Hey all—I would be interested in the "write state" function working with
combinations of PDB structures and inline models (built by importing from
JME or via model kit mode), for docking purposes. Given the recent work
that's been done on "dragminimize" and "dragminimizemolecule," it seems like
a natural next step.
However, currently, it's not working. I can append a molecule built in JME
to a PDB structure, drag it around, and even dragminimize, but upon saving
the state file to recover it later, most of the structure has disappeared!
Try loading the attached state file...this was an example of one of my
attempts. I also played around with modifying a PDB structure in model kit
mode; the resulting state file was mostly OK, but produced garbled results
at the point of modification.
This feels like an epic undertaking, so if it's something that can't be done
in the short term, that's cool. I'd like to see it in the long term, though.
Thanks and cheers!
Mike
--
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign
# Jmol state version 12.0.19 2010-10-13 12:38;
# fullName = "jmolApplet0__353044619318098__";
# documentBase =
"http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx";;
# codeBase = "http://butane.chem.illinois.edu/jsmoore/jmol-12.0.19/";;
function _setWindowState() {
# height 300;
# width 300;
stateVersion = 1200019;
background [xffffff];
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
set ambientPercent 45;
set diffusePercent 84;
set specular true;
set specularPercent 22;
set specularPower 40;
set specularExponent 6;
set zShadePower 1;
statusReporting = true;
}
function _setFileState() {
set allowEmbeddedScripts false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set autoBond true;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultLattice {0.0 0.0 0.0};
set defaultLoadFilter "";
set defaultLoadScript "";
set defaultVDW Auto;
set forceAutoBond false;
#set defaultDirectory "";
#set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";;
#set smilesUrlFormat
"http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";;
#set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
#set edsUrlCutoff
"load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split('
')[2]";
set minBondDistance 0.4;
set minimizationCriterion 0.0010;
set minimizationSteps 100;
set pdbGetHeader false;
set pdbSequential false;
set percentVdwAtom 23;
set smallMoleculeMaxAtoms 40000;
set smartAromatic true;
load /*file*/"http://www.pdb.org/pdb/files/1CA2.pdb";;
set allowEmbeddedScripts false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set autoBond true;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultLattice {0.0 0.0 0.0};
set defaultLoadFilter "";
set defaultLoadScript "";
set defaultVDW Auto;
set forceAutoBond false;
#set defaultDirectory "";
#set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";;
#set smilesUrlFormat
"http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";;
#set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
#set edsUrlCutoff
"load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split('
')[2]";
set minBondDistance 0.4;
set minimizationCriterion 0.0010;
set minimizationSteps 100;
set pdbGetHeader false;
set pdbSequential false;
set percentVdwAtom 23;
set smallMoleculeMaxAtoms 40000;
set smartAromatic true;
load data "model inline"
Jmol Model Kit
Jmol version 12.0.19 2010-10-13 12:38
EXTRACT: ({2207:2224})
18 18 0 0 0
5.9100924 -10.34723 -0.040026 C
5.9100914 -8.813674 0.0389630 C
4.649765 -8.243278 -0.628186 C
3.3894353 -8.81368 0.0389596 C
3.3894382 -10.34723 -0.040012 C
4.6497674 -10.91757 0.6271547 C
6.81498 -10.74849 0.4648995 H
5.938323 -10.66269 -1.106526 H
6.815003 -8.412387 -0.465885 H
5.938293 -8.498272 1.1054844 H
4.649797 -8.509049 -1.708641 H
4.6497774 -7.135599 -0.543885 H
2.4845235 -8.412394 -0.465889 H
3.3612537 -8.49827 1.1054779 H
3.3612165 -10.66270 -1.106508 H
2.4845543 -10.74849 0.4649247 H
4.6497846 -12.02527 0.5430842 H
4.649803 -10.65149 1.7075456 H
1 2 1
2 3 1
3 4 1
4 5 1
5 6 1
6 1 1
7 1 1
8 1 1
9 2 1
10 2 1
11 3 1
12 3 1
13 4 1
14 4 1
15 5 1
16 5 1
17 6 1
18 6 1
end "model inline";
}
function _setModelState() {
select ({0:2038});
Spacefill 0.0;
select BONDS ({0:2 4:2103});
wireframe 0.0;
measures delete;
select *; set measures nanometers;
font measures 15.0 SansSerif Plain;
select ({0:2038});
Cartoon on;
color Cartoon opaque structure;
boundBox off;
font boundBox 14.0 SansSerif Plain;
boundBox off;
frank on;
font frank 16.0 SansSerif Bold;
select *;
frame 1.1; moveto -1.0 {0 0 1 0} 130.0 0.0 0.0 {-9.6675 -1.6742415 15.94043}
33.434658 {0.0 0.0 0.0} 17.150644 -2.9701893 0.0;
frame 2.1; moveto -1.0 {0 0 1 0} 130.0 0.0 0.0 {-9.6675 -1.6742415 15.94043}
33.434658 {0.0 0.0 0.0} 17.150644 -2.9701893 0.0;
set fontScaling false;
}
function _setFrameState() {
# frame state;
# modelCount 2;
# first 1.1;
# last 2.1;
frame RANGE 1.1 2.1;
animation DIRECTION +1;
animation FPS 10;
animation MODE ONCE 0.0 0.0;
frame 0;
animation OFF;
}
function _setPerspectiveState() {
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth true;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {-30.402 -22.225 -10.542999} {15.806 23.178 44.217} # volume
= 114885.484;
center {-9.551675 -1.7382016 15.811473};
moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {-7.2980003 0.47649956 16.837} 33.399685
{0.0 0.0 0.0} 0.0 0.0 0.0;
save orientation "default"
moveto 0.0 { -494 -849 -186 114.07} 130.0 0.0 0.0 {-9.551675 -1.7382016
15.811473} 33.256035 {0.0 0.0 0.0} 22.989202 11.748764 0.0;;
slab 100;depth 0;
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY
0; set navZ 0; set navFps 10;
}
function _setSelectionState() {
hide ({2040:2206});
select ({2207:2224});
set hideNotSelected false;
}
function _setState() {
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setModelState;
_setFrameState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
}
_setState;
------------------------------------------------------------------------------
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