Re: [ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: SHELEX .pdb and .res output and MLPHARE HA file
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2007-12-20

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From: Peter leadlay pfl10 {- at -} MOLE {- dot -} BIO {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-12-20

Subject: Re: SHELEX .pdb and .res output and MLPHARE HA file
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-12-20

You probably dont need to refine the positions but i guess there is no
harm in it.. You do need to refine the ano occupancy which reflects the
f" values.
Your sites 2 and 4 are quite close so the MSE might be disordered?
It doesnt really matter what you call the atom type since nothing is on
the absolute scale..

The shelx.ha needed for MLPHARE would read something like this:
Atom_type x y z
"Real_occup" " Anom_occup" BFAC
ATOM SE 0.265762 0.232712 0.087886 0
1 BFAC 20
and so on

Eleanor

Partha Chakrabarti wrote:
> Hiya,
>
> I used shelex C/D/E on a SAD data, and wanted to refile the positions in
> MLPHARE before going for AddSOLVE. Confused with the output of two shelex
> files.
>
> shelx1.pdb file says
>
> CRYST1 50.050 65.520 105.180 90.00 90.00 90.00
> SCALE1 0.019980 0.000000 0.000000 0.00000
> SCALE2 0.000000 0.015263 0.000000 0.00000
> SCALE3 0.000000 0.000000 0.009508 0.00000
> HETATM 1 S HAT 1 13.301 15.247 9.244 1.000 20.00
> HETATM 2 S HAT 2 11.528 28.067 11.167 0.803 20.00
> HETATM 3 S HAT 3 15.167 5.763 19.810 0.613 20.00
> HETATM 4 S HAT 4 13.307 30.233 13.293 0.599 20.00
> HETATM 5 S HAT 5 12.792 19.519 4.781 0.572 20.00
> HETATM 6 S HAT 6 13.273 15.312 20.083 0.373 20.00
> END
>
>
> shelxd_fa.res file says:
>
> REM TRY 37 CC 37.28 CC(weak) 19.64 TIME 56 SECS
> REM
> TITL eba28_4_shelxc_fa.ins SAD in C2221
> CELL 0.98000 50.05 65.52 105.18 90.00 90.00 90.00
> LATT -7
> SYMM -X, -Y, 1/2+Z
> SYMM -X, Y, 1/2-Z
> SYMM X, -Y, -Z
> SFAC SE
> UNIT 128
> SE01 1 0.265762 0.232712 0.087886 1.0000 0.2
> SE02 1 0.230339 0.428368 0.106166 0.8032 0.2
> SE03 1 0.303047 0.087959 0.188342 0.6130 0.2
> SE04 1 0.265884 0.461433 0.126384 0.5992 0.2
> SE05 1 0.255577 0.297905 0.045451 0.5723 0.2
> SE06 1 0.265198 0.233696 0.190944 0.3728 0.2
> HKLF 3
> END
>
> I have only 4 Se atoms, as judged from cell content analysis, so I guess I
> do see some Sulphurs. What should I do with atom identifiers in MLPHARE?
>
> Cheers, Partha
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: SHELEX .pdb and .res output and MLPHARE HA file
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2007-12-20

Next message:
Subject: Postdoctoral Research position, University of Cambridge
From: Peter leadlay pfl10 {- at -} MOLE {- dot -} BIO {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-12-20