Skip to content

Commit

Permalink
talk
Browse files Browse the repository at this point in the history
  • Loading branch information
@dkoes
dkoes committed Mar 14, 2024
1 parent 14ebf43 commit f4a00f8
Show file tree
Hide file tree
Showing 28 changed files with 56,938 additions and 2 deletions.
1,016 changes: 1,016 additions & 0 deletions paper/talk/1fas.pqr
View file

Large diffs are not rendered by default.

2,298 changes: 2,298 additions & 0 deletions paper/talk/1lo6.pdb
View file

Large diffs are not rendered by default.

Binary file added paper/talk/1lo6_2FOFC.ccp4
View file
Binary file not shown.
2,761 changes: 2,761 additions & 0 deletions paper/talk/3dmol.ipynb
View file

Large diffs are not rendered by default.

17,805 changes: 17,805 additions & 0 deletions paper/talk/3dmol.slides.html
View file

Large diffs are not rendered by default.

Binary file added paper/talk/4csv.ccp4.gz
View file
Binary file not shown.
2,500 changes: 2,500 additions & 0 deletions paper/talk/4csv.pdb
View file

Large diffs are not rendered by default.

1,313 changes: 1,313 additions & 0 deletions paper/talk/Dt.cube
View file

Large diffs are not rendered by default.

1,313 changes: 1,313 additions & 0 deletions paper/talk/ESP.cube
View file

Large diffs are not rendered by default.

36 changes: 36 additions & 0 deletions paper/talk/TODO
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
full screen correct
zoom correct on cif grid
autozoom at end

# Molecular Dynamics Trajectories

Topology (.gro, .prmtop, .pdb) loaded separately from trajectory (.mdcr, netcdf, mdserv URL).


<br><br><br><br><br><br><br><br><br><br><br><br><br><br>

%%html
<div style="height: 400px; width: 100%; z-index: -1;" class='viewerbackground' id='mdsim' ></div>

<script>
$3Dmolpromise.then(function() {
var mdviewer = $3Dmol.createViewer('mdsim');
$3Dmol.get("https://3dmol.csb.pitt.edu/mdsrv/file/data/md.gro", function (data){
var m = mdviewer.addModel(data, "gro");
m.setStyle({cartoon:{},stick:{}});
m.setStyle({resn:"SOL"},{sphere:{opacity:0.5}});

mdviewer.zoomTo();
mdviewer.render( );
var url = "https://3dmol.csb.pitt.edu/mdsrv/";
var pathToFile = "data/md.xtc";

m.setCoordinatesFromURL(url, pathToFile)
.then(function() {
mdviewer.zoomTo();
mdviewer.animate();
}).catch().then(function() {});
});
});
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
5,608 changes: 5,608 additions & 0 deletions paper/talk/af.pdb
View file

Large diffs are not rendered by default.

21,194 changes: 21,194 additions & 0 deletions paper/talk/benzene-homo.cube
View file

Large diffs are not rendered by default.

222 changes: 222 additions & 0 deletions paper/talk/cifex.cif
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,222 @@
data_HKUST-1Fm-3m
_audit_creation_method 'generated by CrystalMaker X for macOS'
_cell_length_a 26.343000
_cell_length_b 26.343000
_cell_length_c 26.343000
_cell_angle_alpha 90.000000
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000

_symmetry_space_group_name_H-M 'F m -3 m'

loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'+z,+x,+y'
'+y,+z,+x'
'+x,+y,-z'
'+z,+x,-y'
'+y,+z,-x'
'-x,+y,+z'
'-z,+x,+y'
'-y,+z,+x'
'-x,+y,-z'
'-z,+x,-y'
'-y,+z,-x'
'+y,+x,+z'
'+x,+z,+y'
'+z,+y,+x'
'+y,+x,-z'
'+x,+z,-y'
'+z,+y,-x'
'+y,-x,+z'
'+x,-z,+y'
'+z,-y,+x'
'+y,-x,-z'
'+x,-z,-y'
'+z,-y,-x'
'-x,-y,-z'
'-z,-x,-y'
'-y,-z,-x'
'-x,-y,+z'
'-z,-x,+y'
'-y,-z,+x'
'+x,-y,-z'
'+z,-x,-y'
'+y,-z,-x'
'+x,-y,+z'
'+z,-x,+y'
'+y,-z,+x'
'-y,-x,-z'
'-x,-z,-y'
'-z,-y,-x'
'-y,-x,+z'
'-x,-z,+y'
'-z,-y,+x'
'-y,+x,-z'
'-x,+z,-y'
'-z,+y,-x'
'-y,+x,+z'
'-x,+z,+y'
'-z,+y,+x'
'+x,1/2+y,1/2+z'
'1/2+x,1/2+y,+z'
'1/2+x,+y,1/2+z'
'+z,1/2+x,1/2+y'
'1/2+z,1/2+x,+y'
'1/2+z,+x,1/2+y'
'+y,1/2+z,1/2+x'
'1/2+y,1/2+z,+x'
'1/2+y,+z,1/2+x'
'+x,1/2+y,1/2-z'
'1/2+x,1/2+y,-z'
'1/2+x,+y,1/2-z'
'+z,1/2+x,1/2-y'
'1/2+z,1/2+x,-y'
'1/2+z,+x,1/2-y'
'+y,1/2+z,1/2-x'
'1/2+y,1/2+z,-x'
'1/2+y,+z,1/2-x'
'-x,1/2+y,1/2+z'
'1/2-x,1/2+y,+z'
'1/2-x,+y,1/2+z'
'-z,1/2+x,1/2+y'
'1/2-z,1/2+x,+y'
'1/2-z,+x,1/2+y'
'-y,1/2+z,1/2+x'
'1/2-y,1/2+z,+x'
'1/2-y,+z,1/2+x'
'-x,1/2+y,1/2-z'
'1/2-x,1/2+y,-z'
'1/2-x,+y,1/2-z'
'-z,1/2+x,1/2-y'
'1/2-z,1/2+x,-y'
'1/2-z,+x,1/2-y'
'-y,1/2+z,1/2-x'
'1/2-y,1/2+z,-x'
'1/2-y,+z,1/2-x'
'+y,1/2+x,1/2+z'
'1/2+y,1/2+x,+z'
'1/2+y,+x,1/2+z'
'+x,1/2+z,1/2+y'
'1/2+x,1/2+z,+y'
'1/2+x,+z,1/2+y'
'+z,1/2+y,1/2+x'
'1/2+z,1/2+y,+x'
'1/2+z,+y,1/2+x'
'+y,1/2+x,1/2-z'
'1/2+y,1/2+x,-z'
'1/2+y,+x,1/2-z'
'+x,1/2+z,1/2-y'
'1/2+x,1/2+z,-y'
'1/2+x,+z,1/2-y'
'+z,1/2+y,1/2-x'
'1/2+z,1/2+y,-x'
'1/2+z,+y,1/2-x'
'+y,1/2-x,1/2+z'
'1/2+y,1/2-x,+z'
'1/2+y,-x,1/2+z'
'+x,1/2-z,1/2+y'
'1/2+x,1/2-z,+y'
'1/2+x,-z,1/2+y'
'+z,1/2-y,1/2+x'
'1/2+z,1/2-y,+x'
'1/2+z,-y,1/2+x'
'+y,1/2-x,1/2-z'
'1/2+y,1/2-x,-z'
'1/2+y,-x,1/2-z'
'+x,1/2-z,1/2-y'
'1/2+x,1/2-z,-y'
'1/2+x,-z,1/2-y'
'+z,1/2-y,1/2-x'
'1/2+z,1/2-y,-x'
'1/2+z,-y,1/2-x'
'-x,1/2-y,1/2-z'
'1/2-x,1/2-y,-z'
'1/2-x,-y,1/2-z'
'-z,1/2-x,1/2-y'
'1/2-z,1/2-x,-y'
'1/2-z,-x,1/2-y'
'-y,1/2-z,1/2-x'
'1/2-y,1/2-z,-x'
'1/2-y,-z,1/2-x'
'-x,1/2-y,1/2+z'
'1/2-x,1/2-y,+z'
'1/2-x,-y,1/2+z'
'-z,1/2-x,1/2+y'
'1/2-z,1/2-x,+y'
'1/2-z,-x,1/2+y'
'-y,1/2-z,1/2+x'
'1/2-y,1/2-z,+x'
'1/2-y,-z,1/2+x'
'+x,1/2-y,1/2-z'
'1/2+x,1/2-y,-z'
'1/2+x,-y,1/2-z'
'+z,1/2-x,1/2-y'
'1/2+z,1/2-x,-y'
'1/2+z,-x,1/2-y'
'+y,1/2-z,1/2-x'
'1/2+y,1/2-z,-x'
'1/2+y,-z,1/2-x'
'+x,1/2-y,1/2+z'
'1/2+x,1/2-y,+z'
'1/2+x,-y,1/2+z'
'+z,1/2-x,1/2+y'
'1/2+z,1/2-x,+y'
'1/2+z,-x,1/2+y'
'+y,1/2-z,1/2+x'
'1/2+y,1/2-z,+x'
'1/2+y,-z,1/2+x'
'-y,1/2-x,1/2-z'
'1/2-y,1/2-x,-z'
'1/2-y,-x,1/2-z'
'-x,1/2-z,1/2-y'
'1/2-x,1/2-z,-y'
'1/2-x,-z,1/2-y'
'-z,1/2-y,1/2-x'
'1/2-z,1/2-y,-x'
'1/2-z,-y,1/2-x'
'-y,1/2-x,1/2+z'
'1/2-y,1/2-x,+z'
'1/2-y,-x,1/2+z'
'-x,1/2-z,1/2+y'
'1/2-x,1/2-z,+y'
'1/2-x,-z,1/2+y'
'-z,1/2-y,1/2+x'
'1/2-z,1/2-y,+x'
'1/2-z,-y,1/2+x'
'-y,1/2+x,1/2-z'
'1/2-y,1/2+x,-z'
'1/2-y,+x,1/2-z'
'-x,1/2+z,1/2-y'
'1/2-x,1/2+z,-y'
'1/2-x,+z,1/2-y'
'-z,1/2+y,1/2-x'
'1/2-z,1/2+y,-x'
'1/2-z,+y,1/2-x'
'-y,1/2+x,1/2+z'
'1/2-y,1/2+x,+z'
'1/2-y,+x,1/2+z'
'-x,1/2+z,1/2+y'
'1/2-x,1/2+z,+y'
'1/2-x,+z,1/2+y'
'-z,1/2+y,1/2+x'
'1/2-z,1/2+y,+x'
'1/2-z,+y,1/2+x'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C C 1.0 0.3219926 0.1780074 0.8870003
C_1 C 1.0 0.2968056 0.2031944 0.9313006
C_2 C 1.0 0.3654956 0.1993983 0.8654956
Cu Cu 1.0 0.2852655 0.7852655 0.5
H H 1.0 0.036243 0.1414797 0.8585203
H_1 H 1.0 0.3802054 0.2280018 0.8802054
O O 1.0 0.3166401 0.2431291 0.9477565
O_1 O 1.0 0.3434024 0.8434024 0.5

Binary file added paper/talk/colab.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added paper/talk/develop.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit f4a00f8

Please sign in to comment.