Hi Michaela, I opened you atomic model and map and used Chimera command vop cover #1 atom #0 and it extended the map to cover the water that was outside the original unit cell map. Tom
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
---------- Původní e-mail ---------- Od: Elaine Meng <meng@cgl.ucsf.edu> Komu: ela.nekardova@gmail.com Datum: 14. 3. 2018 17:28:23 Předmět: Re: [Chimera-users] problem with ccp4 map fitting
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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