Hi Ian
Yes I realized that too. But the way he formulated it was rather
ambiguous so I still posted that. (But using "appears to reflect" )
By the way, attached is the first of the Chimera type programs from 35
years back...
Cheers
Marin
On 10/09/2018 07:58, Ian Tickle wrote:
>
> Hi Marin
>
> I was about to comment on that too but then I realised that Pavel is
> referring to the map _contours_ (which is what most people using a
> map visualisation program like Coot actually see). So the contoured
> map does represent an iso-potential surface. I'm sure Pavel is aware
> that the original cryo-EM maps are 3-dimensional objects.
>
> Cheers
>
> -- Ian
>
> On Mon, 10 Sep 2018 at 10:49, Marin van Heel
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>
> Unfortunately,
>
> The problem here lies primarily in the answer given, not so much
> in the question asked by a newcomer:
>
> "1) In cryo-EM maps are not electron density maps but surfaces
> representing electric potential. "
>
> The answer appears to reflect the widespread misunderstanding that
> EM images (and hence cryo-EM maps) only show the surfaces not the
> internal density of the complexes we study.
> In my Imperial College/Leiden University lecture notes, I have
> always used the below slide to illustrate this point.
>
> Cheers,
>
> Marin
>
>
>
>
>
> On 10/09/2018 01:38, Pavel Afonine wrote:
>> Hi,
>>
>> Is there any sever available to create electron density maps
>> for cryo-em structures?
>>
>>
>> The questions are nonsensical. Here is why:
>>
>> 1) In cryo-EM maps are not electron density maps but surfaces
>> representing electric potential.
>>
>> 2) Creating such a map is essentially carrying on from cryo-EM
>> experiment and obtaining the 3D reconstruction.
>>
>> Are you really sure about what you are asking for?
>>
>> Or, we should create the maps from mmCIF.
>>
>>
>> mmCIF is a file format. It may contain representations of
>> rabbits, boysenberries or some diffraction data. So.. how you
>> think it may be related to cryo-EM, in your particular case?
>>
>> I am particularly interested in those cryo-em structures with
>> high resolution, like 2.6~2.8A.
>>
>>
>> Sure, all are excited about high-res cryo-EM!!!
>>
>> Please give me an education.
>>
>>
>> Sure. One of available universities can do this.
>>
>> Cheers,
>> Pavel
>>
>>
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>>
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>
> --
> ==============================================================
>
> Prof Dr Ir Marin van Heel
>
> Laboratório Nacional de Nanotecnologia - LNNano
> CNPEM/LNNano, Campinas, Brazil
>
> Skype: Marin.van.Heel
> email: marin.vanheel(A_T)gmail.com <http://gmail.com>
> marin.vanheel(A_T)lnnano.cnpem.br <http://lnnano.cnpem.br>
> and: mvh.office(A_T)gmail.com <http://gmail.com>
>
> --------------------------------------------------
> Emeritus Professor of Cryo-EM Data Processing
> Leiden University
> --------------------------------------------------
> Emeritus Professor of Structural Biology
> Imperial College London
> Faculty of Natural Sciences
> email: m.vanheel(A_T)imperial.ac.uk <http://imperial.ac.uk>
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>
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==============================================================
Prof Dr Ir Marin van Heel
Laboratório Nacional de Nanotecnologia - LNNano
CNPEM/LNNano, Campinas, Brazil
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and: mvh.office(A_T)gmail.com
--------------------------------------------------
Emeritus Professor of Cryo-EM Data Processing
Leiden University
Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
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Imperial College London
Faculty of Natural Sciences
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