Re: [Jmol-developers] surface

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

Miguel wrote:

>>>Q: Do you mean 'alone' as if the other atoms were not in the file?
>>>
>>>      
>>>
>>Yes
>>
>>    
>>
>>>If so, then that is not compatible with RasMol/Chime behavior.
>>>
>>>      
>>>
>>but of much more use
>>
>>    
>>
>>>Q: Is that what you want?
>>>
>>>      
>>>
>>yes, I want to be able to visualize binding pockets (where solvent
>>and/or a ligand is in contact with the protein under experimental
>>conditions)
>>    
>>
>
>OK
>
>Q: Is this high-priority or low-priority for you?
>
>  
>
my priority list:
-. MessageCallBack output at least compatible to RasMol
    echo
    show selected group *
    set picking
    correct PDB atom number
-. access to the color scheme
    set helix color red (now color structure should use red for helix parts)
    set carbon color green (from now on color cpk should use green for 
carbons)
-. rockets with
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1ne6
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
    at javax.vecmath.Tuple3f.set(Tuple3f.java:161)
-. surface rendering
-. script access to distances, angles, torsions ... surface area ...*--> 
MessageCallBack
    center [0.0, 0.0, 0.0]  output *-->
-. color hbonds type
-. general use of atom expression, e.g.
    bond 23:A.CA 23:A.O1
-. further operators for advanced scripting bound and count *-->
-. --noscript
    (size should be viewer size)
-. molecule
-. script accessing PDB file
-. stereo
Regards, Jan