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

[Eric M. <em...@mi...>]

Thanks, Bob ... but I have so many projects lined up they'll keep me 
busy for a long time.

So if anyone else (Angel?) wants to write those macros, dive right in 
and the rest of us will appreciate!

Best regards, -Eric

On 7/31/20 7:51 PM, Robert Hanson via Jmol-users wrote:
> 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... 
> <mailto: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
>
>
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