Right, thank you! I've just checked interphase for Chimera-X but it looks less intuitive. I am going to make a separate question regarding it. Yours with thanks Enrico Il giorno mer 5 lug 2023 alle ore 18:25 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
For missing-segments modeling specifically, there is no real difference.
However, if you mean for molecular modeling in general, it depends what features you need. ChimeraX has almost all (but not all) of the Chimera features, but additionally has several completely new tools and features, better performance on large data, fancier lighting options, etc.'
One example of new feature is that the ChimeraX interface to Modeller allows comparative modeling of multi-chain complexes, whereas the Chimera interface to Modeller only allows modeling a single protein chain.
See ChimeraX vs Chimera discussion here: <https://www.rbvi.ucsf.edu/chimerax/progress.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
I hope this helps, Elaine
On Jul 5, 2023, at 9:17 AM, Enrico Martinez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you very much Elaine ! I am going to check it and report the results asap. One question: are there any advantages of using the Modeller interface implemented in the ChimeraX ? Many thanks in advance Enrico
Il giorno mer 5 lug 2023 alle ore 18:09 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, The interface is pretty easy, you wouldn't need a tutorial -- just show the tool, choose the options, etc. There are detailed help pages in the User Guide. But I will include some of the help information here:
(1) open your structure
(2) show Sequence of the chain of interest, e.g. from Favorites menu. If you opened the structure from the PDB, it typically has the whole sequence (from SEQRES lines in the file) even though the 3D structure does not, and the missing parts will be black outline boxes. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
(2b) if the full sequence is not already known from the PDB file, i.e. it doesn't have SEQRES information in it, then instead of showing the sequence from the structure, you could just open your FASTA file instead. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> Then you would need to make sure the sequence is associated with the structure chain, using the Sequence Viewer menu Structure... Associations. Then proceed with #3 below.
(3) in Sequence Viewer menu, choose Structure... Modeller (loops/refinement) and in the resulting dialog are choices to fill in the missing segments <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#modeller> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building>
If you look in the tutorials list, you can see that there is a tutorial for comparative modeling with Modeller (tutorial #8 in index link below), but comparative modeling is much more complicated than simply adding missing segments. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
ChimeraX also has a Modeller interface, although the details of how to use it are slightly different than for Chimera. 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 5, 2023, at 3:29 AM, Enrico Martinez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera Users!
I would like to try MODELLER interphase implemented in the Chimera for prediction of the segments missed in input PDB structure having as the input: the pdb structure with missed N and C terminal fragments (everything in one chain), as well as the full sequence of the protein in FASTA.
Could you please provide me with a link to the tutorial (or just explain a very basic workflow here .. ), which simply explains how I could predict the model based on the data and save the predicted solutions in pdb format ?
Many thanks in advance Cheers
Enrico
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