at 7.35p EDT on 2004 February 25 Wednesday Miguel Howard said:in RasMol2.7.2.1 the show command reports various information, but a parameter model is not implemented
sorry - this does not work in Chime.Huh? You said "Chime can only 'show' all models" ...different perspectives, eh? :-)select (model=1,model=2,model=3)Q: In Chime, can you only show one model, or can you show several
wireframe 0.3
:-) To my way of thinking, this is showing all of the models ... but some of them just happen to be turned off.
so from your perspective, I would say Chime can only 'show' all models,
though it can 'display' various combinations of models.
But can't I also say
show model 1
As an alternate mechanism of restricting the rendering to a single model?
show model
simply messages a list of the model numbers in the file. it does not affect
display or selection at all. (adding a number does not affect this.)
it is just the same in RasMol2.7.2.1 use restrict and select to alter rendering of individual MODELs
no, just mech 1 works.There are two different mechanisms for displaying the first model of a multi-model file:
load someMultiModel.pdb show model all; restrict model=1; wireframe .3
OR load someMultiModel.pdb select *; wireframe .3; show model 1
Please confirm whether or not this is true.
when a multi-model file is loaded, Chime displays all models in wireframe cpk
color by default. 'show model' does not change this; the only way to affect
the display of a model on screen is via restrict, or select combined with a
rendering command (like wireframe). RasMol 2.7 may work differently...
In the animation of a reaction like:if we want to do something like that, we need a resume command which is a restrict which does not forget the rendering styleA--B C ---> A---B---C ---> A B--C
When you load the structures as wireframe and then set 'wireframe 0.1' within the first frames of the animation, sometimes the bond B---C is shown as 'wireframe 0' because the bond wasn't formed when the wireframe-command was given.
# do some rendering
select *
wireframe 0.1
select ligand and model>2
cpk
select nucleic and (*/1 or model>6)
wireframe 0.5
# animation
anim on
resume */1
delay 0.3
resume */2
delay 0.3
...
loop
but then it would be easier to do something like this
# animation list of selections loopmode frametime
anim qw(*/1 */2 */3 */4 */5 */6 */7 */8 */9&(nucleic|hetero) */10&(nucleic|hetero) */11&(nucleic|hetero) ) rock 0.3
(but this is not compatible :-)
Q: In the existing version of Chime, are there commands to manipulate theI never used .xyz files with chime.
individual atoms in the individual frames of a multi-frame .xyz file?
PDB files are used as "poor mans animations" using 10 frames as MODELs instead of trajectories of 200.
http://www.umass.edu/microbio/chime/explorer/morfdoc.htm
I consider vmd the best program for movie creating out of trajectories
http://www.ks.uiuc.edu/Research/vmd/
and how they implemented animate (never used, but the GUI)
http://www.ks.uiuc.edu/Research/vmd/current/ug/node106.html
Regards, Jan
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