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

Fri Jul 30 10:19:09 PDT 2021

Dear Tom,

Oops, I understand now. 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 Fri, Jul 30, 2021 at 10:13 AM Tom Goddard <goddard at sonic.net> wrote:

> The marker serial_number attribute in ChimeraX daily builds is the
> marker's id number which also equals its residue number.  Your files show
> id numbers like 2240 and 4834, nothing in the range of 1 to 73.  So of
> course selecting the serial range 1-73 won't specify anything.
>
> So if your markers in #1 have ids 2240 to 2312 (73 total) and in #2 have
> ids 4834 to 4908 (75 total) and you wanted to exclude the last two markers
> of #2 in the alignment then use command
>
> align #1 to #3:4834-4906
>
>   Tom
>
>
> On Jul 30, 2021, at 9:52 AM, Cardiff Jiang via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> 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
>> >>>> _______________________________________________
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>> >>>
>> >>
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