cif file from pdb-ihm, the integrative structure
Dear all, I am trying to analyze the structures that were deposited in the https://pdb-ihm.org Such as the entry: 8zza The chimeraX (version 1.7 to 1.10) cannot read the CIF file with warning information warning No mmCIF models found. While it succeeded in opening it after adding the option format ihm. But they are the start model, restraints, and results, which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? Best wishes
On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote:
I am trying to analyze the structures that were deposited in the 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 https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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 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> 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 the 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 https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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participants (3)
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Ben Webb -
Tom Goddard -
Yaowang Li