[Chimera-users] problem with ccp4 map fitting

Tom Goddard goddard at sonic.net
Thu Mar 29 14:54:08 PDT 2018

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.


> 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 at ibt.cas.cz
> ---------- Původní e-mail ----------
> Od: Elaine Meng <meng at cgl.ucsf.edu>
> Komu: ela.nekardova at 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 at gmail.com> <ela.nekardova at 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 
> <coot_map.ccp4><coot_geom.pdb>_______________________________________________
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