[Jmol-developers] Re: center and center selected

[Jan Reichert]

Dan Bolser wrote:
Should I send the file in an email?
On Fri, 2 Jul 2004, Dan Bolser wrote:
 

Sorry, here is the attachment (hopefully not too big)
Dan.
On Fri, 2 Jul 2004, Dan Bolser wrote:
   

Thanks both for clear responses. However, the problem persists (I didn't
describe in enough detail).
Attached is the file I am looking at in xyz format (domain1.xyz).
It contains a bunch of CA atoms from one of the domains of pdb 1RYP. These
are of type C. I have also included a N whose position is the geometrc
average center of the CA atoms.
If I type 

select all
center selected
I clearly see the molecule is rotating about the nitrogen...
My calculated center = 

40.18108780487804, 
-134.62689268292684,
69.39078048780488

rasmol show center
[-266,-972,481]
     

hmm, may be [nm]*250, this is bad in RasMol, it should be A (but I only 
needed it for combining molecules and than, arbitrary units are OK, too.

Hmmm...
If I type 

center
Same as select all \n center selected right?
Wrong...
I see the molecule clearly not rotating about the nitrogen.
This structure also shows the garbled command line clicking most atoms,
which is a real pain, so be warned. I have to look directly into a binary
file and scroll down until my terminal is fixed.
Maybe this is an xyz problem?
Version 2.7.2.1.1 January 2004
Final experiment
rasmol center all ... is wrong too, just like center on its own.
In case you are wondering I am looking at bounding spheres, which is why I
would like to select within(arbitary,nitrogen).
Cheers,
Dan.

On Fri, 2 Jul 2004, Miguel wrote:
     

Dan wrote:
       

select carbon
center
center selected
Why would the above two commands have different results?
         

My understanding is ...
The center command takes an arbitrary expression as an argument. The
center is set to the geometric average (unweighted center of gravity). If
no argument is passed then it defaults to 'all'.
The following are equivalent:
center
center *
center all
AND
select all
center selected
       

in RasMol2.7.2
center [0,0,0]
would do the same, too, which is very useful in combining multiple 
molecules, I think it was a good idea to implement this in Jmol

There is nothing special about 'selected' ... it simply refers to the
selected set.
The following are equivalent:
center carbon
center *.c??  # this may not be exactly correct, but you get the idea
center (carbon or oxygen) and !oxygen
AND
select carbon
center selected
       

any way to dump the current center point?
         

In RasMol there is the useful command
show center
which echoes the current center relative to the startup, 'center all' 
e.g. "centre [-100,-129,242]"
It would be nice if the
center
command would echo the new center coordinates to the MessageCallBack 
function.
Regards, Jan

saying 'center' or 'center all' resets it to the default value that is
used at startup.
       

and, hopefully
center [0.0, 0.0, 0.0]
:-)
Miguel
       


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