[3dem] making a density map from atomic model

Fri Nov 5 12:23:18 PDT 2021

Dear Jacopo,

in Xmipp you have also EASFs (Electron Atomic Scattering Factors) as 
kernels. These are supposed to be accurate descriptions of how the atoms 
are seen by electrons in the microscope. The program is 
xmipp_volume_from_pdb, it is also conveniently accessed through Scipion 
(convert pdb protocol).

Kind regards, Carlos Oscar

El 05/11/2021 a las 18:12, wriggers at biomachina.org escribió:
>
> Hello Jacopo,
>
> You can use pdb2vol in Situs, see 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__situs.biomachina.org_fguide.html-23pdb2vol&d=DwIDaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KFh_X33rN_HKrqfTMPnga8kEAoUuLamWMXsJVA4ls3dQClDzQ390f_ZhCv10Nuq7&s=jar5oNa8SALopTln6NOK625dRGvQ8uTsLnIHzMkU3yQ&e=  
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__situs.biomachina.org_fguide.html-23pdb2vol&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=W9BajcCUg97lZL15V0uc8OxTATxv3FwFidAvxkJzh59bgI56H57GX5fMoOg8-HJm&s=H1PfQuwvAUOVl8gmoIOuFM-EaPNrnoSaQtbkWSxKDv8&e=>. 
> There are various convolution kernels that can be used for different 
> purposes like Gaussian, hard sphere etc.
>
> Regards,
>
> Willy
>
> Willy Wriggers, Ph.D.
>
> Frank Batten Chair of Biomedical Engineering
>
> Dept. of Mechanical and Aerospace Engineering
>
> Old Dominion University
>
> 238 Kaufman Hall
>
> Norfolk, Virginia 23529
>
> Office: 757-683-6759
>
> _https://urldefense.proofpoint.com/v2/url?u=http-3A__situs.biomachina.org&d=DwIDaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KFh_X33rN_HKrqfTMPnga8kEAoUuLamWMXsJVA4ls3dQClDzQ390f_ZhCv10Nuq7&s=-uLH20ZQo8BWhsB6-8YNiNkKfsEndoMaATI9GR1mzmM&e=  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__situs.biomachina.org&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=W9BajcCUg97lZL15V0uc8OxTATxv3FwFidAvxkJzh59bgI56H57GX5fMoOg8-HJm&s=CAqZnKdEexNXcKSc6BEl9ZKim0KD7YnxzFE1L7yr89w&e=>_
>
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> *On Behalf Of *Marino 
> Jacopo (PSI)
> *Sent:* Friday, November 5, 2021 12:47 PM
> *To:* 3dem at ncmir.ucsd.edu
> *Subject:* [3dem] making a density map from atomic model
>
> Hi – what program would you use to make a density map from an atomic 
> model, and are there differences in the output depending on the 
> program used ?
>
> Many thanks and kind regards,
>
> Jacopo
>
>
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