There is no atomic model in 8zza, and so ChimeraX cannot visualize it. (Tom and I know this because Tom works on ChimeraX, and I deposited the 8zza structure.) You can certainly fit an atomic model to the deposited bead model if you like, and perhaps that is what Molstar is doing, but it would be an overinterpretation of the data. Ben On 5/13/25 7:33 PM, Yaowang Li via ChimeraX-users wrote:
Agreed, but has information on proteins and AAs
yaowang
*From:*Tom Goddard <goddard@sonic.net> *Sent:* Wednesday, May 14, 2025 9:37 AM *To:* Yaowang Li <liyaowang2911@163.com> *Subject:* Re: [chimerax-users] cif file from pdb-ihm, the integrative structure
Molstar is showing a tube through the beads of the coarse grain model.
Tom
On May 13, 2025, at 6:28 PM, Yaowang Li <liyaowang2911@163.com <mailto:liyaowang2911@163.com>> wrote:
Hi Tom
The chimerax indeed can open the file, and I succeeded in opening it yesterday, same as you showed.
Although the molstar program displays the atomic model, it is hard to analyze.
Yaowang
<image001.png>
*From:*Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> *Sent:*Wednesday, May 14, 2025 9:17 AM *To:*Yaowang Li <liyaowang2911@163.com <mailto:liyaowang2911@163.com>> *Cc:*Ben Webb <ben@salilab.org <mailto:ben@salilab.org>>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax- users@cgl.ucsf.edu>> *Subject:*Re: [chimerax-users] cif file from pdb-ihm, the integrative structure
Hi Yaowang,
You can open the 8zza IHM model in ChimeraX using
open 8zza from pdbdev
If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use
open 8zza from pdbihm
I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out.
As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits.
Tom
IHM 8zza shown in ChimeraX:
<image003.jpg>
On May 13, 2025, at 6:08 PM, Yaowang Li <liyaowang2911@163.com <mailto:liyaowang2911@163.com>> wrote:
Hi, Ben and Tom
Thank you for your help.
“Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure.
In short, I just want to get the atomic model, not the coarse- grained model.
Best wishes,
Yaowang
*From:*chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu <mailto:chimerax-users- bounces+liyaowang2911=163.com@cgl.ucsf.edu><chimerax-users- bounces+liyaowang2911=163.com@cgl.ucsf.edu <mailto:chimerax- users-bounces+liyaowang2911=163.com@cgl.ucsf.edu>>*On Behalf Of*Tom Goddard via ChimeraX-users *Sent:*Wednesday, May 14, 2025 2:01 AM *To:*liyaowang2911@163.com <mailto:liyaowang2911@163.com> *Cc:*chimerax-users@cgl.ucsf.edu <mailto:chimerax- users@cgl.ucsf.edu> *Subject:*[chimerax-users] Re: cif file from pdb-ihm, the integrative structure
Hi Yaowang,
As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 <https:// www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661>
ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/ Downloads/8zza.cif format ihm" it will show you the coarse grain model.
Tom
On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax- users@cgl.ucsf.edu>> wrote:
On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote:
I am trying to analyze the structures that were deposited in thehttps://pdb-ihm.org <https://pdb- ihm.org/><https://pdb-ihm.org <https://pdb-ihm.org/>> Such as the entry: 8zza [...] which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out?
8zza is a model of the yeast nuclear pore complex. As you have observed, it is a coarse-grained model, not atomic. I'm not sure what you mean by "real structural model" but the resolution of the data in 2018 was such that only a coarse-grained structure was possible. That's what was deposited and that's what ChimeraX will show you. What are you trying to do?
Ben -- ben@salilab.org <mailto:ben@salilab.org>https://salilab.org/ ~ben/ <https://salilab.org/~ben/> "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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