To embed a 3d scene in a web page

save scene.glb` #in chimera

Then in the html

  <script type="module" src="https://ajax.googleapis.com/ajax/libs/model-viewer/3.1.1/model-viewer.min.js"></script>

  <model-viewer alt="3D View of ChimeraX scene.glb file" src="scene.glb" style="width: 600px; height: 400px" shadow-intensity="1" camera-controls touch-action="pan-y"></model-viewer>

for more informations see web page

To display backbone only for selection and ribbon for the rest of the mode

sel :84-87,184-188
disp sel & backbone;  ~ribbon sel

This Python code will select the atoms directly bonded to the currently selected atom:

from chimerax.atomic import selected_atoms
selected_atoms(session).neighbors.selecteds = True

To figure out roughly whether ChimeraX will be able to handle your trajectory, multiply 24 (bytes) x #atoms x #frames and compare that to the size of your computer's memory. You could cut down on the total memory use by using the "step" argument of the open command to read only every Nth frame, but for some coordinate formats it will still temporarily read all frames, which could still be problematic if the trajectory is massive. (ML, Eric Pettersen)

in afold, plddt is encoded by bfactor. It is an atom property, so you need to do (@@bfactor)

Most co-factors bind allosterically and do not interact with the ligand, so we can usually delete them. Common co-factors and additives include cations (sodium and calcium most commonly), anions (usually chloride), sugars, ADP, ATP, orotic acid, steroids, NAD, NADP, FAD, SAH, SAM and vitamins. It’s pretty common for proteins to have multiple co-factors around.

action -> set pivot for fixing the f****ing visualiation issues

@n,ca,c,o backbone atoms

sel backbone & (aliphatic-primary-amine | @oxt) ; sel up to select first and last residue of all chains

info residues sel #This shows information on selected residues in the log

bond :cys@sg reasonable true #I think create bonds where bonds should be

alphafold contacts /C to /B distance 5.0 #when a json has been loaded, display the PAE for all atom pairs (/B./C) whose distance is 5.0A. lower is better, cold (blue) is better.

sel :a-b & backbone #select backbone in the a-b range

cartoon suppress false #prevent backbone suppression when displaying cartoons

transparency sel N target c # makes the ribbon (target c) associated to selection(sel) N% transparent

ribbon ::seq_rmsd<=18 #show only residues(::) whose rmsd is equal to or lower than 18 A

sel zone #1:1403 5; sel up; disp sel select only atoms whose dicance from res 1403 of model 1 is lower than 5, then select the residues these atoms belong to, and finally display the residues themselves.

color byattribute seq_rmsd #1 palette blue:red:yellow key TRUE color model one based on rmsd from template; also add a key.

sel #1 & ribbon #select all #1 ribbons

contacts /A@C* restrict :LIG@C* distance 3.8 reveal true name vdW show all contacts between carbons on chain a (/A@C*) and ligand (LIG) carbonds (:BTN@C*) at a distance of 3.8 angstroms (i.e. vdW, that ranges between 2 and 4)

contacts :MET restrict #1@N*,O* distance 3.5 reveal true name metalbonds color gold #show all contacts between the metal (MET) and any nitrogen or oxigen atom of model #1 at a distance of 3.5 Angstrom (distance in [3,4] is good)

contacts :CYS@S* restrict :CYS@S* distance 3.8 reveal true name disB radius 1 dashes 0 color yellow

cofr centerOfView set center of view as molecule center of rotation

rangecolor kdHydrophobicity min dodger blue 0 white max orange red # Display hydrophobicity range see this for reference

First find the center of mass of the something:

measure center $thing

then create a cube.cmm file

<marker_set name="cube">
<marker id="1" x="x-" y="y-" z="z-" radius="0.1"/>
<marker id="2" x="x+" y="y-" z="z-" radius="0.1"/>
<marker id="3" x="x-" y="y+" z="z-" radius="0.1"/>
<marker id="4" x="x+" y="y+" z="z-" radius="0.1"/>
<marker id="5" x="x-" y="y-" z="z+" radius="0.1"/>
<marker id="6" x="x+" y="y-" z="z+" radius="0.1"/>
<marker id="7" x="x-" y="y+" z="z+" radius="0.1"/>
<marker id="8" x="x+" y="y+" z="z+" radius="0.1"/>
<link id1="1" id2="2" radius="0.1"/>
<link id1="2" id2="4" radius="0.1"/>
<link id1="4" id2="3" radius="0.1"/>
<link id1="3" id2="1" radius="0.1"/>
<link id1="5" id2="6" radius="0.1"/>
<link id1="6" id2="8" radius="0.1"/>
<link id1="8" id2="7" radius="0.1"/>
<link id1="7" id2="5" radius="0.1"/>
<link id1="1" id2="5" radius="0.1"/>
<link id1="2" id2="6" radius="0.1"/>
<link id1="3" id2="7" radius="0.1"/>
<link id1="4" id2="8" radius="0.1"/>
</marker_set>

with coordinates:

x- : (xcenter - x_size/2)
x+ : (xcenter - x_size/2)
y- : (ycenter - y_size/2)
y+ : (ycenter - y_size/2)
z- : (zcenter - z_size/2)
z+ : (zcenter - z_size/2)