Re: [Jmol-users] 11.5.33 -- filtered LOAD command, biological ASU (biomolecules) and thermal ellipsoids

[Rolf H. <rh...@fl...>]

Bob Hanson wrote:
> Jmol users, exciting news on three fronts:
> 
> 
> load FILTER
> selection of biomolecules from PDB files
> thermal (and otherwise) ellipsoids and spheres
> 

I have tested loading of biomolecules again with the extra-large entry
'1m4x'. With revision 9356 (application, Java 1.4.2_03) the biomolecule
looked fine now (in contrast to revision 9339).

I noticed two things while testing it:

1) It is almost impossible to apply any commands using the console if
there are about 2,000,000 atoms. After loading '1m4x' with filter option
"*.CA; BIOMOLECULE 1" I tried to apply command "color chain". It just
finished its work after 4 hours...
In contrast it took only about 1 minute to apply the corresponding
command using the popup menu.

2) There is a huge difference in load time and memory usage between
loading the biological unit file for '1m4x' provided by the PDB and
loading the asymmetric unit file with the biomolecule filter option:

  a) biological unit file, all atoms, 1680 models
  b) biological unit file, only CA atoms, 1680 models
  c) asymnetric unit file, filter "BIOMOLECULE 1", 1 model
  d) asymmetric unit file, filter "*.CA; BIOMOLECULE 1", 1 model

     | No. of Atoms | Memory    | Load Time
 ----|--------------------------------------
  a) | ~16,000,000  | >120   GB | >3 hours
  b) |  ~2,000,000  |   83   GB | 30 min.
  c) | ~16,000,000  |   19   GB | 55 min.
  d) |  ~2,000,000  |    2.5 GB |  5 min.

(The listed memory usage is the usage of the whole JavaVM immediately
after loading the structure, before any commands were applied.)

I am wondering about this huge difference in memory usage (~40 times)
because all atoms can still be manipulated separately in case c) and d).

Regards,
Rolf