Here's the scoop:
It turns out that the code for "auto" -- specifically creating regular
bonds or hydrogen bonds -- does not pass through the part of the
"connect" method that distinguishes "modify" from "create". So
whenever you have "auto", Any of "modify" or "create" or
"modifyOrCreate" is ignored.
so if you say
connect modify hbonds auto (*) (*)
Jmol ignores "modify" and processes just
connect hbonds auto (*) (*)
Similarly, if you say
connect modify single delete (*) (*)
Jmol will ignore "modify" and just process
connect single delete (*) (*)
Whether this is a "bug" or a "feature" is a matter of opinion. The
scripting language in Jmol tends to be rather "loose" by design. You
can do things that might not make a lot of sense, and they are just
ignored. For example, you can say
set picking distance and whatever else you want to say
and the command evaluator will only process
set picking distance
-Bob
Miguel wrote:
>>
>>>>I agree, but what does
>>>>connect modify hbonds auto (*) (*)
>>>>with existing (CONECT record or connect min max create hbond
(selection)
>>>>(selection) hbonds)?
>>>>
>>>>
>>>
>>>This would only modify an existing bond.
>>>
>>>So, if there were a covalent bond someplace, it would get modified and
>>>become an hbond.
>>>
>>>No new hbond would be created.
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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