Re: [Jmol-developers] label formatting options

[Miguel <mi...@jm...>]

> Thanks, Miguel. Here is what I found. Please indicate the ones that
should not be included in the documentation or should be listed as "not
yet implemented"

The ones that say 'for internal use' should not be listed.

> or that I don't quite have it right with. The list here is just in the
order of switches in Atoms.java.
>
> In addition, is there a way of delivering such information to a message
callback? Something like:
>
> select *
> report %a %x %y %z\n
>
> Labels are nice, but....

Give me more specific detail about what you want.

> Bob
>
> %i;number assigned this atom (1,2,3,...)
This is the atom sequence number in a PDB file. Other file types start at
1 per model.

> %a;atomic symbol (H,C,N,...; same as %e)

This is the atom name. Depends upon the file type. For pdb files it is the
name used for the atom. If you try gaussian files then it will be a combo
of the atom name and the atom number.

If the file does not define an atom name (like mol or xyz) then it uses
the element symbol.

> %e;atomic symbol (H,C,N,...; same as %a)

correct ... 'e' is for element

> %x;x-coordinate
> %y:y-coordinate
> %z:z-coordinate

I don't think these are implemented in RasMol/Chime.


> %X:atom index (not implemented?)

For Jmol internal use only.

> %C:formal charge
> %P:partial charge

I think these default to 0.

> %V:Van der Waals radius (1.7 for O; in Angstroms)
> %I:Bonding radius (0.68 for O; in Angstroms)

These do not exist in RasMol/Chime.

> %b:B-factor/temperature (specified in PDB file; same as %t)
> %t:B-factor/temperature (specified in PDB file; same as %b)

There are a few other file types that support b factor.

It is not clear to me what the difference is, but there *is* some
difference between temperature and b-factor. But the waters seem to have
been muddied somewhat by RasMol, and we probably need to maintain this
somewhat for backwards compatibility.

> %q:occupancy (crystallographic information)

This is an integer value 0-100 representing a percentage.

> %c:chain/strand ID (A, B, C,...; same as %s)
> %s:chain/strand ID (A, B, C,...; same as %c)

I did not know that %s was there ... but I believe you.

> %L:chain/strand length (not implemented?)

This is actually polymer length. And it is implemented for polymers.

We need to be careful about our terminology.

Chain means absolutely nothing. For example, according to the .pdb format
all of the HOH atoms are usually in the same chain.

We need to use the word 'polymer' to mean a real chain.

> %M:model tag (start with "/"; file-type dependent)

Correct. This is currently a number ... (as defined in .pdb files). But I
am in the process of changing it to be a string (to better support other
file types). Hence the name 'modelTag'

> %m:"<X>"

Who knows?

> %n:protein group (VAL, ARG, HOH, etc.)
> %r:sequential number in Rasmol chain (1,2,3,...)

Actually, this is the 'residue' number in .pdb speak. It should include an
insertion code if one is present.

> %U:atom identity (protein: "N[LEU]:C" nitrogen atom of leucine on chain
C, DNA: "P[G]:A", phosphorus atom on guanine of chain A; mol file: "H 3"
atom 3 (hydrogen), animation: "3/7" third atom of frame 7)

> %{string}:client property "string?"

This is to allow the display of arbitrary client properties. It currently
only takes effect if someone has hooked Jmol into CDK.



Very good work.


Miguel