Re: [Jmol-users] Re: JMol deployment at University of Cambridge

[Jan R. <jr...@im...>]

Miguel wrote:

>Warwick,
>
>I have taken the liberty to cc the jmol-users mailing list so that others
>may benefit from seeing these answers.
>
>  
>
>>The University of Cambridge Centre for Applied Research in Education
>>    
>>
>Technologies (CARET) and the University of Cambridge Department of Plant
>Sciences are putting together web based teaching materials around the
>topic of protein biochemistry, structure and function.
>
>Very good. My primary motiviation for working on Jmol is to have it used for
>web-based instruction.
>
>  
>
>>We are having a serious look at JMol 10 as a MDL Chime replacement and
>>    
>>
>are
>  
>
>>very much impressed with the Beta program  - we would much prefer to run
>>    
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>the course using JMol rather than CHIME.
>
>I will do whatever I can to make sure that you use Jmol instead of Chime.
>
>  
>
>>However, there are a couple of
>>features that are vital to us and may (?) be in the current beta release
>>    
>>
>(version 10, beta 9), but are not visible to us yet. If you can point us
>in
>  
>
>>the right direction about the proposed support for these features, that
>>    
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>would be very helpful - thank you.
>
>OK
>
>  
>
>>1. In CHIME, clicking on an atom in a protein makes the atom number,
>>    
>>
>residue type and residue (amino acid) number appear in the browser
>status
>  
>
>>bar. However with the JMol applet only the atom number and residue type,
>>    
>>
>but not the residue number appear. Is there a way to determing  residue
>(amino acid) number in the JMol applet?
>
>That sounds like an oversight ... or a bug.
>
>Not to worry ... it is easily addressed.
>
>I am not a Chime user, so I need people to help me out on Chime-related
>issues.
>
>
>Q: Does Chime display something different from what RasMol displays?
>  
>
no, but no Model info

>Q: *Exactly* what appears in the status bar when one clicks on an atom in
>Chime?
>  
>
using 1az0 which still behaves strange in Jmol
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1az0&SCOP=SCOP%201.65

RasMol:
Atom:    CA   4070   Hetero:   CA   283
or if there is a chain,
Atom:    CA   1834   Group:   LYS   245   Chain:   A
and if there would be a Model,
Atom:    CA   1834   Group:   LYS   245   Chain:   A    Model: 1
would be added

Chime status line looks just the same, but didn't show any Model info
Atom: CA   4070   Hetero:   CA   283
Atom:    CA   1834   Group:   LYS   245   Chain:   A

Jmol:Hoover, I think it would be a nice idea to add the residue number 
e.g. CA   [CA]283
CA [CA]
Jmol:pickCallBack, the numbers are still wrong
atom 4065
CA CA 72448 Chain:
Jmol:Status
CA CA 72448 Chain:

>Q: Does it depend upon whether or not there are multiple models loaded?
>  
>
no, but if there is model information RasMol will display it

>Q: What does Chime display
>  
>
Chime does not display model information, which I consider as bug.

>  
>
>>2. In CHIME, clicking on an atom in a protein makes the atom number etc
>>    
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>appear in the browser status bar, for all structure renderings
>(wireframe,
>  
>
>>spacefill etc) . However with the JMol applet atom number etc is
>>    
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>displayed
>  
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>>only for ball and stick, spacefill, but not for wireframe, cartoon or
>>    
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>stick.  Is there a way to enable the labelling with wireframes, cartoons
>and stick rendering?
>
>Jmol should be reporting the atom number in the case of wireframe, if not,
>then it is a bug.
>  
>
numbering in Jmol should be fixed with priority, because you can't do 
interactive select without the correct pickCallBack information.

>I was not aware that Chime reported atom/group numbers when one clicked on
>a cartoon (or other secondary structure shape).
>  
>
it does

>That will be a little more difficult to do ... but I am sure that we can
>get it done.
>
>Q: *Exactly* what is reported in the status bar when one clicks on a
>cartoon? Info about the alpha carbon atom of the residue?
>  
>
The same info you get clicking directly on the *.CA

>
>
>I encourage you to join the jmol-users mailing list and post additional
>questions there. Particularly on things related to Chime, there are other
>people who can help explain things.
>
>And welcome to Jmol!
>
>  
>
Regards, Jan