Dear Bob, > questions answered in line below...
Sorry for the delay; I looked back in the R.E.D. code. > Jmol doesn't need atom symbols, but as you can imagine, CA for calcium and > CA for alpha carbon is not conducive to unambiguous resolution of elements > without that key field. There are no rules about atom names having to start > with element symbols, so Jmol can only apply a reasonable guess algorithm to > get elements when that element field data is missing. Yes, you are right... > - Many small molecules are written in the PDB file format without >> these chemical elements > > Yes, but for them the atom name "CA1" is interpreted as calcium, as you > would expect. Same for Ce1, Cd1, Cf1. How could Jmol be expected to read > those as carbons? In fact, R.E.D. deals only with chemical elements up to Bromine; this means there is only one ambiguity in our case; CA for calcium versus CA for alpha carbon. >> - VMD and LEaP (for instance) do not need chemical elements to >> recognize atom names > > And they will make the same mistake -- or not recognize cerium as a possible > atom. VMD has all sorts of known problems figuring out elements from atom > names. ok, as we work in the field of organic & bio-organic molecules we do not encounter these problems, I see. > Jmol does this already. but you can't throw generic "PDB-like" files at it > and expect it to know that CA1 means alpha carbon and not calcium. One could > suggest that ATOM requires CA be alpha carbon and HETATM might not, but it > turns out that's not workable, either. ok > Jmol recognizes that if you start "CA1" in column 13, then you must mean > calcium, and if you start it in column 14, you mean alpha carbon. That is, > columns 12 and 13 indicate atom symbol. So that's an option. (The atom names > are spit out by many programs in this way -- all the RCSB PDB files are like > this, for example, even if it is not in the specs.) This system breaks down > for certain hydrogen atoms that are named as, for example, "HH11" or "HO5'". > For "HO5'" Jmol checks to see if this is a HETATM (so this is read as > holmium, or ATOM (so this is read as hydrogen). Obviously the best situation > is to create proper PDB files and have that colum 77/78 data. > >> Consequently, this means that Jmol can already recognize some atom >> names without chemical elements. Is it not possible to extend this >> feature to more general atom names? > > Right, that's because Jmol has a fallback option. The rule is that the atom > symbol should appear right-justified in > columns 13 and 14. But if that's not the case, as here, then the algorithm > looks next at just the character in column 13. In this case C and H. > > By the way, are you sure ATOM is appropriate for a benzene ring? According > to the specs we have: > > The ATOM records present the atomic coordinates for standard residues (see > http://deposit.pdb.org/public-component-erf.cif). > > Everything else should be HETATM. The only difference that makes for Jmol is > for four-letter > atom names that are therefore forced to start in column 13, start with H, > but aren't hydrogen. Like, > for example, HE for helium or "hydrogen E". In that case, if it is HETATM, > Jmol chooses helium; if it is ATOM, it chooses H. ok Thanks for all these explanations. all makes perfect sense. I have modified R.E.D. IV so that the PDB format generated always contains chemical elements so that Jmol does what we want. regards, Francois ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users