[phenixbb] phenix.pdbtools

Pavel Afonine PAfonine at lbl.gov
Wed Aug 20 16:22:39 PDT 2008


Hi Jianghai,

the message tells there are 707 bonds with the length more than the 
cutoff. The cutoff is actually a big number - a unit cell period. So, I 
presume there must be something very weird with your PDB file. If you 
want me to debug it - please send me the file and I will look into this 
problem right away.

Pavel.


On 8/20/2008 1:59 PM, Jianghai Zhu wrote:
> Hi,
>
> I am trying to use phenix.pdbtools to calculate the geometry  
> statistics for a model from Rosetta. "phenix.pdbtools --show-geometry- 
> statistics foo.pdb" stopped with a message "Sorry: Number of bonds  
> with excessive lengths: 707".  Anybody know what happened there?
>
> Thanks.
>
> -- Jianghai
>
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   



More information about the phenixbb mailing list