Yes - contacts or distang gives you a list of distances. PISA a list of h
bonds and salt bridges - all with associated sym ops.
But none produce a complete table - PISA output prob the best.
Eleanor
distang gives you this sort of information but i guess it is far too
detailed?
R 125 NA R5 NH1 A 3.599 X,Y,Z 1.00
25.73
R 125 NA H 121 OA 3.493 X,Y,Z 1.00
26.73
R 125 NA A 122 CA 3.767 X,Y,Z 1.00
24.41
R 125 NA A 122 OA 3.199 X,Y,Z 1.00
24.69
R 125 NA W 123 CA 3.509 X,Y,Z 1.00
25.05
R 125 CA A A 122 OA 3.926 X,Y,Z 1.00
26.28
R 125 CB A A 122 OA 3.569 X,Y,Z 1.00
28.11
R 125 NE A N 113 OD1 A 3.934 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
34.82
R 125 CZ A N 113 OD1 A 3.360 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
35.77
R 125 CZ A A 122 NA 3.964 X,Y,Z 1.00
31.89
R 125 CZ A A 122 CA A 3.631 X,Y,Z 1.00
32.07
R 125 NH1 A N 113 OD1 A 3.592 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
36.32
R 125 NH1 A A 122 CA A 3.714 X,Y,Z 1.00
32.62
R 125 NH1 A A 122 CB A 3.745 X,Y,Z 1.00
32.41
R 125 NH2 A N 113 CG A 3.947 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
32.44
R 125 NH2 A N 113 OD1 A 3.274 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
34.03
On Wed, 19 May 2021 at 10:19, Hari shankar <
465d10db143e-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear Misha,
>
> There is a program in ccp4 called contacts that will give you this
> information. You can alter entry parameters to show you the relevant
> information.
>
> I think you can also try PISA server from EMBL-EBI.
>
> I reckon both these programs show you all distances and you may have to
> manually pick out the shortest ones.
>
> Regards
> Hari
>
> On Wednesday, May 19, 2021, 16:54, Isupov, Michail
> wrote:
>
>
> Hi
>
> I am wondering if there is a simple program that would convert a pdb file
> into a matrix that
>
> shows the smallest distance between all pairs of amino-acid side chains?
>
> Thanks,
> Misha
>
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