[Jmol-developers] [ jmol-Feature Requests-3425296 ] bonds ID numbers
Feature Requests item #3425296, was opened at 2011-10-18 09:23
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
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Please note that this message will contain a full copy of the comment thread,
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Category: Jmol extensions
Group: None
Status: Open
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];
--
Comment By: Bob Hanson (hansonr)
Date: 2011-11-01 06:51
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
--
Comment By: berlin (berlin222)
Date: 2011-11-01 06:14
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.
--
Comment By: Bob Hanson (hansonr)
Date: 2011-10-27 09:10
Message:
almost. You need to surround that math expression with @{ }
select bonds @{ {atomno=1 or atomno=2}.bonds }
color bonds opaque [0,200,0]
--
Comment By: berlin (berlin222)
Date: 2011-10-27 06:31
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 berlin222...@gmail.com 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!
--
Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 03:56
Message:
BTW, Robert replied on the developers ML:
You most easily select bonds using:
x = {atomno=1 or atomno=2}.bonds
or the like.
--
Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 03:55
Message:
berlin222, thanx for posting here. Got your email, but my reply was
bounced.
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379136aid=3425296group_id=23629
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[Jmol-developers] [ jmol-Feature Requests-3425296 ] bonds ID numbers
Feature Requests item #3425296, was opened at 2011-10-18 09:23
Message generated for change (Settings changed) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379136aid=3425296group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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];
--
Comment By: Bob Hanson (hansonr)
Date: 2011-11-01 06:51
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
--
Comment By: berlin (berlin222)
Date: 2011-11-01 06:14
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.
--
Comment By: Bob Hanson (hansonr)
Date: 2011-10-27 09:10
Message:
almost. You need to surround that math expression with @{ }
select bonds @{ {atomno=1 or atomno=2}.bonds }
color bonds opaque [0,200,0]
--
Comment By: berlin (berlin222)
Date: 2011-10-27 06:31
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 berlin222...@gmail.com 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!
--
Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 03:56
Message:
BTW, Robert replied on the developers ML:
You most easily select bonds using:
x = {atomno=1 or atomno=2}.bonds
or the like.
--
Comment By: Egon Willighagen (egonw)
Date: 2011-10-19 03:55
Message:
berlin222, thanx for posting here. Got your email, but my reply was
bounced.
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379136aid=3425296group_id=23629
--
RSAreg; Conference 2012
Save #36;700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1
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Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
Hi, On Sun, Oct 30, 2011 at 08:44:29PM +0100, Michael Banck wrote: I took a look at packaging 12.2 (congrats!) for Debian/Ubuntu, and realized it now requires the naga NIO asynchronous sockets implementation. I know you bundle the jar in your release tarball, but we have to remove all binary jars and repackage the tarball prior to build as per Debian policy and in order to comply with the Debian Free Software Guidelines. Naga has not yet been packaged for Debian, and as neither their subversion repository nor their release jarfiles have any copyright/license information (the website says MIT), this will likely not be accepted into the Debian/Ubuntu repositories for now. I have filed issue http://code.google.com/p/naga/issues/detail?id=12 to that effect. The naga maintainer has now added the requested copyright information, and we uploaded naga to Debian. Also, jmol-12.2 is now in Debian and should get synced to Ubuntu in the next days. Thanks a lot for your efforts, Michael -- RSAreg; Conference 2012 Save #36;700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
That's great. I think I'll leave it as a reflection interface anyway. Adds a bit of flexibility. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- RSAreg; Conference 2012 Save #36;700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
