Markus Rudolph wrote:
>
> Hello,
>
> long ago I had a case when HG1 etc. were interpreted as mercury by phaser.
>
> Could that be relevant to your case?
I hope not.
However, as I have already seen EPMR handle some Hydrogen as Carbon,
I am ready to see anything happening! :(
I will have a quick look to see if I can make Phaser
output atom numbers from what was read from the PDB.
Regards,
F.
> Regards,
>
> Markus
>
> On Tue, 12 Jan 2010, Francois Berenger wrote:
>
>> Hello,
>>
>> I have 4 molecules.
>> If I use Phaser's AUTO_MR with all default parameters on them,
>> I get the following scores:
>>
>> no_modif remove_H
>> molecule RFZ TFZ RFZ TFZ
>> 1 6.9 9.6 7.0 9.4
>> 2 5.2 5.9 5.4 6.2
>> 3 4.2 4.5 4.7 5.2
>> 4 4.9 6.8 5.2 6.7
>>
>> Hence, here are my existential questions, given that I heard
>> many times "H is transparent for X-rays":
>> * should I always remove H before running Phaser?
>> * why?
>>
>> Here are a few lines of one of my PDBs containing H, in case it is
>> misinterpreted by Phaser:
>> ---
>> ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00
>> ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00
>> ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00
>> ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00
>> ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00
>> ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00
>> ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 ---
>>
>> Thanks a lot,
>> Francois.
>>
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