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

[Cardiff Jiang]

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
> > > _______________________________________________
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>
>
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