<html><body><span lang="EN-GB">Dear Elaine,</span>
<p><span lang="EN-GB"><br></span></p><p><span lang="EN-GB">Thank you for your answer. Please accept my
apologies for the delayed reply. <span style="mso-spacerun:yes"> </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><span lang="EN-GB"><br></span></p><p><span lang="EN-GB">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>
<p><span lang="EN-GB"> </span></p>
<p><span lang="EN-GB">Best regards,</span></p>
<p><span lang="EN-GB">Michaela </span></p>
<br>-- <br>Institute of Biotechnology of the CAS, v. v. i.<br>Laboratory of Biomolecular Recognition<br>Address:<br>Průmyslová 595<br>252 50 Vestec<br>The Czech Republic <br>Email: nekardovam@ibt.cas.cz<br><br><br><br><aside>
---------- Původní e-mail ----------<br>
Od: Elaine Meng <meng@cgl.ucsf.edu><br>
Komu: ela.nekardova@gmail.com<br>
Datum: 14. 3. 2018 17:28:23<br>
Předmět: Re: [Chimera-users] problem with ccp4 map fitting
</aside><br><blockquote data-email="meng@cgl.ucsf.edu">Dear Michaela,
<br>Sessions do not include the map file, so you would have to attach that in addition to the session file.
<br>
<br>However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”:
<br><http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html>
<br>
<br>The following might also be useful, but I haven’t tried the script to see what it does:
<br><http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.html>
<br>
<br>I hope this helps,
<br>Elaine
<br>-----
<br>Elaine C. Meng, Ph.D.
<br>UCSF Chimera(X) team
<br>Department of Pharmaceutical Chemistry
<br>University of California, San Francisco
<br>
<br>> On Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@gmail.com> wrote:
<br>>
<br>> Dears,
<br>> 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>> Thank you in advance for your help.
<br>> Best regards,
<br>> Michaela Nekardova
<br>
<br></blockquote></body></html>