[chimerax-users] How to Align Chromosome Models with Different Number of Atoms?

Fri Jul 30 09:52:15 PDT 2021

Dear Elaine,

Unfortunately again, I can't align two models with different numbers of
atoms. Please assist.

This is the error message:
[image: image.png]

This is the beginning of the .cmm file for model #1:
[image: image.png]

This is the beginning of the .cmm file for model #3:
[image: image.png]

Thank you!

Best regards,

Zichen “Cardiff” Jiang

Undergraduate Class of 2023 | Biology with a Specialization in
Bioinformatics

Division of Biological Sciences

University of California, San Diego

On Mon, Mar 29, 2021 at 8:43 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Cardiff,
> It is exactly as Boris said (thanks Boris!) and as I already said in the
> previous answer:
>  (1) there is no way to best-fit one model to multiple other models at the
> same time.
>  (2) to superimpose them all together you have to choose one model as the
> reference, and then for each match, always use that one as the "to" model
> in the command.
>
> Elaine
>
> > On Mar 29, 2021, at 12:34 AM, Boris Steipe <boris.steipe at utoronto.ca>
> wrote:
> >
> > Ummm ... that won't actually work the way you write it. Be careful about
> the direction of the superposition. You have to declare one reference
> protein, and always rotate/translate onto the same coordinate set. So,
> follow what Elaine wrote exactly. 2 ON 1, then 3 ON 1 etc.
> >
> > For most purposes that is going to give you a good enough solution. But
> it's not the best one can do, in the same way that a pairwise set of
> sequence alignments is not going to give you an optimal global alignment.
> In particular, the details are going to depend on the reference model, so
> any kind of quantitative analysis is no longer reliable.
> >
> > In general, the problem has conflicting objectives and no principled way
> to resolve them. If you must, you can use some online tool - PDB eFold at
> the EBI comes to mind:
> https://urldefense.com/v3/__https://www.ebi.ac.uk/msd-srv/ssm/__;!!Mih3wA!VDojOzNI9ZXd3gJbVtpZk3gY-AXW6z6Mnuiy0dgiWjtAIfthf3sZ8izx8ypvquAg$
> >
> > But, given all the tradeoffs, the "best" strategy really depends on the
> exact problem you are trying to solve.
> >
> > TLDR; Multiple sequence alignments, and multiple structure
> superpositions, are dark arts.
> >
> >
> > :-)
> >
> >
> >
> >
> >
> >
> >> On 2021-03-29, at 11:58, Cardiff Jiang <z8jiang at ucsd.edu> wrote:
> >>
> >> EXTERNAL EMAIL:
> >> Dear Elaine,
> >>
> >> Just to check if I understood you correctly. I can only superimpose
> model #1 to #2 in one pairwise alignment job. Then with a separate pairwise
> alignment job, I can superimpose #1 to #3. I cannot superimpose more than
> two models simultaneously. Is my understanding correct? Thank you.
> >>
> >> Best regards,
> >> Zichen "Cardiff" Jiang
> >>
> >> On Sun, Mar 28, 2021 at 6:24 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >> Hi Cardiff,
> >> You can only do pairwise alignments.  There is no way to best-fit one
> model to multiple others at the same time.
> >>
> >> However, you can still superimpose all of the models together by
> picking one as the reference (the one that stays in place) and then
> matching each of the other three to that one. E.g. if #1 is the reference,
> you could match #2 to #1, then #3 to #1, then #4 to #1.
> >>
> >> I hope this helps,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Mar 28, 2021, at 3:17 PM, Cardiff Jiang <z8jiang at ucsd.edu> wrote:
> >>>
> >>> Dear Elaine,
> >>>
> >>> Thank you for your help! The individual balls/ beads of the genome
> models turn out to be atoms.
> >>>
> >>> Is it possible to align four genome models, each with a different
> number of "atoms"? The smallest atom count is 49 and using the following
> command sequentially didn't work. The commands aligned model #1 to #2, then
> separated #1 from #2, finally aligned #1 to #3, and so on:
> >>> align #1 to #2 #1@@serial_number>=1 & #1@@serial_number<=49  #2@@serial_number>=1
> & #2@@serial_number<=49
> >>> align #1 to #2 #1@@serial_number>=1 & #1@@serial_number<=49  #3@@serial_number>=1
> & #3@@serial_number<=49
> >>>
> >>> Combining the sequential commands together results in "Unequal number
> of atoms to pair, 49 and 0":
> >>> align #1 to #2-4 #1@@serial_number>=1 & #1@@serial_number<=49 #2@@serial_number>=1
> & #2@@serial_number<= 49 #3@@serial_number>=1 & #3@@serial_number<=49 #4@@serial_number>=1
> & #4@@serial_number<= 49
> >>>
> >>> How should I align four models to each other? Thank you.
> >>>
> >>> Best regards,
> >>> Zichen "Cardiff" Jiang
> >>>
> >>> On Sat, Mar 27, 2021 at 6:35 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>> Hi Cardiff,
> >>> It is impossible to tell from a picture what the atoms are named or
> how the residues are numbered.  You have to figure out how to specify an
> equal number of "atoms" from the two files, based on how the atoms are
> named and how the residues are numbered.  Matchmaker is for biopolymers
> (proteins or nucleic acids made of real atoms, not your chromosome models),
> so you would need to use "align" after figuring out how to specify equal
> numbers of "atoms."
> >>>
> >>> You might need to look at your PDB files in a text editor to
> understand its naming/numbering.  Do they really contain 40 residues?  Or
> is each one really a single residue with 40 atoms?
> >>>
> >>> "#1:1-40" specifies residues numbered 1-40 in model #1 because the
> colon symbol ":" means residues. Command "select #1:1-40" will report how
> many "atoms" that specifies.  It might be 0 atoms if the specification is
> wrong.  If you really meant "atoms" numbered 1-40 (not residues) the atom
> specification should instead be "#1@@serial_number>=1 & #1@
> @serial_number<=40"
> >>>
> >>> How to specify atoms in the command line, where # : @ are symbols for
> hierarchical levels model residue atom, and @@ refers to atom attributes:
> >>> <
> https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html__;!!Mih3wA!RYB58EhB-zYqHVp_yrqydhbVxbphw5nBtvKXW9lzRfrV6VCXRpMW0mfZVh0Ft8b3$
> >
> >>>
> >>> I hope this helps,
> >>> Elaine
> >>> -----
> >>> Elaine C. Meng, Ph.D.
> >>> UCSF Chimera(X) team
> >>> Department of Pharmaceutical Chemistry
> >>> University of California, San Francisco
> >>>
> >>>> On Mar 27, 2021, at 11:45 AM, Cardiff Jiang <z8jiang at ucsd.edu> wrote:
> >>>>
> >>>> Dear ChimeraX User List,
> >>>>
> >>>> How can I compare two chromosome 3D models (PDB files) that have
> different numbers of "atoms"?
> >>>>
> >>>> Matchmaker tool reports, "Reference and/or match model contains no
> nucleic or amino acid chains. Use the command-line 'align' command to
> superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal
> number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering
> true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms
> paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired
> for alignment."
> >>>>
> >>>> How should I compare two chromosome 3D models below? Thank you.
> >>>> <image.png>
> >>>>
> >>>> Best regards,
> >>>> Zichen "Cardiff" Jiang
> >>>> _______________________________________________
> >>>> ChimeraX-users mailing list
> >>>> ChimeraX-users at cgl.ucsf.edu
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> >>>
> >>
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> >
> >
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