[Chimera-users] combine models

[Francesco Pietra]

Hi Elaine:
chimerax furnished me, from the mmCIF file, a clean, complete pdb, a task
that all software that I tried could not do correctly (i.e., not all
proteins were extracted from the mmCIF file).

The pdb could not be opened with chimera (for the reasons you said, I
suppose), but opened with either Jmol or vmd.
With the latter, I cut a sphere of 30A around the "small molecule" of my
interest and with this sphere.pdb I went back to chimera
to visualize (all OK).

The longest part was installing chimerax on Debian amd64, but finally it
succeeded by, step by step, installing what was lacking in the system, and
changing to a desktop because the vintage VAIO has a too old graphic card
not accepting OpenGL graphics 3.3.

Thanks a lot
francesco

On Sun, Apr 11, 2021 at 1:44 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Actually, let me revise that answer: I realized that if there are too many
> chains for the PDB to put them into one PDB file, there may also be too
> many chains for combine to make them into one model in Chimera (it will
> also run out of valid chain IDs).  That is likely the problem, for which I
> don't have a solution.
>
> Elaine
>
> > On Apr 10, 2021, at 4:31 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Francesco,
> > It's not possible to identify the problem without the specific data.  If
> this is a PDB entry, what is the ID so we can try opening the mmCIF?
> >
> > Or, if this is not in the public database, please use Help... Report a
> Bug and attach a session that has all the bundle.pdb loaded into Chimera,
> and then in the description say how you combined them and what the problem
> is with the combined result.
> >
> > Before you do that, make sure that you are displaying everything in the
> combined result.  Maybe the parts that seem to be missing were just hidden.
> >
> > I should mention that ChimeraX is much better with mmCIF and very large
> complexes than Chimera, but maybe you are planning to use analysis features
> that are only in Chimera (not yet in ChimeraX).
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >> On Apr 10, 2021, at 10:37 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >>
> >> Of course I tried to open the corresponding mmCIF, but CHIMERA
> candidate 1.15 build 42258 linux64 answered that the cif file [line 3]
> appears in tag name entry.id and it was not opened
> >>
> >> ---------- Forwarded message ---------
> >> From: Francesco Pietra <chiendarret at gmail.com>
> >> Date: Sat, Apr 10, 2021 at 6:45 PM
> >> Subject: combine models
> >> To: chimera <chimera-users at cgl.ucsf.edu>
> >>
> >>
> >> Hi
> >> (1) I am faced by the coordinates for a nucleics/protein assembly being
> given in several bundle.pdb, while I need a sequential, continuous pdb file
> that comprises all nucleotides and proteins, not made of models
> >>
> >> (2) If I load all the bundles to chimera, I see all expected ligands
> around the small molecule.
> >>
> >> (3) With all models selected, copy/combine (adopting default first
> model as reference and allowing renaming chains) generates a new model. The
> new  model laks some proteins that should lie near the ligand, as described
> at (2).
> >>
> >> I feel that I am missing something.
> >>
> >> Thanks for advice
> >> francesco pietra
> >
> >
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