You are quite right - LSQKAB must be wrong to report a RMS
Distance?/deviation? for a GLY side chain - will look into it and
correct I hope.. Thanks for noticing it and pointing the bug out
Eleanor
Nathalie Colloc'h wrote:
> Hello all,
>
> I have still a question about LSQKAB
> Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for
> glycine side chains ?
>
> thanks a lot
>
> nathalie
>
>
> Eleanor Dodson a écrit :
>> Q1) Rms xyz and rmsd mean exactly the same . And as for what you
>> should report - that depends on the problem. As long as you state
>> clearly what has been fitted ( all atoms, CAs, loops excluded etc etc )
>>
>> Q2) The algorithms for SSM and LSQKAB are different - SSM fits
>> secondary structure elements only, then checks the rmsd of all CAs.
>> This is particularly useful for fitting homolous proteins.
>>
>> LSQKAB requires a list of all the atoms to be matched and that "rms
>> xyz" considers all those atoms and only those.
>> If you want a report of all differences you must click for that on
>> the GUI.
>> And as you say this is helpful for finding differences in different
>> copies of the same molecule.
>> Eleanor
>>
>
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