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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Hello Jacopo,<o:p></o:p></p><p class=MsoNormal>You can use pdb2vol in Situs, see <a href="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=">https://situs.biomachina.org/fguide.html#pdb2vol</a>. There are various convolution kernels that can be used for different purposes like Gaussian, hard sphere etc. <o:p></o:p></p><p class=MsoNormal>Regards,<o:p></o:p></p><p class=MsoNormal>Willy<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:#0033CC'>Willy Wriggers, Ph.D.</span><o:p></o:p></p><p class=MsoNormal><span style='color:#0033CC'>Frank Batten Chair</span> <span style='color:#0033CC'>of Biomedical Engineering<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0033CC'>Dept. of Mechanical and Aerospace Engineering</span><o:p></o:p></p><p class=MsoNormal><span style='color:#0033CC'>Old Dominion University</span><o:p></o:p></p><p class=MsoNormal><span style='color:#0033CC'>238 Kaufman Hall</span><o:p></o:p></p><p class=MsoNormal><span style='color:#0033CC'>Norfolk, Virginia 23529</span><o:p></o:p></p><p class=MsoNormal><span style='color:#0033CC'>Office: 757-683-6759</span><o:p></o:p></p><p class=MsoNormal><u><span style='color:blue'><a href="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=">http://situs.biomachina.org</a></span></u><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> <b>On Behalf Of </b>Marino Jacopo (PSI)<br><b>Sent:</b> Friday, November 5, 2021 12:47 PM<br><b>To:</b> 3dem@ncmir.ucsd.edu<br><b>Subject:</b> [3dem] making a density map from atomic model<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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 ?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks and kind regards,<o:p></o:p></p><p class=MsoNormal>Jacopo<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>