Hello, I think you mean "interface" ... interphase is a different thing relating to the cell cycle. :-) There are two different tools (Modeller interfaces), and you might be looking at the wrong one: (A) Modeller Comparative is for comparative or homology modeling using one or more template structures. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> (B) Model Loops is for adding missing segments or generating alternative conformations of loops. It does not use a template. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html> For adding missing segments, you still need a structure (the one with the missing segments) as well as its full sequence. If you got the structure from the PDB it probably has the full sequence information already. So you would (1) open the structure (2) show its sequence (menu: Tools... Sequence... Show Sequence Viewer, choose the chain of interest) ... or you can show its sequence with a command, e.g.: seq chain #1/A (3) in the Sequence Viewer window, you can see the missing segments are in black outline boxes. You can start Model Loops using the context menu in the sequence window (Ctrl-click or right-click depending on what kind of computer you have). In the context menu it is Tools... Model Loops. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> ...or you can start Model Loops using the ChimeraX main menu: Tools... Sequence... Model Loops. Details of how to use that tool are in the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html> If you did not get the structure from the PDB it may be missing the full sequence information. In that case you would have to open the sequence separately instead of step #2 above. If you have a sequence file (e.g. FASTA) you can open that. Or, you can figure UniProt sequence ID for this structure and fetch that sequence. E.g. if I go to the uniprot website and figure out that I need the sequence for LDLR_HUMAN then in ChimeraX I can use command: open uniprot:LDLR_HUMAN ...to show the sequence. Then you would need to make sure that sequence is associated with your structure, as explained in the Sequence Viewer documentation, before going on to step #3 above. Sequence-structure association: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 13, 2023, at 2:46 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am trying to use the Modeller interphase of the Chimera-X, with the aim to model missed segments from the input PDB structure. I have very basic questions:
1) In the top, there is a Sequence Alignment dialog box but I don't understand how to provide the alignment there. Should it be the alignment of the sequence of the target pdb (template) ? If so, how could it be obtained supposing that I have i) a pdb with missing fragments as well as ii) the full sequence.
Many thanks in advance
Enrico