[modeller_usage] How Modeller avoid CA clashes?

[Yun He <>]

When the distance between two adjacent CA atoms (i.e. Ca_i and Ca_i+1) is 
shorter than 3.6 Angstrom, the two residues may take part in clashes. These 
are severely unrealistic geometry, however, cis-proline may be an exception 
usually.

When we use Modeller to build model, the default model routine (automodel 
class) seems only to check the improper chain breaks (the distance between 
two adjacent CA atoms is larger than 8 Angstrom) of templates, but not check 
the CA clashes of generated models. And the models sometimes have the CA 
clashes problem. How could Modeller avoid such improper geometry? Add some 
distance restraints by hand?

A typical example:
T0345, a target just released of CASP7. Two templates with very high 
similarities (id% > 65%) are found, 2F8A and 1GP1.
Here is my alignment file of 1GP1_A and T0345
--------------
>P1;1GP1A
structure:1gp1:10:A:192:A:GLUTATHIONE PEROXIDASE:NA:2.00:0.171
---RTVYAFSARPLAGGEPFNLSSLRGKVLLIENVASL-GTTVRDYTQMNDLQRRLGPRGLVV
LGFPCNQFGHQENAKNEEILNCLKYVRPGGGFEPNFMLFEKCEVNGEKAHPLFAFLREVLPTP
SDDATALMTDPKFITWSPVCRNDVSWNFEKFLVGPDGVPVRRYSRRFLTIDIEPDIETLL-*

>P1;T0345
sequence:T0345:1: :185: :T0345: :2.00:-1.00
MIAKSFYDLSAINL-DGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF-PRRLVV
LGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYP
YDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK*
---------------
There are two cis-prolines (PRO:97, PRO:150) in each chain of 1GP1, 
correspondingly, there are two prolines on the same sites of T0345 (PRO:89, 
PRO:142), and residues around these prolines are very conserved, so I think 
the prolines in T0345 should be also cis-proline. After building models from 
this alignment, I have checked the CA clashes of models, and found that there 
are two clashes: 
--
           pair                  distance       
  88 ARG:  ===   89 PRO:          2.798 A
 141 SER:  ===  142 PRO:          2.803 A
--
However there are NO CA clashes occurred in 1GP1. How do the two clashes 
happen?
Are there some means to avoid these clashes?



Best regards,

Yun
2006/06/30