Hi Mohamed
The RMSD of the electron density (or difference density) is calculated by
the FFT program using the standard equation that I referenced. I would
guess that what you see in Coot is copied either from the map header or the
FFT log file.
I'm not clear what you mean when you refer to 'the e/A^3'. The RMSD (as
does the electron density from which it's calculated) consists of a pure
number and a unit of measure, e.g. '1.234 A^-3' (why it's not '1.234 eA^-3'
we won't go into here: suffice it to say that 'e' is a unit of charge and
'electron density' is not the same as 'charge density', while an electron,
or 'e-', is not a unit of measure at all, it's a sub-atomic particle: see
Wikipedia/Non-SI_units_mentioned_in_the_SI and Wikipedia/electron). The
relation between 'RMSD' and 'A^-3' is simply that the latter is the unit of
the former, exactly analogous to the relation between 'distance' and
'metre'.
Yes '3 sigma' in this context is not correct: it's '3 RMSD', and indeed
COOT itself uses the latter terminology (which you see any time you change
the contour level), so I'm not clear where you got that from. The
uncertainty ('sigma') of the density does have a value, though this is not
estimated by any of the standard programs AFAIK. However one thing is
certain: it's unlikely to equal the RMSD!
Cheers
-- Ian
On 19 April 2018 at 15:25, Mohamed Ibrahim <mohamed.ibra...@hu-berlin.de>
wrote:
> Hi Ian,
>
> Thanks a lot for your answers. They are very informative. I am afraid that
> I was looking in the wrong direction to figure out what I seek. So, I am
> reforming my question; I am trying to figure out whether the relation
> between the RMSD and the e/A^3 is linear or not. Therefore, I was looking
> for how does COOT calculate the RMSD, hoping to find the relation between
> RMSD and e/A^3. If you could refer to me a reference that is related to
> this, it will be great.
> One more question, you mentioned that " it shouldn't be called sigma
> because it's not an uncertainty ", so when we say, for example, this map
> is contoured at 3 sigma, this is a wrong statement?
>
> Cheers,
>
> On Thu, Apr 19, 2018 at 2:57 PM, Ian Tickle <ianj...@gmail.com> wrote:
>
>>
>> Hi, first maps are produced by Refmac, not Coot, and second it shouldn't
>> be called sigma because it's not an uncertainty, it's a root-mean-square
>> deviation from the mean. The equation for the RMSD can be found in any
>> basic text on statistics, e.g. just type 'RMSD' in Wikipedia.
>>
>> Cheers
>>
>> -- Ian
>>
>>
>> On 19 April 2018 at 13:20, Mohamed Ibrahim <mohamed.ibra...@hu-berlin.de>
>> wrote:
>>
>>> Dear COOT users,
>>>
>>> Do you know how to extract the equations that COOT uses for generating
>>> the maps and calculating the sigma values?
>>>
>>> Best regards,
>>> Mohamed
>>>
>>> --
>>>
>>> --
>>> *----------------------------------*
>>> *Mohamed Ibrahim *
>>>
>>> *Humboldt University *
>>> *Berlin, Germany *
>>>
>>> *Tel: +49 30 209347931 *
>>>
>>
>>
>
>
> --
>
> --
> *----------------------------------*
> *Mohamed Ibrahim *
>
> *Humboldt University *
> *Berlin, Germany *
>
> *Tel: +49 30 209347931 *
>
