Feature Requests item #3425296, was opened at 2011-10-18 07:23
Message generated for change (Comment added) made by berlin222
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Category: Jmol extensions
Group: None
Status: Closed
Priority: 5
Private: No
Submitted By: berlin (berlin222)
Assigned to: Nicolas (nicove)
Summary: bonds ID numbers
Initial Comment:
it would very nice if it could tell us the definition of bond ID numbers.
I want to use the bond ID numbers to set the color of each bonds.
But can not make sure of the bond ID numbers is represent which bonds.
So I can not continue my work.
Example:
the *.spt file can set up the color of bonds like this:
select BONDS ({0:100});
color bonds opaque [0,200,0];
select BONDS ({101});
color bonds opaque [200,100,0];
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Comment By: berlin (berlin222)
Date: 2011-11-04 19:21
Message:
I am using the version 12.2.0,
select and set bonds in function _setModelState of "*.spt" files.
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Comment By: Bob Hanson (hansonr)
Date: 2011-11-01 04:51
Message:
Ah, yes, that has been there forever. Your initial question was about bond
identifiers and the BONDS command, but what you were really asking was "How
can I color specific bonds specific colors."
select bonds @{ {atomno=1 or atomno=2}.bonds }
has worked since at least version 11.1. I forgot to ask, what version are
you using? Here is an example from 12.2:
load $caffeine
select bonds @{ {atomno=1 or atomno=2}.bonds }
color bonds yellow
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Comment By: berlin (berlin222)
Date: 2011-11-01 04:14
Message:
thanks you all!
"select bonds @{ {atomno=1 or atomno=2}.bonds }" is not work too.
But, I got the way:
"
select ({2 3});
color bonds opaque [0,200,0];
"
select the bond of atom 2 and 3, and set its color.
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Comment By: Bob Hanson (hansonr)
Date: 2011-10-27 07:10
Message:
almost. You need to surround that math expression with @{ }
select bonds @{ {atomno=1 or atomno=2}.bonds }
color bonds opaque [0,200,0]
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Comment By: berlin (berlin222)
Date: 2011-10-27 04:31
Message:
egonw, thanks you very much.
I can't get your email may due to the server of "yahoo.com.cn" have some
trouble. maybe, the email of "[email protected]" would get your email.
do you mean can select and color bonds by:
"
select bonds ({{atomno=1 or atomno=2}.bonds});
color bonds opaque [0,200,0];
"
but it does not work.
may you help more!
thanx!
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Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 01:56
Message:
BTW, Robert replied on the developers ML:
"You most easily select bonds using:
x = {atomno=1 or atomno=2}.bonds
or the like."
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Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 01:55
Message:
berlin222, thanx for posting here. Got your email, but my reply was
bounced.
----------------------------------------------------------------------
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https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3425296&group_id=23629
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