[3dem] making a density map from atomic model

[wriggers at biomachina.org]

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=DwIFaQ&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=DwIFaQ&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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