[Jmol-developers] [ jmol-Feature Requests-3036296 ] complete molecule fragments

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Feature Requests item #3036296, was opened at 2010-07-28 17:18
Message generated for change (Comment added) made by hansonr
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Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: complete molecule fragments

Initial Comment:
Unless I've missed it, a simple method to fill a unit-cell and then complete any molecular fragments that straddles the cell boundaries would be great. Presently I might have one hydrogen from a water molecule near a cell face; given the information that this atom should be connected to an O and that to another H, it should be possible to complete the fragment, as is done simply in Diamond.

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>Comment By: Bob Hanson (hansonr)
Date: 2010-07-30 01:00

Message:
Glad to be of assistance.

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Comment By: Nobody/Anonymous (nobody)
Date: 2010-07-29 19:35

Message:
Magnificent sir, thankyou!

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Comment By: Bob Hanson (hansonr)
Date: 2010-07-29 07:55

Message:
It is simple enough to do this. The defaults are there for a reason -- that
we want to represent the file data as directly as possible, without any
assumptions about what the user "probably" wants. To do as you suggest, you
would simply do the following:

load "myfile.cif" {444 666 1}    
display within(molecule, cell=555)  

# loading a 3x3x3 set of unit cells
# display only the molecules that have one or more atoms within the unit
cell.

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