Something about the symmetry you gave with "sym" is not correct for your alphafold model. I don't think you can simply measure the center of some other assembly and then use it on your alphafold model, because even if you think the capsid has exactly the same symmetry and size, your alphafold model might not be in the same location or orientation or location as 2xvr asymmetric unit. You could try superimposing your alphafold model onto the 2xvr asymmetric unit (e.g. with Matchmaker) before using "sym" but I'm not completely sure that would work very well either. If the conformation is somewhat different the packing may be poor. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 22, 2025, at 12:23 AM, 王雪 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Dr. Elaine, Thank you very much for your prompt and detailed answers to my previous questions—I greatly appreciate your guidance and the time you have taken to assist me. I am writing because I have encountered an unexpected issue in my current modeling workflow. Using AlphaFold3, I predicted the monomeric structure of the T7 phage capsid protein Gp10, and I then employed the experimentally determined capsid model (PDB ID: 2xvr) as my template. After obtaining the center coordinates of the 2xvr assembly via the “measure center” command, I issued the following ChimeraX command to generate an icosahedral shell: “sym #2 I,n25 center 386.40,386.40,386.40 copies true” However, the resulting shell exhibits several conspicuous, symmetric voids (please see the attached screenshots). I am unsure whether these holes arise from an error in my modeling procedure or if they reflect intrinsic features of the monomeric structure itself. Would you be so kind as to advise me on how best to troubleshoot this issue? For your convenience, I have attached: 2xvr.jpg: a snapshot of the capsid protein model directly from the PDB entry Protein_all_1.jpg: the ChimeraX–generated icosahedral assembly showing the voids Any suggestions you might have regarding alternative commands, validation steps, or checks on the monomer structure would be extremely helpful. Thank you again for your invaluable support. I look forward to your expert advice. Sincerely, Wang Xue South China Agricultural University July 22, 2025
At 2025-07-20 23:42:32, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
You can access the locally downloaded copy with the ChimeraX Help menu or "help" command, for example: menu: Help... User Guide, or command "help volume"
Elaine
On Jul 20, 2025, at 8:05 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Sorry no, there is no PDF -- the User Guide is a collection of HTML pages only, and has not been assembled into a single document. These are all included in your local download of the software package, so you do not need to be online.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 19, 2025, at 9:43 PM, 王雪 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF RBVI Team,
My name is Wang Xue, and I am a graduate student at South China Agricultural University. I have been learning to use UCSF ChimeraX to build the icosahedral capsid model of viral proteins. In the course of my studies, I discovered that the ChimeraX documentation and User Manual are provided as a collection of HTML files. While these are extremely helpful, I find that having a single, paginated PDF version would greatly facilitate offline review, bookmarking, and printing of the chapters I most frequently consult.
Would it be possible for you to share the complete ChimeraX User Manual in PDF format? If such a version is already available, I would be grateful if you could direct me to its download link. Otherwise, I would very much appreciate your assistance in providing a consolidated PDF.
Thank you for your help and for all the work you do in maintaining this valuable resource. I look forward to continuing to explore ChimeraX’s powerful features.
Sincerely, Wang Xue South China Agricultural University July 20, 2025