VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Thu Oct 27 2005 - 15:26:01 CDT

Thanks for the response,

Yes, sorry, I did do that loop, as implied by the closing brace I did
include.
I'm still messing with this. Perhaps it is because I am assuming
something about how
VMD sets/resets the origin? -- If the original molecule was not
actually centered at (0,0,0), VMD will
happily put the axes at the center of the molecule when you load it
(if you 'set axes origin') even though it isn't
actually the origin?

Cheers,

Mike

On Oct 27, 2005, at 12:47 PM, Marc Q. Ma wrote:

> charles,
>
> interesting. did you use the for loop?
> for { set i 0 } { $i < 3 } { incr i } {
>
>
> Marc
> On Oct 27, 2005, at 1:57 PM, Charles McCallum wrote:
>
>
>>
>> Hi there, I'm trying to cut a PBC box out of a cube of waters
>> surrounding a molecule. I'm using the Gramicidin A example
>> (http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/).
>>
>> I've carefully arranged my molecule to the origin of the large
>> water box. I'm now trying to chop off all the waters outside this
>> (octahedral box) with the tcl commands
>>
>> set sel [atomselect top \
>> "water and same residue as (not hydrogen and (x < -14.99 or x
>> > 14.99))"]
>> $sel set beta 1
>> $all move [transaxis z 120]
>> }
>>
>> I have previously defined "all" in the usual way.
>>
>> I expect this to rotate on the z-axis, leaving a octahedral box,
>> essentially centered on my molecule. What I get is unexpected ---
>> it seems that the rotation axis has been shifted off the z-axis.
>> Here is a picture of the result (small 60k image), showing the
>> *removed* waters:
>>
>> <unknown.jpg>
>> I have lined up the VMD axes at the origin. Why isn't it centered
>> where I expect?
>>
>> Cheers,
>>
>> Mike
>> --
>> C. Michael McCallum http://chemistry.cop.uop.edu/cmccallum.html
>> Associate Professor
>> Department of Chemistry, UOP
>> mmccallum .at. pacific .dot. edu (209) 946-2636
>> v / (209) 946-2607 fax
>>
>> <hole.jpg>
> 

--
C. Michael McCallum           http://chemistry.cop.uop.edu/ 
cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax