#203 Jmol 13.0.10 compoundname loads wrong structures

None
closed
nobody
None
5
2013-03-26
2013-02-17
Anonymous
No

glucitol,D-glucitol,D-galactitol,D-mannitol,sorbitol name searches all of them load the D-MANNITOL structure.
The problem I have seems to be general for all alditols: the c2 configuration is always (R) nomatter what.
The JSmol HTML site does the same thing to me.
Is there something to be fixed there or something for me to learn??
Thanks for any response
akis farkoius

Discussion

  • Angel Herraez
    Angel Herraez
    2013-02-18

    Hello, Akis
    Loading by name depends on connection to the CACTUS database, so any problems you find depend on how are the molecules stored/defined there.
    The address is
    http://cactus.nci.nih.gov/chemical/structure

     
  • Angel Herraez
    Angel Herraez
    2013-02-18

    I'm not seeing the problem: try
    load files $D-mannitol $L-mannitol
    Both C2 and C5 are R in frame 1, and S in frame 2
    (Jmol application, 13.0.8)

     
  • Bob Hanson
    Bob Hanson
    2013-02-18

    Jmol uses an OPSIN server at the NIH to interpret these names. It's excellent for many cases, but carbohydrates are a work in progress. Please contact Peter Murry-Rust at Cambridge, UK, if you are interested in OPSIN. http://opsin.ch.cam.ac.uk/information.html

     
  • Bob Hanson
    Bob Hanson
    2013-03-26

    • status: open --> closed
    • milestone: -->