  surfapbs1 takes a few seconds to calculate,  
but it appears.

but then if I run this subsequently:

model 2.1
define ligand2 (hetero and not (solvent,[CA])) and model=2.1
define bsregion2 model=2.1 and (protein and within(12.0,ligand2))
isosurface surfapbs2 select(bsregion2) model 2.1 solvent 0.8


surfapbs2 appears instantaneously...but surfapbs1 disappears.

and oddly, if I do the same for the third model:

model 3.1
define ligand3 (hetero and not (solvent,[CA])) and model=3.1
define bsregion3 model=3.1 and (protein and within(12.0,ligand3))
isosurface surfapbs3 select(bsregion3) model 3.1 solvent 0.8


Jmol says surfapbs3 was created, but it never appears.  in the end,  
the only visible surface is associated with model 2.1.  stepping  
through the frames confirms this.  however, if I send this:

isosurface surfapbs3
isosurface delete

then the surface disappears.  it seems like Jmol is copying each new  
isosurface over top of the previous.


I thought I had this working earlier in the week, but perhaps not.   
can anyone see what I've messed up?  I've been banging against this  
for most of the day/night, and I'm a bit frustrated.


many, many thanks for any help.  my head hurts.

tim
-- 
Timothy Driscoll                                em: mo...@vb...
Virginia Bioinformatics Institute               ph: 540-231-3007
Bioinformatics I: M-1                           im: molvisions
Washington St., Blacksburg, VA 24061

04-16-07.  We will not forget you.