Re: [ccp4bb]: Protein Dimensions

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

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hi michael:

i had a closer look. when i use amore and moleman2 i get exactly the same
result, which is expected because both use the same methods (this test uses
molcule A from pdb entry 1PMP):

AMORE: 43 * 38 * 34
Minimal Box   :    42.93    38.06    34.17
Rotation      :   344.43   102.82    54.13

MOLEMAN2: 43 * 38 * 34
 Crowther Alpha Beta Gamma               164.429    -102.813    -125.865
       Item    Average     St.Dev        Min        Max
    X-coord      0.000      9.380    -19.609     23.317
    Y-coord      0.000      8.235    -18.104     19.951
    Z-coord      0.000      6.718    -19.281     14.887

if you calculate (Max - Min) for X, Y and Z you get the same results as in
AMORE (i will change MOLEMAN2 so it lists those numbers in the STats command).
Also, as one would hope, the rotations needed to align the inertia axes are
clearly related: alpha,beta,gamma for MOLEMAN2 are equal to
alpha-180,-beta,gamma-180 for AMORE

if you only use CA atoms, MOLEMAN2 gives dimensions: 39 * 32 * 26

i checked the CNS input file molecule_extent.inp, but this only lists the min
and max values of the X, Y and Z coordinates in the structure *as is* (i.e.,
not along the inertia axes). this should be identical to using the STats
command in MOLEMAN2 without aligning the molecule first. so this is not a
solution to your original problem.

> Thanks for your help, moleman2 worked great, although the results from the
> different methods are somewhat different:
> 
> >From CNS (molecule_extent): 48 x 46 x 66

CNS doesn't align inertia axes with X, Y and Z, so these are not the numbers
you want

> >From AMORE (minimal box): 74 x 48 x 47
> >From moleman2: 66 x 41 x 37

given that i obtain identical results with both programs, i suspect you didn't
use exactly the same set of atoms in both programs (modulo waters ? CA-only ?
with/out ligand ?)

> They are all in the same ballpark but is this type of error normal?  On another
> note, can you run your PACMAN program noninteractively with a script?  If so
> how? Information on this is lacking in the online documentation.

yep, just like any other program under Unix (that's why it isn't documented
separately). for an example, see the use of PACMAN to get rid of obviously
clashing molecular replacement solutions in the auto_amore script
(ftp://xray.bmc.uu.se/pub/gerard/omac/auto_amore.com)

--gerard

(ps: cc-ing this mail to ccp4bb since it may be of interest to others)

******************************************************************
                        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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