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
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