VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Nov 23 2011 - 11:25:22 CST

You can also use the norm {nx,ny,nz}, distance, and center {ox,oy,oz}
from the clip plane tool, and define the selection as:
all and (nx*(x-ox)+ny*(y-oy)+nz*(z-oz)-distance>0).

This only selects the atoms behind/(in front of) the plane.

On Nov 23, 2011, at 7:22 AM, John Stone wrote:

>
> Hi,
> You can use spatial atom selections to do much the same thing as a
> user-defined clipping plane, but removing entire atoms and not just
> clipping their drawn geometry. The syntax for making such atom
> selections
> is described in the VMD User's Guide, but here are a few examples of
> simple spatial atom selections, some of which combine math functions:
> "z > 0"
> "not water and x > 0"
> "sqrt(x*x + y*y + z*z) < 30"
> "protein and ((z > 0 and (x/z < -0.5)) or z < 20)"
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Nov 23, 2011 at 02:48:33AM -0800, Philippe Bopp / temporary
> wrote:
>> Hi all,
>>
>> a day's worth of googling could not solve this one:
>>
>> I would like to clip a representation in VdW (and/or) CPK
>> without the black spots that (it seems to me) occur when
>> a sphere is cut by a clip plane (see attached). In other
>> words, I would like the VdW/CPK-atom to be removed as
>> soon as any part of its sphere is cut by a clip plane, not only
>> when the center is above/below the plane.
>>
>> I could also live with something like an atomselect that
>> refers to the clip plane, but could not find that
>> either. A piece of tcl code (at which I am not good at all)
>> would also be welcome.
>>
>> thanks
>>
>> Philippe
>>
>>
>> -----------------
>> Philippe A. Bopp
>>
>> philippebopp AT yahoo.com (private)
>> Philippe.Bopp AT u-bordeaux1.fr (office)
>> -----------------
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078