Miguel wrote:
Scott wrote:
...
I've been working on a Javascript that includes a loop similar to the
following:
- XMLHTTP server request for newly generated model
- append new model to string containing all previous models
- get view
- loadInline(concatenated model)
- Jmol script call to set view to the previous and to restore the
previous rendering style
- repeat
OK, I think I get the idea.
Q: Why are you catting in JavaScript and using loadInline rather than
doing a 'load some-concatenation-cgi?foo' where the concatenation is
performed on the web server?
I think this is a CGI job, but if JavaScript string handling is OK, why not.
...
Let's talk about/work on these things one at a time.
First, let's work on the 'append an additional model' problem. One or two
other people have asked for the same thing.
At this point I'll warn that RasMol2.7.2 has the "molecule" concept, you
could load up to five structure assemblies which could be rendered *and*
manipulated independently.
Let's assume that we have some script command that will load an additional
file without clearing the first one ...
How should model numbers be handled? ...
Q: What should the model number of the 2nd file be?
In this case, I think MODELs are required, I think this is a CGI job to
generate the model numbers, but molecule could be implemented, too, may
be at start without independent manipulation which is in RasMolScript
achieved by
set rotate all
the rendering commands are directed to a specific molecule #number#
after the
molecule <#number#>
command is given.
Q: What happens if there are explicit model numbers in subsequent files,
but those model numbers are already used?
the molecule may contain MODELs but addressing is independent
Regarding scale & centering ...
Q: What happens if the coordinates of the 2nd model are completely
unrelated to the coordinates of the first? For example, the first one
loaded is centered at 10000,10000,10000 and the second one loaded is
centered at -10000,-10000,-10000 ?
all follow up molecules should be moved the same amount as the first one
e.g. 10000,10000,10000
if independent movement of molecules is implemented it would be easy to do
set rotate molecule
molecule 2
select all
# all of molecule 2
center selected
if desired, but in many case it is desired to start with an assembly in
one PDB file, split up the chains in to individual files e.g.
restrict *:A
save 2buj_A.pdb
restrict *:B
save 2buj_B.pdb
and load them as independent molecules to test rotations and
translations between the molecules, they should be assembled relative to
each others after loading as in the original single PDB file.
(in theory this may be achieved by recalculation of center and zoom
after joining the molecules, too, which may be implemented by repeating
movement of the first molecule to all following and than recalculate
center and zoom for the assembly)
Q: What scaling should be used? (by scaling I mean, pixels per angstrom)
the same as with molecule 1
Q: What happens if the first model loaded is HOH and the 2nd model loaded
is some huge protein?
it is up to authors responsibility to design useful loading sequences
(load the largest molecule first), otherwise do a
zoom 5
Regards, Jan
P.S. about publication quality images: though RasMol isn't really that
good image quality, the
cat rasmolwritescript.RAZ | rasmol -nodisplay
command sequence is an easy way to get GIF images with a CGI mechanism.
Besides the -nodisplay switch, Jmol application would need the
write <format>
command. format could be PNG or POVRay ...
or script (this would be helpful to generate a jmolwritescript.JMZ)
and an
exit
command.
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