[Chimera-users] Contact/clash detection for HETATMs

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 5 10:20:55 PST 2008

Hi Jonathan,
It does not matter if the atoms are in ATOM or HETATM records in the  
PDB file.  For example:
(using commands)

open 4hhb
col byatom
show :hem z<5
findclash :hem overlap 0.2

The HEM residues are all in HETATM records.  I doublechecked just now  
and it also works in the Find Clashes/Contacts GUI.

There must be something else going on with your file.  You could send  
it to me if you want...
Otherwise (1) are you sure there are contacts within your specified  
parameters?  (2) is your PDB format correct?

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 4, 2008, at 1:06 PM, Jonathan Magasin wrote:

> Hello,
> I'm trying to use the clashes/contacts tool to explore
> valid phi/psi angles for L- and D-Ala (as part of a
> homework assignment; developing a Ramachandran plot
> for each).  The tool worked great for L-Ala but does
> not report any contacts for D-Ala.  (For each, I've
> snipped just the relevant sections out of a larger
> PDB.  I'm using default params for collision
> detection, with detection calculated for any
> movement.)
> The difference in the PDB's for L-Ala and D-Ala is
> that the latter are in HETATM records.  I did include
> the CONNECT info (to explicitly tell Chimera how
> HETATMs bond) but that did not help.
> Perhaps there's something else I must include, or some
> modification I can make to the HETATMS (element
> labeling?) so that collision detection will work as
> with peptides?  Or is this a known limitation?  (Is
> there a list of known limitations?  I'm a new user.)
> I'm not
> Note that the distance tool works for D-Ala.  If I can
> get collision detection to work, it take much less
> time.
> Thanks in advance.
>   -Jonathan

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