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

[Cardiff Jiang]

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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