FyD wrote: > At http://q4md-forcefieldtools.org/RED/index-test.php, one can see the > DMSO molecule (Tripos mol2 file format loaded). > > I am surprised by the color of the carbons/hydrogens is pink
That's Jmol color for non-identified elements. > I guess it is because the name of > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 It's usually an issue with misaligned atom names (at least in pdb format, I'm not used to mol2). Check the mol2 format specification. > Does it mean that only the chemical symbols are recognized as atom names ? > So what about atom names in amino-acids such as CA, CB etc... Absolutely not. CA are read as "carbon, type CA i.e. alpha carbon of proteins". But in PDB, there is a space before the C; if you shift it one character to the left, it would be read as calcium. In addition, pdb has a field specific for the element symbol (close to column 79) which will be used in preference to that dedcue form the atom name. mol2 may have one too. 1. Check your mol2 format and whatever program is generating it. 2. Open the file in another viewer and see how it reads it, or even export it again to mol2 3. Edit the mol2 file and insert/delete a blank column where appropriate ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
