<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Dear Jacopo,</p>
<p>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).</p>
<p>Kind regards, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 05/11/2021 a las 18:12,
<a class="moz-txt-link-abbreviated" href="mailto:wriggers@biomachina.org">wriggers@biomachina.org</a> escribió:<br>
</div>
<blockquote type="cite"
cite="mid:002101d7d268$5201a430$f604ec90$@biomachina.org">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<style>@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}span.EmailStyle21
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}div.WordSection1
{page:WordSection1;}</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<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="
moz-do-not-send="true">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="
moz-do-not-send="true">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
<a class="moz-txt-link-rfc2396E" href="mailto:3dem-bounces@ncmir.ucsd.edu"><3dem-bounces@ncmir.ucsd.edu></a> <b>On Behalf Of </b>Marino
Jacopo (PSI)<br>
<b>Sent:</b> Friday, November 5, 2021 12:47 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
3dem mailing list
<a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>
<a class="moz-txt-link-freetext" href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a>
</pre>
</blockquote>
</body>
</html>