Hi Henrike,
I use CCP4's "contact" program:
#!/bin/bash
# find bad contacts: list all CA-CA distances < 3.8A between non-adjacent
residues
# in a well-folded protein, these should be very rare (1 contact in 1000
residues)
# KD 20.12.21
grep CA $1 > /tmp/temp.pdb
contact xyzin /tmp/temp.pdb <<EOF | awk '/LIST OF CONTACTS/,/FONT
COLOR/{print}' | grep -v FONT
MODE IRES
LIMIT 0 3.8
EOF
rm /tmp/temp.pdb
If you are interested in non-CA atoms, modify accordingly. But this should give
you the idea.
HTH,
Kay
On Thu, 14 Jul 2022 17:52:40 +0200, Henrike Wagler
<[email protected]> wrote:
>Dear all,
>
>
>We are looking into a way to find clashes / bumps between protein chains
>(closer than van der Waals contacts).
>
>Ideally, we would like to that with a script, for example, reading in a
>pdb file, and giving back the number of clashes.
>Of course, this is possible within Coot or PyMol, but maybe there is a
>software as part of CCP4 that we can directly use with a script.
>
>Apologies if there an obvious solution that we are currently not aware of.
>
>Many thanks
>
>Best,
>Henrike Wagler
>
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