> 2. I need some advice on how to proceed with fixing the predefined set
> 'protein'. should I try to include all of the known modified residue
> names in the JmolConstants file? seems like an awful kludge, though
> maybe that's the only way.
>
> some background info, from the PDB FAQ:
[snip]
>
> in an ideal world, Jmol would read the MODRES records and add the
> contents to the protein set.
OK, I just read the spec on MODRES. It doesn't seem too bad. The only
issue is that there currently are no data structures that describe these
3-letter residue names. The only real attribute they have is their
position in
JmolConstants.predefinedGroup3Names ...
> by default (esp for files with no MODRES
> records), anything with an alpha carbon and amino group bound in the
> backbone of a protein chain would be considered protein.
This might make it somewhat easier ... in fact, most of the data
structures to support this are already in place.
I build a data structure called viewer.pdb.PdbChain which exactly
corresponds to the chain specifications in the .pdb file. A 'chain' in
this context can contain HETATMs, water, etc.
I also build a data structure called viewer.pdb.PdbPolymer which is
similar, but not the same. It is the data structure for a real *chain*.
In order for a residue to make it into a PdbPolymer it needs to have:
- amino nitrogen
- alpha carbon
- carbonyl carbon
- carbonyl oxygen
This should happen independent of the group name.
Here is how you can test this out:
1. load up a model that has a modified residue
(with or without a MODRES record ...
this record type is currently ignored)
2. turn on backbone
3. see whether or not the residue appears in the backbone
If it does, then most of the work is done.
Q: Can you please add a small file that contains a modified protein
residue to the
samples directory ... with a name like modifiedProteinResidue.pdb
you said:
> anything with an alpha carbon and amino group bound in the
> backbone of a protein chain would be considered protein
Q: Are there cases where something can get into the protein chain without
having
N-C-C=O ?
Q: If so, what are the criteria for determining whether or not something
is in the polymer chain?
Q: How important are modified residues?
> what do you think?
I think we can fit this in.
> is this a reasonable task?
I think this is a good task for us to implement together.
It would be very helpful for you to run the tests above.
I will probably need to make at least some of the modifications to the
data structures because they will be somewhat complicated.
Miguel
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