Sandbox 5 Eric Martz: Difference between revisions

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<div style="background-color:pink; padding: 3px;border-width: 1px;border-color: black;border-style:solid;">
<div style="background-color:#ffd8d8;border-width:1px;border-color:#b00000;border-style:solid;padding:5px;">
This page is '''reserved''' for a collaboration between Moran Shalev and Eric Martz.
This page is reserved for Eric Martz and Jaim Prilusky.
</div>
</div>
<br>
This page displays part of the A site of the bacterial ribosome. The morph begins with the ligand-free moiety (from [[3bnl]]) and ends with the moiety complexed with an aminoglycoside (from [[1j7t]]).
<br><br>
<applet load='Moran_asite_par_morph.pdb' size='400' frame='true' align='right' caption='Insert caption here'
scene='Sandbox_5_Eric_Martz/Morph_asite_par_nopar/1' />


The initial scene is without PAR. Toggle Quality ON for improved displays. Be sure to rotate the morphs with the mouse to watch them from various perspectives.
<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs|morphed]] to the oxy form ([[1hho]]). Element colors: {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_Fe}}'
<ul>
scene='Sandbox_5_Eric_Martz/Heme/4' />
<li>
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par_bound/1'>PAR bound</scene>.
</li><li>
Without PAR (<scene name='Sandbox_5_Eric_Martz/Morph_asite_par_nopar/1'>restore initial scene</scene>).
</li><li>
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par_both_models/1'>Both empirical models</scene>.
</li><li>
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par/5'>Morph, wireframe RNA</scene>. <font color='red'>Sometimes you have to scroll the browser a little to start the animation.</font>
</li><li>
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par/6'>Morph, cartoon RNA</scene>.
{{Template:Button Toggle Animation2}}
</li>
</ul>
You can ''popup'' any of the above scenes. When popping up the morph, toggle quality OFF. It has little effect on quality in a large Jmol, but it does slow the morph animation considerably.


==Technical: Morphing==
This is a [[Morphs#Linear_Interpolation|linear interpolation morph]] showing the oxygenation/deoxygenation of heme in the beta chain of human hemoglobin. Chain B of [[1hga]] (deoxygenated, 2.1 &Aring;) was morphed to chain B of [[1hho]] (oxygenated, 2.1 &Aring;). The two chains were aligned on three carbon atoms in the heme.


The morph adds, to the two empirical models, 8 interpolated frames generated by the Yale Morph Server (see [[Morphs]]). To the 10 models of the morph was added an 11th model containing only PAR, for purposes of showing it as a translucent "background" during the morph animation. The resulting 11-model PDB file was 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 morph should then animate with the desired appearance in the SAT, namely, model 1.11 (translucent PAR) should be the constant background model, and it should not be included in the animation as the last frame (without RNA). The result was then saved as a scene, leaving "animate" '''unchecked'''. (The "animate" option is using a command, 'anim on', that resets the frame range to all frames. I have requested that is use instead 'frame play' which does not.)
The two carboxy groups on the heme, and one other carbon atom, were "frozen" because their positions in the two starting models differ for unimportant reasons, and their morph movements are distracting.


If you use the SAT to edit the representation or coloring of the morph, you will need to enter the command "frame play" in the Jmol Console just before saving the scene, leaving "animate" '''unchecked'''.
For more details about the morph PDB file: see
[[Image:Hb_heme_morph.pdb]].


The script below was developed in the Jmol ''application'' (Jmol.jar). The script will play offline if you put the PDB file, Jmol.jar, and the script in a file named 1.spt all in one directory, then double click Jmol.jar, then open the Script Console (right click on the black Jmol, then click Console on Jmol's menu), and enter (in the bottom box) "script 1.spt".
{{Template:Button Toggle Animation2}}
{{Clear}}
* <scene name='Sandbox_5_Eric_Martz/Heme/5'>Protein as backbone trace</scene>. (Protein color key below)
<pre>
* <scene name='Sandbox_5_Eric_Martz/Heme/6'>Protein spacefilled</scene>. (Protein color key below)
# The Yale Morph Server numbered the models 0-10. However, model/frame 0 has
* <scene name='Sandbox_5_Eric_Martz/Heme/4'>Initial scene</scene> (heme only).
# a special meaning in Jmol, namely, all models. In order to reduce confusion,
{{Template:ColorKey_N2CRainbow}}
# 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;
==Jmol Notes==
There are some formatting problems in this PDB file. Select iron with "hem.fe" (10 atoms, one in each model) and molecular oxygen with "hem.o?" (2 atoms, model 10 only). Iron is not recognized as such by Jmol and needed to be colored E06633. The two his sidechains shown are his62 and his92. Those sidechains can be selected with "select sidechain and (his63,his92)" or "select twohis". The iron-coordinating nitrogens in these his sidechains can be selected as "twohisn" or (his63.ne2,his92.ne2). Hmmm, it seems the [[SAT]] is destroying the defined tokens twohis and twohisn in the saved state scripts. Those worked prior to saving.


#frame 1.11 is the ligand PAR by itself.
If the last two atoms in the PDB file (molecular oxygen) were copied into a MODEL 11, they could be shown translucent throughout the animation, becoming opaque only in model 10. The script would need to include something like this (untested)
# 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.
*set backgroundModel 11
frame play;
*frame range 1 10
</pre>
*frame play # must be used instead of "animation on" which resets the frame range to "all".

Latest revision as of 21:34, 18 July 2010

This page is reserved for Eric Martz and Jaim Prilusky.

Human deoxy-hemoglobin (1hga) morphed to the oxy form (1hho). Element colors: C O N Fe

Drag the structure with the mouse to rotate

This is a linear interpolation morph showing the oxygenation/deoxygenation of heme in the beta chain of human hemoglobin. Chain B of 1hga (deoxygenated, 2.1 Å) was morphed to chain B of 1hho (oxygenated, 2.1 Å). The two chains were aligned on three carbon atoms in the heme.

The two carboxy groups on the heme, and one other carbon atom, were "frozen" because their positions in the two starting models differ for unimportant reasons, and their morph movements are distracting.

For more details about the morph PDB file: see File:Hb heme morph.pdb.

  • . (Protein color key below)
  • . (Protein color key below)
  • (heme only).
N               C

Jmol NotesJmol Notes

There are some formatting problems in this PDB file. Select iron with "hem.fe" (10 atoms, one in each model) and molecular oxygen with "hem.o?" (2 atoms, model 10 only). Iron is not recognized as such by Jmol and needed to be colored E06633. The two his sidechains shown are his62 and his92. Those sidechains can be selected with "select sidechain and (his63,his92)" or "select twohis". The iron-coordinating nitrogens in these his sidechains can be selected as "twohisn" or (his63.ne2,his92.ne2). Hmmm, it seems the SAT is destroying the defined tokens twohis and twohisn in the saved state scripts. Those worked prior to saving.

If the last two atoms in the PDB file (molecular oxygen) were copied into a MODEL 11, they could be shown translucent throughout the animation, becoming opaque only in model 10. The script would need to include something like this (untested)

  • set backgroundModel 11
  • frame range 1 10
  • frame play # must be used instead of "animation on" which resets the frame range to "all".

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Eric Martz
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