Lines Matching refs:atoms
455 # bug fix: load trajectory {0 -1 1} not loading any models if first model has 0 atoms
507 # print 'there are ' + all.length + ' atoms'
743 # print ({*} < 100 ? "a small molecule" : "at least 100 atoms")
839 # yes yes yes atomID special atom IDs for PDB atoms assigned by Jmol
991 # new feature: load XYZ ... loads just the XYZ coordinates, in sequence, based on selected atoms.
1016 # --operates on previously selected atoms only
1022 # new feature: select within(-0.1, {1/2 1/2 1/2}) -- negative distance within selects atoms based o…
1023 …-0.1, atomno=3) -- negative distance within selects atoms based on unitcell coordinates of all ato…
1024 # new feature: select within(-0.1, true, atomno=3) -- negative distance within model selects atoms …
1083 # bug fix: Hall lattice operation (SHELX only) could place atoms in unexpected unit cell
1084 # bug fix: unitCell normalization error could miss some atoms in multi-unit cell visualizations
1092 # bug fix: calculate hbonds can fail when group does not have O or OXT atoms
1151 # new feature: frame ALIGN {atoms} -- aligns frames around designated atoms in each frame
1160 # around code that might be running and deleting atoms or bonds while some other
1214 # bug fix: measure n1 n2 n3 n4 with just numbers selecting atoms in frame 1 rather than current fr…
1241 # bug fix: MO calculation with selected atoms can fail
1242 # bug fix: picked atoms automatically selected -- bug in 11.7.24
1287 # ALT_LEFT or CTRL_ALT_RIGHT highlights atoms and rotates them
1288 # ALT_SHIFT_LEFT highlights atoms and translates them
1566 # for any atoms A--X- - -Y where A is attached to X,
1661 # bug fix: AMBER molecular dynamics topology file misreads P atoms
1708 # -- quaternion is created based on three atoms or coordinates
1887 # new feature: draw ramachandran includes planes connecting atoms.
1994 # bug fix: application rubberband selecting inappropriately selects atoms not visible
2186 # bug fix: quaternion frame "n" recognizes file-based H atoms on N for frame definition
2314 # bug fix: state script fails to save data for atoms created using the quaternion command
2491 # -- No atoms selected!
2492 # -- <n> atoms selected!
2526 # (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()})
2538 # new feature: set drawPicking now enables measuring among atoms and DRAW points
2556 # bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value)
2631 # The first format loads only those atoms matching a specific filter or set of
2789 # draw circle {molecule=1} mesh nofill # around specified atoms
2802 # minimization CLEAR releases constraints and fixed atoms
2911 # bug fix: zap {atom expression} for not including all atoms in a model in the selection
2917 # new feature: zap {atom expression} # zaps models associated with given atoms.
2962 # bug fix: write PDB format incorrectly writes atoms with 4-length names
2973 # bug fix: write PDB format incorrectly writes atoms with 4-length names
3094 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms
3209 # for proteins, just the helix or turn or sheet containing those atoms;
3299 …bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected atoms
3431 # bug fix: symop=0NNN not returning all atoms with translation NNN
3434 # box containing symop=1555, not the atoms themselves.
3590 # bug fix: multimodel files could have connected atoms between different models.
3632 # bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms
3639 # bug fix: new boundbox command with small numbers of atoms
3644 …mol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for this set of atoms
3676 # bug fix: POVRAY and other buttons aren't enabled when there are no atoms but instead draw objects…
3697 # bug fix for selecting atoms of atomsets using [-n] or [0]
3827 # if the array is shorter than the number of atoms selected, then
3828 # only that number of atoms are affected
3843 # bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms.
3876 # bug fix: slabbed atoms are now capped in povray output.
3877 # Note: In CPK mode atoms overlap, but are capped at the same height.
3922 # color atoms @{xlist[n]};
3932 # bug fix: 0-diameter atoms displayed as single pixels when perspectiveDepth = false
4043 # All the atoms, bonds, and models are now in ModelSet.
4113 # new feature: select ISAROMATIC # selects aromatic atoms
4187 # allows finding atoms within a specified distance of other atoms in OTHER models:
4268 # color atoms blue
4273 # color atoms cpk
4431 # new feature: aPlane.distance({some atoms})
4451 # color atoms "byresidue_Jmol"
4461 # color atoms "byElement_Mine"
4541 # color atoms property partialcharge "rwb" range -1.0 1.0
4545 # color atoms property partialcharge "rwb" range 1.0 -1.0
4611 # color atoms property partialcharge "user" range -1.0 1.0
4915 # bug fix for symop=nijk selecting base atoms when not appropriate
4917 # bug fix for adding atoms but mads[] going stale
4929 # bug fix for load append with spacegroups causing atoms to be repositioned
4940 # bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0}
5020 # adds capability to define a property for selected atoms:
5142 # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
5144 # normal Jmol autobonding would not properly connect atoms, but
5150 # new bonds are created that are between atoms that were created
5164 # the same number of atoms. Atom locations can also be updated on the
5169 # of atoms.
5399 # jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3)
5431 # about 58% of the full package. All that gets you is atoms, bonds,
5448 # x = {*}.atoms.max #the last atom
5509 # {oxygen} and {molecule=1} ==> all oxygen atoms in the first molecule
5513 # x is now the center point of all oxygen atoms in the first molecule
5589 # adds connected() both for finding atoms and for identifying bonds:
5594 # x.atoms
5661 # Now that we can move atoms so easily, we don't want those measurements getting stale.
5721 # x = {carbon}[3][5] # the third through fifth carbon atoms
5722 # x = {carbon}[3][0] # the third through last carbon atoms
5789 # You can select atoms from an atom expression using [n].
5819 # atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL
5877 # and it will AUTOMATICALLY update with new values as you select different atoms.