Re: [ccp4bb]: LSQMAN- Comparing waters!

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

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hi,

you need to use two pdb files that contain both your protein and your water.
then you first superimpose the two using the protein atoms, and subsequently
you can compare the water structure with the WAters command. see
http://xray.bmc.uu.se/usf/lsqman_man.html#S70

--dvd

> Hi Everyone,
> I am trying to use LSQMAN to compare water molecules between two of my 
> structures.
> Here's how the *.pdb files read-
> ----------
> ATOM  12446  O   WAT S2320      55.807  24.270 -71.680  1.00 36.11      S
> ----------
> Here's the error message I get following the EXplicit command-
> LSQMAN > ex m1 a1-889 m2 a1-3130
>  Explicit fit of M1 A1-889
>  And             M2 A1-3130
>  Atom types     | CA | N  | C  | O  | CB |
>  B-factor range used: -1000.00 - 10000.00 A2
>  ERROR --- Zone ignored in range2 : A1-3130
>  Nr of atoms to match  : (          0)
>  Nr skipped (B limits) : (          0)
>  ERROR --- Less than three atoms; cannot match
> ----------
> What am I doing wrong ? Any suggestions ?
> Thanks very much.
> Raji

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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