[Jmol-developers] proposed changes: measure/monitor, connect, bondorder, model, frame

[Bob H. <ha...@st...>]

First, thank you to all those who responded to my request for 
suggestions both
online, offline, and by phone.

Comments are requested on possible changes to five commands:

measure/monitor
connect
bondorder
model
frame

-----------------
measure/monitor:

action: marks a distance, angle, or dihedral angle with line and/or label
Currently requires up to four integer numbers.

  monitor 2087 2088

proposed change: add the capability of specifying atom
selection sets instead of integers, thus:

  monitor ([LIP]3:A.O5) ([LIP]3:A.O6)

effect on current implementation: none

status: implemented at 
<http://www.stolaf.edu/people/hansonr/jmol/test/json/express.htm>


-----------------
connect:

action: creates/removes bonds and changes bond order
Currently requires a previous select command

proposed change 1: add the option to specify minimum and maximum
distances between atoms:

  select (carbon and atomno<5)
  connect 1.2 2.0 DOUBLE (oxygen)

proposed change 2: add the option to specify both sets of
atoms as parameters:

  connect 1.2 2.0 DOUBLE (carbon and atomno<5) (oxygen)

proposed change 3: add the EXISTS option to restrict operation
to bonds already in existance, not make new bonds.

  connect 1.2 2.0 DOUBLE EXISTS (carbon) (oxygen)

effect on current implementation: none

status: implemented at 
<http://www.stolaf.edu/people/hansonr/jmol/test/json/express.htm>


-----------------
bondorder:

action: undocumented "set bondmode"-dependent bond order changes

proposed change: remove command -- this is better handled with connect.

status: waiting for comment; not implemented in prototype


-----------------
model:

action: allows selection of a specific model "N" or displays all models.
Allows limited navigation with "next" and "-1". The number "N" is the model
number specified on the MODEL line of a PDB file or, for other file formats,
just the serial index to the model in the file, starting with 1.

proposed change: add options RANGE, PREVIOUS, PLAY, PLAYREV, PAUSE

  model RANGE 10 20

specifies the starting model and ending model for animations and (possibly?)
for MODEL ALL; displays the first model. If the first number is greater
than the second,

  model RANGE 20 10

plays animation in the specified order, starting in this case with model 20.

   model PREVIOUS

same as "model -1"

  model PLAY  [model number]

starts animation at the specified model number or the current model, if not
specified, and plays only within the range, if previously specified. Plays
in current direction (as specified by the "animation DIRECTION" command).

  model PLAYREV  [model number]

starts animation at the specified model number or the current model, if not
specified, and plays only within the range, if previously specified, but
reverses direction from the current direction (as specified by the
"animation DIRECTION" command).

effect on current implementation: none

status: implemented at 
<http://www.stolaf.edu/people/hansonr/jmol/test/json/express.htm>

comment: this change makes standard "tape-recorder"-like functionality
possible, with the added feature that you can select the range of models
to play through, and you could have start/stop/play/reverse controls.


-----------------
frame:

action: currently just a synonym for "model" and "animation frame".

proposed change 1: keep the synonym to "animation frame" but with
the change that the numbers specified refer to the actual sequential
position of the model in the file, not the PDB MODEL number. So "frame 1"
is the first frame, etc.

proposed change 2: add RANGE, PREVIOUS, PLAY, PLAYREV, PAUSE as for the 
model
command. This just makes the two commands identical, except for what the
number refers to.

effect on current implementation: none for most users; users with PDB files
that specify unusual numbers in the MODEL line should use model, not frame,
to access models using these numbers.

status: waiting for comment; not implemented in prototype


-------------------
question: Should the RANGE in the model and frame commands also
determine which models are displayed when the command "frame ALL"
or "model ALL" is invoked?

Bob Hanson