<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Michaela,<div class=""><br class=""></div><div class=""> I opened you atomic model and map and used Chimera command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop cover #1 atom #0</div><div class=""><br class=""></div><div class="">and it extended the map to cover the water that was outside the original unit cell map.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="54D03499-2496-488F-9B70-2596264F9909" src="cid:8327C505-744C-48F7-B8A7-F13DBC217AA9@cgl.ucsf.edu" class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 27, 2018, at 6:47 AM, Michaela wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><span lang="EN-GB" class="">Dear Elaine,</span><p class=""><span lang="EN-GB" class=""><br class=""></span></p><p class=""><span lang="EN-GB" class="">Thank you for your answer. Please accept my
apologies for the delayed reply. <span style="mso-spacerun:yes" class=""> </span>Probably
I did a mistake when I saved the session because the map was included. I work
with Chimera briefly. The first link describes the same or similar problem but
in my case, the suggested solution depicts the map not quite correctly. I understand
that Chimera was created for a different purpose than crystallography.
Unfortunately, the COOT graphics is unacceptable for papers and websites. I have
used Pymol but a map fitting and other options have certain imperfections as
well. I work on a bioinformatics study based on analysis of tens of map files with
the described problem. </span></p><p class=""><span lang="EN-GB" class=""><br class=""></span></p><p class=""><span lang="EN-GB" class="">In case that you find the problem
interesting, I am sending you the files: the map of water density and the
dinucleotide with its hydration sites. </span></p><div class=""><span lang="EN-GB" class=""> </span><br class="webkit-block-placeholder"></div><p class=""><span lang="EN-GB" class="">Best regards,</span></p><p class=""><span lang="EN-GB" class="">Michaela </span></p>
<br class="">-- <br class="">Institute of Biotechnology of the CAS, v. v. i.<br class="">Laboratory of Biomolecular Recognition<br class="">Address:<br class="">Průmyslová 595<br class="">252 50 Vestec<br class="">The Czech Republic <br class=""><a href="mailto:nekardovam@ibt.cas.cz" class="">Email: nekardovam@ibt.cas.cz</a><br class=""><br class=""><br class=""><br class=""><aside class="">
---------- Původní e-mail ----------<br class="">
Od: Elaine Meng <meng@cgl.ucsf.edu><br class="">
Komu: ela.nekardova@gmail.com<br class="">
Datum: 14. 3. 2018 17:28:23<br class="">
Předmět: Re: [Chimera-users] problem with ccp4 map fitting
</aside><br class=""><blockquote data-email="meng@cgl.ucsf.edu" class="">Dear Michaela,
<br class="">Sessions do not include the map file, so you would have to attach that in addition to the session file.
<br class="">
<br class="">However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”:
<br class=""><http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html>
<br class="">
<br class="">The following might also be useful, but I haven’t tried the script to see what it does:
<br class=""><http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.html>
<br class="">
<br class="">I hope this helps,
<br class="">Elaine
<br class="">-----
<br class="">Elaine C. Meng, Ph.D.
<br class="">UCSF Chimera(X) team
<br class="">Department of Pharmaceutical Chemistry
<br class="">University of California, San Francisco
<br class="">
<br class="">> On Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@gmail.com> wrote:
<br class="">>
<br class="">> Dears,
<br class="">> I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please?
<br class="">> Thank you in advance for your help.
<br class="">> Best regards,
<br class="">> Michaela Nekardova
<br class="">
<br class=""></blockquote></div><span id="cid:i07757815257509985"><coot_map.ccp4></span><span id="cid:D283AC4F-4E94-48DA-90D2-176B8166BC8C@cgl.ucsf.edu"><coot_geom.pdb></span>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>