Re: [Jmol-users] FASTA sequences? Missing residues?

[Robert H. <ha...@st...>]

Eric, this is very cool. It occurs to me that perhaps you would be
interested in developing one or more macros for Jmol.  A macro is a script
with a URL that is distributed with Jmol so that works in both Java and
JavaScript. It allows power users like you to share their good ideas in a
way that is (reasonably) accessible for the rest of us. I think you could
make a(nother) huge contribution with macros if you were interested.

All you do is make a script that creates functions and then also adds
enough description to make them useful. A recent one I made is called
TOPOND -- for solid-state computational crystallography. If you type

MACRO topond

or just

MACRO

you can see what I am talking about. (I see MACRO crystal doesn't exist,
though.)

Bob


On Fri, Jul 31, 2020 at 11:57 AM Eric Martz <em...@mi...>
wrote:

> Dear Bob,
>
> I often find it useful to extract the one-letter amino acid sequence from
> the ATOM records in a PDB file with Jmol, using " print {*.ca}.group1".
>
> This lists one residue per line. I have figured out how to convert this
> listing to a FASTA format paragraph, but for some this may be an obstacle.
> So (1) I suggest an option to print the residues in FASTA format like this
> >filename.pdb (or filename.cif)
> ABCDEFG.....
>
> Perhaps "print {*.ca}.group1fasta" would be the command?
>
> (2) Maybe this would be too much fuss to implement, but it would also be
> extremely useful to generate a sequence alignment between the SEQRES (full
> experimental sequence) and the ATOMs, that is residues that have
> coordinates. In such an alignment, there would be gaps where residues are
> listed in SEQRES but missing ATOM coordinates (typically due to disorder in
> the electron density map). In our example, suppose residues CDE lack
> coordinates. Then the output would be
> >filename.pdb SEQRES
> ABCDEFG...
> >filename.pdb ATOM
> AB---FG...
>
> (FASTA requires a description line starting ">" in column 1, above the
> sequence paragraph.) Such an alignment can be copied and pasted directly
> into e.g. http://MSAReveal.Org for flexible display options.
>
> As an alternative to generating the alignment from the SEQRES and ATOM
> records, for mmCIF files, this is alignment is included in the file under
> *_pdbx_poly_seq_scheme* and would merely need to be converted from
> columnar 3-letter codes to paragraph 1-letter FASTA format. It would be OK
> to require CIF files for such output, since CIF files are available for all
> published PDB entries.
>
> Thanks for considering these suggestions, -Eric
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900