Hi Rob and Angel, Thank you for clarifying this.
To address Rob's question about what functions of the various file formats are ignored, I'm no expert on the .pdb format, but in reading the .pdb file spec here: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf it appears that there are approximately a gajillion possible record types and fields within those records, including some kinds of annotations. For example, bibliographic citations, MDLTY, REVDAT, REMARK, etc. Not that I would find most of these fields very useful - just answering the question and thereby asking if I am misunderstanding something about .pdb. I guess these generally are not visual annotations/labels as I am thinking of. Assuming that none of the molecular model formats support saving either general visible annotations or atom labels, and that the solution is to write an SPT, JMOL or PNGJ, as Rob suggested, that would be perfect if JMol was the only program other users needed. But, the actual modeling may have been done in GROMACS, HyperChem, VMD, etc. So, the problem is round-tripping. If someone gives me a .pdb, I can't annotate it (nor probably do many other things) and give it back them as a .pdb, or anything that they can use without losing my changes. E.g., .spt, .jmol and .pngj do not appear to be on HyperChem's "open" or "save as" list. Same when I just scan down the list of file formats GROMACS uses (http://www.gromacs.org/Documentation/File_Formats). I'm guessing there is no simple answer, but any suggestions would be great. Sincerely, James Ryley, PhD, RPA SumoBrainSolutions Intellectual Property Solutions, Consulting & Data Providers of: AcclaimIP Patent Analytics Platform for Search & Business Intelligence FreePatentsOnline.com Comprehensive Patent Searching Database SumoBrain.com The Convergence of IP and Business Information BioMedSearch.com Worlds Largest Free Biomedical Search Engine OpenThesis.org Upload & Search Global Theses and Dissertations This communication is to be treated as confidential and the information in it may not be used or disclosed except for the purpose for which it has been sent. Nothing contained herein nor on a related web site should be construed as legal or patenting advice. > -----Original Message----- > From: Angel Herráez [mailto:angel.herr...@uah.es] > Sent: Wednesday, May 08, 2013 10:12 AM > To: jmol-users@lists.sourceforge.net > Subject: Re: [Jmol-users] saving annotations and labels > > Hello, James > > Precisely! > PDB format has no place for atom labels or annotations, that why Jmol > cannot save that. > You can save to a "JMOL" file which is a file (actually a gzipped set of files) > that holds everything. Of course, that file can only be opened by Jmol, You > can also save to a special png file (called PNGJ) that includes a snapshot of > the model and will be loaded as an image by external software but as a full > model by Jmol. > > I don't know of any file format that can hold annotations for each atom. > Several allow comments. Maybe the newer MOL3000 has a place, but I never > read about it. > > > This opens up what is perhaps a more general question. I don't think > > JMol always supports all of the possible data fields for the file > > formats it can use. Is there documentation about which features > > should be assumed to work (I'm particularly thinking of when using > > "write CD|MOL|PDB|SDF|V2000|XYZ|XYZRN|XYZVIB " > > Not exhaustive, but for several formats and features there is some > documentation in the Wiki, see http://wiki.jmol.org/index.php/File_formats > and there > Coordinates > Support for bond orders > Support for isotopes > Support for stereochemistry > > As for export, it's msotly just the atom properties that are written to file > (ccordinates, identities...). > > > > ---------------------------------------------------------------------------- -- > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200-page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
