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This is what's used for bulk-solvent mask calculation:<br>
<br>
sources/cctbx_project/cctbx/eltbx/van_der_waals_radii.py<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/15/14, 12:03 PM, Nigel Moriarty
wrote:<br>
</div>
<blockquote
cite="mid:CANkP=2dgXeLR1Cxhf8enGorc9hqXfsupSAXX7R6PQzxEqcbg0g@mail.gmail.com"
type="cite">
<div dir="ltr">Rituparna
<div><br>
</div>
<div>You can find this information in the ener_lib.cif and
geostd_ener_lib.cif (changes to the standard Monomer Library
values to match the Molprobity values). These files are in
$PHENIX/chem_data/mon_lib and $PHENIX/chem_data/geostd
respectively.</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Nigel</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, Aug 15, 2014 at 10:52 AM,
Rituparna Sengupta <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:rsengupta@wisc.edu"
target="_blank">rsengupta@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Hi! </div>
<div><br>
</div>
<div>I'm new to the list. This might be a naive question
to ask, but I'm looking for information about the set of
van der Waal's radii popular with most protein
crystallographers. Is there a certain list that phenix
uses for building from the x-ray structures. If so,
where can I find it. I shall be grateful for any
thoughts or inputs on this. </div>
<div><br>
</div>
<div>Thanks, </div>
<div>Ritu</div>
<div><br>
</div>
<div><br>
</div>
<br clear="all">
<div>
<div dir="ltr"><span
style="color:rgb(0,0,0);font-family:Times;font-size:medium">Rituparna
Sengupta</span>
<div
style="min-height:1em;color:rgb(0,0,0);font-family:Times;font-size:medium"><br>
<div style="min-height:1em">Graduate Student</div>
<div style="min-height:1em">Biophysics Graduate
Program</div>
<div style="min-height:1em">Record Lab</div>
<div style="min-height:1em">Department of
Biochemistry</div>
<div style="min-height:1em">
Biochemical Sciences Building</div>
<div style="min-height:1em">University of
Wisconsin-Madison</div>
</div>
</div>
</div>
</div>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a moz-do-not-send="true"
href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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