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<p>Hi Firdous,</p>
<p>I've been watching this conversation and I think it reached the
point so I'm now curious.. Would you mind sharing the model file
with us so that we evaluate the situation and suggest a way
forward? If you choose to share files, please send it to me and
Nigel, not the whole phenixbb list!</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 6/15/21 22:51, Firdous Tarique
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAAw5XrXw97YLUDZQnO8mjaV=F8pkgp9pzrh+xB=y3hUZ3na+Bg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Nigel
<div><br>
</div>
<div>Thanks for this information. To be more specific. If the
ribosome contains many modified bases then I have to generate
restraints for each of these ligands separately and add them
one by one using the Real Space Refinement Add file menu along
with the map and the whole 40S coordinates and run it. Am I
right ? Is there anyway If the protein contains multiple
ligands and you want to generate for all in a single output
file as it does in refmac, in that case a single cif file
should work for all. I saw one option here but it says it is
generally not preferred to generate restraints for multiple
ligands from the pdb.</div>
<div><br>
</div>
<div>My second question is regarding Elbow which is how to use
it in its best possible way, particularly for determining the
final geometry of the ligand. For example the tool suggests
that one can <b>Use simple optimization</b>, or <b>Optimize
using elbow AM1 QM method</b>, or <b>Optimize using 3rd
party QM package</b>, or <b>Provide final geometry from
file.</b></div>
<div><br>
</div>
<div>What do you think? What to use for a general restraint
generation for a ligand from an already known structure. </div>
<div><br>
</div>
<div>I am new to Phenix, would appreciate it if you please share
with me a general workflow for using eLBOW and how to use it
during refinement.</div>
<div><br>
</div>
<div>Best</div>
<div><br>
</div>
<div>Firdous</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Jun 16, 2021 at 1:19
AM Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov"
moz-do-not-send="true">nwmoriarty@lbl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Firdous
<div><br>
</div>
<div>You need to generate restraints for the missing
entities. You can use eLBOW.</div>
<div><br>
</div>
<div><a href="https://www.youtube.com/watch?v=8qVYTUVKlbQ"
target="_blank" moz-do-not-send="true">https://www.youtube.com/watch?v=8qVYTUVKlbQ</a></div>
<div><br>
</div>
<div>and I can help you.</div>
<div><br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr"><font face="arial, sans-serif">Cheers</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Nigel</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">---</font></div>
<div><font face="arial, sans-serif">Nigel W.
Moriarty<br>
Building 33R0349, Molecular Biophysics
and Integrated Bioimaging</font></div>
<div><font face="arial, sans-serif">Lawrence
Berkeley National Laboratory</font><br>
<font face="arial, sans-serif">Berkeley,
CA 94720-8235</font><br>
<font face="arial, sans-serif">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
href="http://CCI.LBL.gov"
target="_blank" moz-do-not-send="true">CCI.LBL.gov</a></font></div>
</div>
<div><font face="arial, sans-serif"><span
style="color:rgb(73,74,76)">ORCID : </span><font
color="#494a4c"><a
href="https://orcid.org/0000-0001-8857-9464"
target="_blank" moz-do-not-send="true">orcid.org/0000-0001-8857-9464</a></font></font><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
<img
src="https://pxl-mailtracker.com/pixel/u8kp2ZmJoPlqizTZ18O4?rid=u8kp2ZmJoPlqizTZ18O4"
moz-do-not-send="true" width="1" height="1" border="0"></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jun 15, 2021 at
11:14 AM Firdous Tarique <<a
href="mailto:kahkashantarique@gmail.com" target="_blank"
moz-do-not-send="true">kahkashantarique@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi
<div><br>
</div>
<div>I am trying to do real space refinement of a 40S
rigid body docked model in a cryoEM map of 4.8
Angstrom resolution. The PDB contains some modified
nucleic acid bases due to which the program ends with
the following error.</div>
<div><br>
</div>
<div>Fatal problems interpreting model file: Number of
atoms with unknown nonbonded energy type symbols; 52
Please edit the model file to resolve the problems and
/or supply a CIF file with matching restraint
definitions, along with apply_cif_modification and
apply_cif_link parameter definitions if necessary.</div>
<div><br>
</div>
<div>Seems its refinement library is not able to read
the modified bases. Can you please advise how to fix
this problem. What is the best way to update the
library ? Any suggestions are highly appreciated. </div>
<div><br>
</div>
<div>Best</div>
<div><br>
</div>
<div>Firdous</div>
</div>
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