Re: [Jmol-users] The woes of big molecules

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

Hi, Craig,

The Chime syntax for selecting chain 4 is "select :4", not "select *4". The 
former works. The latter (in Chime -- I haven't tried jmol) selects all 
residues numbered 4 but not chain 4.

While on the subject of digits in names, the Chime syntax for selecting a 
group name that includes digits is "select [so3]". "select so3" doesn't 
work! This is because the default interpretation is that the group name is 
letters and the first digit begins a sequence number, as in "select 
asp226". (Recall that group names can be 1-3 letters, e.g. "a" and "ca".)

I have a close to comprehensive intro to select commands in RasMol and 
Chime at
http://www.umass.edu/microbio/rasmol/seleccmd.htm

Worse than digit-named chains, some PDB files have so many chains that both 
upper and lower case letters are used for different chains, and also 
punctuation. Chime can't handle the case distinction, nor the punctuation. 
So, count yourself lucky with "only" 32 chains in 1KQS!

Then there are the cases of 2-letter names aligned in the PDB file's 
3-character field so that Chime can't handle them, such as "ca " vs. " ca"!

Good luck, -Eric

At 3/21/05, you wrote:
>Greetings,
>
>  I've run across another issue arising from my trying to set up some 
> Ribosome pages (I'm still struggling with memory issues on Mac browsers).
>
>  It turns out that there are more chains in the structure 1KQS (and some 
> other ribosome structures) than there are letters in the alphabet. So in 
> addition to the letters A-Z, the authors have used 0, 1, 2, 3, and 4 as 
> chain identifiers.
>
>  However, when I issue the command "select *4", I select all residues 
> numbered "4" in all chains. What are the rules about this, either within 
> the PDB or in Jmol/CHIME? Can chains have numeric designators and if so, 
> how does one select them?
>
>  Clearly, we can't ask the ribosome to consolidate   ;)
>
>Thanks,
>
>Craig
>
>Craig Martin
>Univ of Mass
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Jmol-users mailing list
>Jmo...@li...
>https://lists.sourceforge.net/lists/listinfo/jmol-users

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
       http://bioinformatics.org/mailman/listinfo/molvis-list

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
               http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */