Bob-
I apologize for the incomplete information. The timing problems that I'm
having may actually be Jmol bugs, so I'll document an important case below.
1) I load ethane.
2) I run following Jmol script:
{atomIndex=3}.element = "C";minimize addHydrogens;select hydrogen and
connected({atomIndex=3});delete selected
The script only executes "{atomIndex=3}.element = "C";minimize
addHydrogens;"
If, however, I run the script in two separate steps (I'm using an execute
script text field on my page.), the two sequential steps do what I expected:
Step 1: select hydrogen and connected({atomIndex=3});delete selected;
Step 2: {atomIndex=3}.element = "C";minimize addHydrogens;
As expected, these two steps run separately add a carbon, add hydrogens, and
then delete these hydrogens. I've been calling my encounter with this type
of problem a "timing problem," but timing may not be the problem.
Of course, in this case, there is no need for the delete, but in general,
the steps 1 and 2 are needed - e.g. "{atomIndex=1}.element = "O";minimize
addHydrogens" requires a delete followed by an add.
I checked atomInfo after each step above, and, indeed, the new carbon atom
is atomIndex=3. Just in case I missed something in the atomInfo, I'll paste
the atom info for original ethane and after step 1 below:
Otis
Initial Ethane:
atomInfo *Vector[8]
atomInfo[1].element "carbon"
atomInfo[1].visible true
atomInfo[1].model "1"
atomInfo[1].radius 0.80833334
atomInfo[1].visibilityFlags 13
atomInfo[1].clickabilityFlags 12
atomInfo[1].bondCount 4
atomInfo[1].atomno 1
atomInfo[1].elemno 6
atomInfo[1].z 0.0
atomInfo[1].y 0.0
atomInfo[1].x -0.7615
atomInfo[1].partialCharge -0.067999996
atomInfo[1].sym "C"
atomInfo[1].colix -32762
atomInfo[1].spacefill 0.391
atomInfo[1].coord {-0.7615 0.0 0.0}
atomInfo[1].color "[x909090]"
atomInfo[1].info "[SUBUNIT]1:A.C1 #1"
atomInfo[1].atomIndex 0
atomInfo[1]._ipt 0
atomInfo[1].formalCharge 0
atomInfo[2].element "carbon"
atomInfo[2].visible true
atomInfo[2].model "1"
atomInfo[2].radius 0.80833334
atomInfo[2].visibilityFlags 13
atomInfo[2].clickabilityFlags 12
atomInfo[2].bondCount 4
atomInfo[2].atomno 2
atomInfo[2].elemno 6
atomInfo[2].z 0.0
atomInfo[2].y 0.0
atomInfo[2].x 0.7615
atomInfo[2].partialCharge -0.067999996
atomInfo[2].sym "C"
atomInfo[2].colix -32762
atomInfo[2].spacefill 0.391
atomInfo[2].coord {0.7615 0.0 0.0}
atomInfo[2].color "[x909090]"
atomInfo[2].info "[SUBUNIT]1:A.C2 #2"
atomInfo[2].atomIndex 1
atomInfo[2]._ipt 1
atomInfo[2].formalCharge 0
atomInfo[3].element "hydrogen"
atomInfo[3].visible true
atomInfo[3].model "1"
atomInfo[3].radius 0.525
atomInfo[3].visibilityFlags 13
atomInfo[3].clickabilityFlags 12
atomInfo[3].bondCount 1
atomInfo[3].atomno 3
atomInfo[3].elemno 1
atomInfo[3].z 0.0
atomInfo[3].y 1.0459
atomInfo[3].x -1.1422
atomInfo[3].partialCharge 0.0227
atomInfo[3].sym "H"
atomInfo[3].colix -32767
atomInfo[3].spacefill 0.253
atomInfo[3].coord {-1.1422 1.0459 0.0}
atomInfo[3].color "[xffffff]"
atomInfo[3].info "[SUBUNIT]1:A.H3 #3"
atomInfo[3].atomIndex 2
atomInfo[3]._ipt 2
atomInfo[3].formalCharge 0
atomInfo[4].element "hydrogen"
atomInfo[4].visible true
atomInfo[4].model "1"
atomInfo[4].radius 0.525
atomInfo[4].visibilityFlags 13
atomInfo[4].clickabilityFlags 12
atomInfo[4].bondCount 1
atomInfo[4].atomno 4
atomInfo[4].elemno 1
atomInfo[4].z 0.90500003
atomInfo[4].y -0.52419996
atomInfo[4].x -1.1422
atomInfo[4].partialCharge 0.0227
atomInfo[4].sym "H"
atomInfo[4].colix -32767
atomInfo[4].spacefill 0.253
atomInfo[4].coord {-1.1422 -0.52419996 0.90500003}
atomInfo[4].color "[xffffff]"
atomInfo[4].info "[SUBUNIT]1:A.H4 #4"
atomInfo[4].atomIndex 3
atomInfo[4]._ipt 3
atomInfo[4].formalCharge 0
atomInfo[5].element "hydrogen"
atomInfo[5].visible true
atomInfo[5].model "1"
atomInfo[5].radius 0.525
atomInfo[5].visibilityFlags 13
atomInfo[5].clickabilityFlags 12
atomInfo[5].bondCount 1
atomInfo[5].atomno 5
atomInfo[5].elemno 1
atomInfo[5].z -0.90500003
atomInfo[5].y -0.52419996
atomInfo[5].x -1.1422
atomInfo[5].partialCharge 0.0227
atomInfo[5].sym "H"
atomInfo[5].colix -32767
atomInfo[5].spacefill 0.253
atomInfo[5].coord {-1.1422 -0.52419996 -0.90500003}
atomInfo[5].color "[xffffff]"
atomInfo[5].info "[SUBUNIT]1:A.H5 #5"
atomInfo[5].atomIndex 4
atomInfo[5]._ipt 4
atomInfo[5].formalCharge 0
atomInfo[6].element "hydrogen"
atomInfo[6].visible true
atomInfo[6].model "1"
atomInfo[6].radius 0.525
atomInfo[6].visibilityFlags 13
atomInfo[6].clickabilityFlags 12
atomInfo[6].bondCount 1
atomInfo[6].atomno 6
atomInfo[6].elemno 1
atomInfo[6].z 0.0
atomInfo[6].y -1.0459
atomInfo[6].x 1.1422
atomInfo[6].partialCharge 0.0227
atomInfo[6].sym "H"
atomInfo[6].colix -32767
atomInfo[6].spacefill 0.253
atomInfo[6].coord {1.1422 -1.0459 0.0}
atomInfo[6].color "[xffffff]"
atomInfo[6].info "[SUBUNIT]1:A.H6 #6"
atomInfo[6].atomIndex 5
atomInfo[6]._ipt 5
atomInfo[6].formalCharge 0
atomInfo[7].element "hydrogen"
atomInfo[7].visible true
atomInfo[7].model "1"
atomInfo[7].radius 0.525
atomInfo[7].visibilityFlags 13
atomInfo[7].clickabilityFlags 12
atomInfo[7].bondCount 1
atomInfo[7].atomno 7
atomInfo[7].elemno 1
atomInfo[7].z 0.90500003
atomInfo[7].y 0.52419996
atomInfo[7].x 1.1422
atomInfo[7].partialCharge 0.0227
atomInfo[7].sym "H"
atomInfo[7].colix -32767
atomInfo[7].spacefill 0.253
atomInfo[7].coord {1.1422 0.52419996 0.90500003}
atomInfo[7].color "[xffffff]"
atomInfo[7].info "[SUBUNIT]1:A.H7 #7"
atomInfo[7].atomIndex 6
atomInfo[7]._ipt 6
atomInfo[7].formalCharge 0
atomInfo[8].element "hydrogen"
atomInfo[8].visible true
atomInfo[8].model "1"
atomInfo[8].radius 0.525
atomInfo[8].visibilityFlags 13
atomInfo[8].clickabilityFlags 12
atomInfo[8].bondCount 1
atomInfo[8].atomno 8
atomInfo[8].elemno 1
atomInfo[8].z -0.90500003
atomInfo[8].y 0.52419996
atomInfo[8].x 1.1422
atomInfo[8].partialCharge 0.0227
atomInfo[8].sym "H"
atomInfo[8].colix -32767
atomInfo[8].spacefill 0.253
atomInfo[8].coord {1.1422 0.52419996 -0.90500003}
atomInfo[8].color "[xffffff]"
atomInfo[8].info "[SUBUNIT]1:A.H8 #8"
atomInfo[8].atomIndex 7
atomInfo[8]._ipt 7
atomInfo[8].formalCharge 0
After Step 1:
atomInfo *Vector[11]
atomInfo[1].element "carbon"
atomInfo[1].visible true
atomInfo[1].model "1"
atomInfo[1].radius 0.80833334
atomInfo[1].visibilityFlags 13
atomInfo[1].clickabilityFlags 12
atomInfo[1].bondCount 4
atomInfo[1].atomno 1
atomInfo[1].elemno 6
atomInfo[1].z -0.07662228
atomInfo[1].y 0.044318
atomInfo[1].x -0.7284024
atomInfo[1].partialCharge -0.067999996
atomInfo[1].sym "C"
atomInfo[1].colix -32762
atomInfo[1].spacefill 0.391
atomInfo[1].coord {-0.7284024 0.044318 -0.07662228}
atomInfo[1].color "[x909090]"
atomInfo[1].info "[SUBUNIT]1:A.C1 #1"
atomInfo[1].atomIndex 0
atomInfo[1]._ipt 0
atomInfo[1].formalCharge 0
atomInfo[2].element "carbon"
atomInfo[2].visible true
atomInfo[2].model "1"
atomInfo[2].radius 0.80833334
atomInfo[2].visibilityFlags 13
atomInfo[2].clickabilityFlags 12
atomInfo[2].bondCount 4
atomInfo[2].atomno 2
atomInfo[2].elemno 6
atomInfo[2].z -1.9062017E-4
atomInfo[2].y 0.006451379
atomInfo[2].x 0.6672193
atomInfo[2].partialCharge -0.067999996
atomInfo[2].sym "C"
atomInfo[2].colix -32762
atomInfo[2].spacefill 0.391
atomInfo[2].coord {0.6672193 0.006451379 -1.9062017E-4}
atomInfo[2].color "[x909090]"
atomInfo[2].info "[SUBUNIT]1:A.C2 #2"
atomInfo[2].atomIndex 1
atomInfo[2]._ipt 1
atomInfo[2].formalCharge 0
atomInfo[3].element "hydrogen"
atomInfo[3].visible true
atomInfo[3].model "1"
atomInfo[3].radius 0.525
atomInfo[3].visibilityFlags 13
atomInfo[3].clickabilityFlags 12
atomInfo[3].bondCount 1
atomInfo[3].atomno 3
atomInfo[3].elemno 1
atomInfo[3].z -1.5137201E-5
atomInfo[3].y 0.9515201
atomInfo[3].x -1.1374098
atomInfo[3].partialCharge 0.0227
atomInfo[3].sym "H"
atomInfo[3].colix -32767
atomInfo[3].spacefill 0.253
atomInfo[3].coord {-1.1374098 0.9515201 -1.5137201E-5}
atomInfo[3].color "[xffffff]"
atomInfo[3].info "[SUBUNIT]1:A.H3 #3"
atomInfo[3].atomIndex 2
atomInfo[3]._ipt 2
atomInfo[3].formalCharge 0
atomInfo[4].element "carbon"
atomInfo[4].visible true
atomInfo[4].model "1"
atomInfo[4].radius 0.525
atomInfo[4].visibilityFlags 13
atomInfo[4].clickabilityFlags 12
atomInfo[4].bondCount 4
atomInfo[4].atomno 4
atomInfo[4].elemno 6
atomInfo[4].z 0.98063457
atomInfo[4].y -0.56796104
atomInfo[4].x -1.1781847
atomInfo[4].partialCharge 0.0227
atomInfo[4].sym "C"
atomInfo[4].colix -32762
atomInfo[4].spacefill 0.253
atomInfo[4].coord {-1.1781847 -0.56796104 0.98063457}
atomInfo[4].color "[x909090]"
atomInfo[4].info "[SUBUNIT]1:A.H4 #4"
atomInfo[4].atomIndex 3
atomInfo[4]._ipt 3
atomInfo[4].formalCharge 0
atomInfo[5].element "hydrogen"
atomInfo[5].visible true
atomInfo[5].model "1"
atomInfo[5].radius 0.525
atomInfo[5].visibilityFlags 13
atomInfo[5].clickabilityFlags 12
atomInfo[5].bondCount 1
atomInfo[5].atomno 5
atomInfo[5].elemno 1
atomInfo[5].z -0.8264246
atomInfo[5].y -0.47213003
atomInfo[5].x -1.1354815
atomInfo[5].partialCharge 0.0227
atomInfo[5].sym "H"
atomInfo[5].colix -32767
atomInfo[5].spacefill 0.253
atomInfo[5].coord {-1.1354815 -0.47213003 -0.8264246}
atomInfo[5].color "[xffffff]"
atomInfo[5].info "[SUBUNIT]1:A.H5 #5"
atomInfo[5].atomIndex 4
atomInfo[5]._ipt 4
atomInfo[5].formalCharge 0
atomInfo[6].element "hydrogen"
atomInfo[6].visible true
atomInfo[6].model "1"
atomInfo[6].radius 0.525
atomInfo[6].visibilityFlags 13
atomInfo[6].clickabilityFlags 12
atomInfo[6].bondCount 1
atomInfo[6].atomno 6
atomInfo[6].elemno 1
atomInfo[6].z -0.035207964
atomInfo[6].y -1.041018
atomInfo[6].x 1.2297618
atomInfo[6].partialCharge 0.0227
atomInfo[6].sym "H"
atomInfo[6].colix -32767
atomInfo[6].spacefill 0.253
atomInfo[6].coord {1.2297618 -1.041018 -0.035207964}
atomInfo[6].color "[xffffff]"
atomInfo[6].info "[SUBUNIT]1:A.H6 #6"
atomInfo[6].atomIndex 5
atomInfo[6]._ipt 5
atomInfo[6].formalCharge 0
atomInfo[7].element "hydrogen"
atomInfo[7].visible true
atomInfo[7].model "1"
atomInfo[7].radius 0.525
atomInfo[7].visibilityFlags 13
atomInfo[7].clickabilityFlags 12
atomInfo[7].bondCount 1
atomInfo[7].atomno 7
atomInfo[7].elemno 1
atomInfo[7].z 0.8839429
atomInfo[7].y 0.5514767
atomInfo[7].x 1.2301948
atomInfo[7].partialCharge 0.0227
atomInfo[7].sym "H"
atomInfo[7].colix -32767
atomInfo[7].spacefill 0.253
atomInfo[7].coord {1.2301948 0.5514767 0.8839429}
atomInfo[7].color "[xffffff]"
atomInfo[7].info "[SUBUNIT]1:A.H7 #7"
atomInfo[7].atomIndex 6
atomInfo[7]._ipt 6
atomInfo[7].formalCharge 0
atomInfo[8].element "hydrogen"
atomInfo[8].visible true
atomInfo[8].model "1"
atomInfo[8].radius 0.525
atomInfo[8].visibilityFlags 13
atomInfo[8].clickabilityFlags 12
atomInfo[8].bondCount 1
atomInfo[8].atomno 8
atomInfo[8].elemno 1
atomInfo[8].z -0.8266734
atomInfo[8].y 0.47145042
atomInfo[8].x 1.1457973
atomInfo[8].partialCharge 0.0227
atomInfo[8].sym "H"
atomInfo[8].colix -32767
atomInfo[8].spacefill 0.253
atomInfo[8].coord {1.1457973 0.47145042 -0.8266734}
atomInfo[8].color "[xffffff]"
atomInfo[8].info "[SUBUNIT]1:A.H8 #8"
atomInfo[8].atomIndex 7
atomInfo[8]._ipt 7
atomInfo[8].formalCharge 0
atomInfo[9].element "hydrogen"
atomInfo[9].visible true
atomInfo[9].model "1"
atomInfo[9].radius 0.525
atomInfo[9].visibilityFlags 13
atomInfo[9].clickabilityFlags 12
atomInfo[9].bondCount 1
atomInfo[9].atomno 9
atomInfo[9].elemno 1
atomInfo[9].z 1.0680546
atomInfo[9].y -1.4436048
atomInfo[9].x -0.5607295
atomInfo[9].partialCharge 0.0
atomInfo[9].sym "H"
atomInfo[9].colix -32767
atomInfo[9].spacefill 0.253
atomInfo[9].coord {-0.5607295 -1.4436048 1.0680546}
atomInfo[9].color "[xffffff]"
atomInfo[9].info "H9 #9"
atomInfo[9].atomIndex 8
atomInfo[9]._ipt 8
atomInfo[9].formalCharge 0
atomInfo[10].element "hydrogen"
atomInfo[10].visible true
atomInfo[10].model "1"
atomInfo[10].radius 0.525
atomInfo[10].visibilityFlags 13
atomInfo[10].clickabilityFlags 12
atomInfo[10].bondCount 1
atomInfo[10].atomno 10
atomInfo[10].elemno 1
atomInfo[10].z 1.7802764
atomInfo[10].y 0.13419197
atomInfo[10].x -1.0401628
atomInfo[10].partialCharge 0.0
atomInfo[10].sym "H"
atomInfo[10].colix -32767
atomInfo[10].spacefill 0.253
atomInfo[10].coord {-1.0401628 0.13419197 1.7802764}
atomInfo[10].color "[xffffff]"
atomInfo[10].info "H10 #10"
atomInfo[10].atomIndex 9
atomInfo[10]._ipt 9
atomInfo[10].formalCharge 0
atomInfo[11].element "hydrogen"
atomInfo[11].visible true
atomInfo[11].model "1"
atomInfo[11].radius 0.525
atomInfo[11].visibilityFlags 13
atomInfo[11].clickabilityFlags 12
atomInfo[11].bondCount 1
atomInfo[11].atomno 11
atomInfo[11].elemno 1
atomInfo[11].z 0.7612281
atomInfo[11].y -0.781339
atomInfo[11].x -2.2020159
atomInfo[11].partialCharge 0.0
atomInfo[11].sym "H"
atomInfo[11].colix -32767
atomInfo[11].spacefill 0.253
atomInfo[11].coord {-2.2020159 -0.781339 0.7612281}
atomInfo[11].color "[xffffff]"
atomInfo[11].info "H11 #11"
atomInfo[11].atomIndex 10
atomInfo[11]._ipt 10
atomInfo[11].formalCharge 0
--
Otis Rothenberger
http://chemagic.org
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
