Bob Hanson wrote:
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
great!
connect
faulty
bondorder
don't like that
model
model should be MODEL
frame
I'm fine with sequence number
all should be all, add a token RANGE
-----------------
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)
really great, I like it very much, and more then two selections, e.g. angle
monitor (tyr237:A.CA) (CLA6.MG) (CLA9.MG)
are implemented, too.
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>
if NOTEXISTS would be implemented too, e.g. INCREMENT could be simulated
(in most cases)
connect 1.2 1.36 DOUBLE EXISTS (nitrogen) (carbon)
connect 1.36 1.4 SINGLE NOTEXISTS (*.N???) (carbon)
there is a *problem* with this command, using H2C=CH2 I run
connect 0.0 5.5 DELETE (all) (all)
connect 0.8 1.2 SINGLE (carbon) (hydrogen)
connect 1.2 1.6 DOUBLE (carbon) (carbon)
connect 1.2 3.2 HBOND (carbon) (hydrogen)
now no HBOND (or SINGLE if I tried) was formed though (by simple
distance criteria) there should be
if I tried
connect 1.2 5.5 HBOND (carbon) (hydrogen)
nothing either, but (sometimes !!!) after some experiments with
select carbon
connect 1.2 3.2 DELETE (hydrogen)
connect 1.2 3.2 SINGLE (hydrogen)
connect 1.2 3.2 HBOND (hydrogen)
I failed trying this without the SINGLE intermediate
-----------------
bondorder:
action: undocumented "set bondmode"-dependent bond order changes
proposed change: remove command -- this is better handled with connect.
I agree.
Regards, Jan
...
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