On Wed, May 8, 2013 at 11:23 AM, James Ryley <ja...@ryley.com> wrote:
> Hi Rob and Angel,
>
> Thank you for clarifying this.
>
>
> and thereby asking if I am misunderstanding something about .pdb. I guess
> these generally are not visual annotations/labels as I am thinking of.
>
All those PDB header records are read and accessible to users within Jmol.
>
> 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.
Well, it sounds like you are thinking very generally; once your plan is
refined further, let us know what exactly you are interested in doing. I
suspect you could write scripts that do just about anything. There will be
no general solution to these issues.
> 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.
Right, and they would not expect that, because the format does not support
it. The SDF file format (V2000/V3000) does allow adding customized records,
but that's the only one I know of like that.
http://c4.cabrillo.edu/404/ctfile.pdf
> 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.
>
You will need to write your own file conversion for round tripping. I doubt
it's possible to get annotations through the full cycle.
Bob Hanson
On Wed, May 8, 2013 at 11:23 AM, James Ryley <ja...@ryley.com> wrote:
> 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
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>
> > -----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...).
> >
> >
> >
> >
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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