Dear Bob, > 1) There's no header information that distinguishes this from PDB files > 2) The atom name field overlaps with the B-Factor field. (Kind of amazing to > me that you > would just invalidate that field that way instead of using the > available columns just after it.) > 3) There's no element listed in columns 77-78 > > We don't particularly need (3), but I certainly need (1). I'm not going to > have Jmol check the B-Factor field for a non-number just to do this!
- What if you check for this second column of atom names only for files with the .p2n or .P2N extension. - or we can add a header in the P2N file to distinguish it from the PDB file format; for instance: REMARK P2N FILE FORMAT JMOL COMPATIBLE - We can also adapt the format of the P2N file; if you need to have this second column of atom names located in another set of columns; no problem for R.E.D. which only takes the last column available. ATOM 1 CO1 CHC 1 0.000 0.000 -0.000 CO ATOM 2 N2 CHC 1 1.186 0.866 0.332 N1 and ATOM 1 CO1 CHC 1 0.000 0.000 -0.000 CO ATOM 2 N2 CHC 1 1.186 0.866 0.332 N1 and ATOM 1 CO1 CHC 1 0.000 0.000 -0.000 CO ATOM 2 N2 CHC 1 1.186 0.866 0.332 N1 are all recognized by R.E.D. - the chemical element can be deduced from the one of the two columns of atom names. 1H2 -> H; CB -> C; NH -> N; C'1 -> C; C*1 -> C etc... The ambiguity is for Calcium; we use as name XX Just tell me what you prefer... regards, Francois > On Wed, Nov 10, 2010 at 9:51 AM, FyD <f...@q4md-forcefieldtools.org> wrote: > >> Dear Jmol developers, >> >> I have a request for the Jmol developers... >> >> Jmol handles atom names, charge values, force field atom types & more; >> it recognizes among others the PDB & mol2 file formats. >> >> With the R.E.D. tools & R.E.D. Server we have introduced a new file >> format named P2N file format. >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3 >> >> This P2N file format derives from the PDB file format; the main >> difference is that this P2N file format can handle two types of atom >> names: >> - the first one reflects chemical equivalencing used in RESP input >> generation and RESP/ESP charge derivation >> - the second one conserves atom naming conventions >> >> Do you think Jmol could recognize this P2N file format i.e. could Jmol >> display these two types of atom names independently? >> >> You can find an example of P2N file format @ >> http://q4md-forcefieldtools.org/Tutorial/P2N/Metal-complex/Mol_red1.p2n >> >> The idea would be to allow displaying these two types of atom names as >> Jmol already does for the regular atom names, the charge values and >> the force field atom types using the mol2 file format - such as in the >> follow applet: >> http://q4md-forcefieldtools.org/RED/popup/javaapplet.php >> Atomic charges -> displayed or not displayed >> Force field atom types -> displayed or not >> Atom names -> displayed or not >> >> We could imagine the same approach for the P2N file format i.e. for >> the files with the .p2n and P2N extensions: >> Atom names (1st column) -> displayed or not displayed >> Atom names (2nd column) -> displayed or not >> >> As this P2N file format is only used by the tools from >> q4md-forcefieldtools.org, I would understand Jmol developers would not >> be motivated by this request ;-) no problem with that. >> >> Thank you, >> 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
