On Mar 27, 2018, at 6:47 AM, Michaela wrote:

Dear Elaine,

Thank you for your answer. Please accept my apologies for the delayed reply.  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.

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.

 

Best regards,

Michaela

--
Institute of Biotechnology of the CAS, v. v. i.
Laboratory of Biomolecular Recognition
Address:
Průmyslová 595
252 50 Vestec
The Czech Republic
Email: nekardovam@ibt.cas.cz

Dear Michaela,
Sessions do not include the map file, so you would have to attach that in addition to the session file.

However, I can see what is happening from the image. Please see this previous post, “visualizing maps from Coot in Chimera”:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-July/012514.html>

The following might also be useful, but I haven’t tried the script to see what it does:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 14, 2018, at 7:58 AM, <ela.nekardova@gmail.com> <ela.nekardova@gmail.com> wrote:
>
> Dears,
> 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?
> Thank you in advance for your help.
> Best regards,
> Michaela Nekardova

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