[3dem] making a density map from atomic model
wriggers at biomachina.org
wriggers at biomachina.org
Fri Nov 5 10:12:29 PDT 2021
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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