Sandbox 5 Eric Martz

From Proteopedia

Revision as of 18:09, 20 February 2010

The initial scene is without PAR. Other visualizations:

• Without PAR ().

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Technical: Morphing

The morph adds, to the two empirical models, 7 interpolated frames generated by the Yale Morph Server (see Morphs).The 9 models for the morph were uploaded as Image:Moran asite par morph.pdb. Below is the script for the morph. In the SAT, the uploaded PDB file was loaded, then the Jmol Console was opened, and the script below was pasted in and run (with the "load" command commented out). The result was then saved as a scene, making sure to check "animation".

# The Yale Morph Server numbered the models 0-10. However, model/frame 0 has
# a special meaning in Jmol, namely, all models. In order to reduce confusion,
# I renumbered the models (by hand editing) 1-11.

zap;
color background white;
set antialiasdisplay on; # smoother rendering, speed penalty seems acceptable.

load moran_asite_par_morph.pdb;
spacefill off;
wireframe off;

# don't make par wireframe -- it shows thru the translucent spacefill.
select nucleic;
wireframe 0.1;

select par; # selects it in both the penultimate and ultimate models.
spacefill;

# We want par to appear translucent except in the last frame of the animation,
# where it is bound and should be opaque.
# Method: coordinates for par will be in two models: the next to last model
# (together with RNA), and the last model (by itself).
# par alone is in model 11 = frame 1.11.
# We'll make that translucent and set it as a background model.
# model 10 = frame 1.10 contains the last conformation of RNA plus par.
# We'll make that par opaque. It will show (covering up the translucent par)
# only in the last frame of the animation.

select par and model=11;
color translucent -1;
set backgroundmodel 1.11;

# model 10 is the last model with nucleic, and it also has par.
select par and model=10;
color opaque;

anim mode palindrome;

#frame 1.11 is the ligand PAR by itself.
# set frame range for anim
frame 1.1 1.10; # exclude frame 1.11 from the anim.
#frame range 1.1 1.10; #alternative syntax

# N.B. 'anim on' resets frame range! 'frame play' does not.
frame play;