[Jmol-users] Electron Density for 3hz7

[Eric Martz]

Today, crystallographer Harry Greenblatt kindly looked at the page I made 
yesterday on electron density maps (http://www.umass.edu/molvis/tests/jmol_edm/ 
). He pointed out that the 2 Angstrom resolution example that I chose, 3hz7, 
has an unusually poor electron density (e.g. all those waters and outlying 
residues that have no density at 1 sigma). Checking at MolProbity showed this 
model to have an unusually high number of atomic clashes for its resolution. So 
it is a bad example. I will replace it when I have time. Meanwhile, I have put 
a note about this on the page.

--

Eric Martz, Ph.D.

Professor Emeritus, Microbiology, University of Massachusetts, Amherst

http://martz.molviz.org


  --
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] help displaying jvxl MO

[Grossman, Robert B]

Hi,

I have a JVXL file containing MO data that I am trying to display.  I can see 
the molecule, but I can't see the MO.  I have tried various scripts to turn on 
the MO, to no avail.  Below I have copied the relevant part of my Web page.  I 
am using 'mo HOMO;' as the script, but I have tried several other commands, 
including none, to no avail.  How do I display the MO?  Does the fact that I 
load inline prevent the MO from being displayed?

-- Bob

script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15  2008-11-24 
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, 
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ?\n-32 
-4.286028 -4.170638 -6.45537 ANGSTROMS\n80 0.12402356 0.0 0.0\n80 0.0 0.184445 
0.0\n80 0.0 0.0 0.1257623\n6 6.0 0.0 0.0 0.0\n6 6.0 1.5335295 0.0 0.0\n8 8.0 
2.447 1.1734227 0.0\n6 6.0 2.3022442 2.08224 -1.0298198\n6 6.0 1.9440373 
3.352165 -0.783915\n6 6.0 2.166842 4.391685 -1.8063345\n8 8.0 1.4540279 
5.5320063 -1.5695299\n6 6.0 1.4419276 6.5410266 -2.576349\n6 6.0 0.4292079 
7.5804462 -2.13194\n1 1.0 0.699213 8.036855 -1.1707217\n1 1.0 0.36370665 
8.384962 -2.8751543\n1 1.0 -0.57431144 7.149238 -2.0169382\n1 1.0 2.4541469 
6.9775352 -2.6722505\n1 1.0 1.1674224 6.103718 -3.555268\n8 8.0 2.9358563 
4.365084 -2.7551525\n1 1.0 1.4746284 3.6545703 0.16250335\n1 1.0 2.660351 
1.708333 -1.9975383\n6 6.0 2.025939 -0.95221835 -1.101621\n1 1.0 1.6514318 
-1.9706379 -0.937718\n1 1.0 1.6784323 -0.62881225 -2.0926402\n1 1.0 3.1216602 
-1.0091194 -1.1394216\n1 1.0 1.869836 -0.3798073 0.9982192\n6 6.0 -0.86121655 
0.62561214 -1.0898211\n6 6.0 -0.8380163 2.0938404 -1.2457241\n6 6.0 -0.81681573 
2.6353507 -2.5209484\n7 7.0 -0.79011524 3.084059 -3.6053698\n6 6.0 -1.1576223 
2.898656 -0.16150327\n7 7.0 -1.4360279 3.5764692 0.75561434\n1 1.0 -0.59091145 
0.1594031 -2.0609396\n1 1.0 -1.9027367 0.2891056 -0.885317\n1 1.0 -0.29010567 
-1.0688207 0.08750176\n1 1.0 -0.314506 0.47200906 0.95541835\n-1 35 90 35 90 
Jmol voxel format version 1.4\n# \n0.05 361 -1362 1362 -1.0 1.0 -1.0 1.0 
rendering:isosurface ID homop fill noMesh noDots notFrontOnly frontlit\n 
117879 5 75 6 74 5 6154 7 72 9 71 9 71 9 72 7 75 3 5915 7 72 9 70 11 69 11 69 
11 70 10 71 7 5834 4 74 9 70 11 68 13 67 13 67 13 68 12 69 9 73 5 5754 7 71 11 
68 13 67 13 66 14 67 13 67 13 68 11 71 7 5752 8 71 11 68 13 66 14 66 15 65 15 
66 13 68 11 71 7 334 2 77 4 77 2 5256 8 70 12 68 13 66 14 66 14 66 14 67 13 68 
11 71 7 173 3 75 6 74 7 72 8 73 6 75 4 5176 8 71 11 68 12 67 14 66 14 66 14 67 
12 69 10 73 4 173 6 73 8 71 10 70 9 72 8 73 6 5176 6 72 10 69 11 69 12 68 12 68 
11 70 9 73 5 175 2 75 7 72 9 71 10 70 10 70 9 72 7 5256 6 72 9 71 9 71 9 72 7 
75 2 256 3 75 7 72 9 71 9 71 9 71 9 72 7 5993 7 72 9 71 9 71 9 71 8 74 5 5801 4 
74 7 73 7 29 5 39 7 28 7 40 4 28 8 73 7 73 6 5800 5 74 7 72 9 71 9 71 9 28 4 40 
7 29 5 75 5 77 1 4709 4 77 3 1008 7 72 9 70 10 70 10 71 9 72 7 75 3 4743 3 76 5 
75 5 77 3 928 7 72 9 70 10 70 10 71 9 72 7 75 3 4742 4 76 5 75 5 76 4 928 6 73 
8 71 10 70 10 71 9 72 7 4820 3 77 5 75 5 76 4 929 4 75 7 72 8 72 8 73 7 74 5 
4822 1 78 4 76 4 77 3 1010 5 74 6 74 6 75 5 4982 2 78 2 
279630\nW4?A7Kv(0Dwm)s(RKaX!S@V0QmxtbS9C3Omxtb9B|#HVR:PQ|RBGbHJB!-8:#vKSHeHZQ`a...@tu(DQOaJ[6OJRKgiv\'trpm+r...@f7ob*7gzt4@dX!q:`...@ag|ga{$l{\'-v9-wuv+p2wm...@[s7k]u[Fw,*\'Lq##%$l|R-5pEO=W?69JmAOWTW\'_XQcN[n*cJOw\'m31X,GNHDmuXy^Izv+kA2axMh_lP:ZqF1*-!,lA;p.)w*)E8BQXQleUe,Z60]Nrx[zeCzs(b;23c`]buFGwJ6\/3cg...@a`tvvjk4dj4:,+eS\'c\'e5j-mMYzUSYS*ES9Xc^Hj9!cv|wgBP74=JC\'+g^uny...@kon^c:I2*w,@re=YqVOVpfMXiEKqP2Tntyt{_e125nBUkx4btL\'^\'tFOE{#YXCwPuT[HX|;8XXq*P]T\/O4;9TBwZPXsOS.STEk,e*rMsrUZOT^]s.d7GeQvLo8KU!4ql(*(drzx]gjazd...@g8kn@FWtce=9e2^F;CSlmC.(\/ErmVLLSazymkrw+OcjfT\/H6A]^LK+v#w=Q45JQM,UG`631[smx\/9\'-\']3h\'g9{EKKwDX7t\'y#P^baZLp4S^+DXejjbR6Qx$R^ecZF##uk(=JOK=%x|m)\/K6![mrm[4TINK2tJrk|pN0G()UDG)N#y.7cro?(3N?QDKA:5m!){Wl{yxfSHnw\/BcymJ!Zd-X_ma0_Za6)s46n+]z=eap0dabuyll+gc`e99d].itfk...@lqvz)3$xJgwBoIiIC:WTZ;.`\/[;[%o%\/1.1$$)9S4]Yr{pXu2;@^=FxUl^Jh0rFC6VA]Ca;A3B\/u!dz%.rz7L[`=LdD2))1Dfa1ZFI8P-e(kr-tJc;^rH%|#g$$#8O;In3.;ibxkw)h...@]lqnd\/GICGPinIc!MXjn.bD(Q7Bb[=q]W1%`*45Zz!A1))0a`l...@%w8p$9xr,vxM.MsTf(8\'x#=YN_];G[vysz96LWZVJ5VT.wqH^r:dd2x7N9sRHX-9[OiXX+tjb0C?EfL44;Ll{v{jisss1NEPSN@(0HCpc4=_JFE[)u;K*9Qv9oKovNQxE|,dD[|bRJIReI,T8;4$\'l#T#rgBYT\'x|diBN^FGWn`HQaA9p7IrX1j:iC|*6N1DStklvgLFUz)F,^jlfU7NFw6ixct+;6qXN0-k7RG[K733z%HXj7W;uxg...@zmpfl++n\/\/6`j(S.tiBS;9qARHJ\/3`8gs...@wkt8hpdf.\/*);_]snyS6($+?aU+OAqyiF4bJ|m\'R`{3YB5ahgED38-C1gBbhXS[o|]MHOap]X^q\n|~1361
 \n#---end of jvxl file data---\n# cutoff = 0.05; pointsPerAngstrom = 
8.062984; nSurfaceInts = 361; nBytesData = 3736; bicolor map\n# created using 
Jvxl.java\n# precision: false nColorData 1362\n# isosurface homop cutoff +0.05 
mo homo fill;\n# isosurface ID homop fill noMesh noDots notFrontOnly 
frontlit\n# bytes read: 0; approximate voxel-only input\/output byte ratio: