On Tue, Jun 18, 2013 at 4:44 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> 1. At "calculate hbonds" it is not clear to me what "all other cases"
> means. I think you are saying that if hydrogen atoms are present, and
> if you "select all" instead of "select not hydrogen" before "set
> hbonds rasmol false" and "calculate hbonds", you get the result in
> the 3rd column of the table. Could you please be more explicit in the
> second column of the table, third row?
>
>
*all cases where hydrogens are selected followed by calculate HBONDS
*
> 2. Under "calculate hbonds" section "see also" please add "hbonds".
>
> done
> 3. Under "calculate hbonds" in the second row of the table, please
> add that hbonds between water molecules are not calculated, but
> hbonds between water molecules and non-water entities are calculated.
>
> *pseudo-hydrogen bonds between O or N atoms on proteins and nucleic acid
(but not limited to backbone atoms), and other atoms, including water
oxygens. Psuedo-hydrogen bonds are not calculated between two water
molecules. Uses an algorithm developed for Jmol involving parameters (see
below). These hbonds are not colorable by energy.
*
> 4. Under "calculate hbonds" in the third row, please add that hbonds
> between water hydrogens and water oxygens are calculated.
>
>
*Creates bonds from hydrogen atoms on O or N to other O and N atoms,
regardless of whether they are in macromolecules. When two atom sets are
used, hydrogen atoms must be present in the first set; other atoms in that
set will be ignored. Coloring of standard hydrogen bonds by "energy" is
possible, but the value associated with that color should be be taken as a
true energy. Note that you can add hydrogen atoms to a PDB file using set
pdbAddHydrogens prior to loading a PDB file.*
> 5. Somewhere under "calculate hbonds" please mention that
> "hbondsrasmol" is true by default.
>
>
*select not hydrogen; set hbondsRasmol TRUE; calculate HBONDS* The default
calculation when no hydrogen atoms are selected.
> 5. Under "hbonds" in the section "see also" please add "calculate". I
> know it is redundant but I think one should not have to read every
> word to find which other commands are relevant.
>
> done
> 6. Under "hbonds" please add "hbonds delete" and mention that it
> deletes only hbonds between atoms in the previously selected set.
>
>
hbonds DELETE
*Deletes hydrogen bonds between atoms in the currently selected set of
atoms. Both atoms of a given hydrogen bond need to be selected.
*
*
*
> 7. Under "delete", add that a delete command deletes all atoms
> specified in the command, not just the previously selected subset of
> those atoms.
>
> Yes, that definitely needed some work. Note that there is a bug there;
DELETE by itself is acting as ZAP which is not correct. Surfaces should not
be being deleted.
delete *The DELETE command deletes atoms or identified objects. DELETE by
itself deletes all atoms, similarly to the way select by itself selects all
atoms.
* delete $ [object id]
*Deletes the specified objects (from draw, isosurface, etc. using the ID
parameter). Wildcards may used. For example, delete $d* will delete all
identified objects starting with the letter d. delete $* deletes all such
objects.*
delete [atom-expression]
*Deletes the specified atoms. For example: DELETE hydrogen or DELETE atomno
> 30 . Note that delete by itself deletes all atoms, similarly to the way
select by itself selects all atoms.*
> 8. Under "calculate hydrogen" please add that all hydrogens are
> added, not just those appropriate for the previously selected set of atoms.
>
>
calculate HYDROGENS [atom-expression]{default: *}
*Adds hydrogens at calculated positions based on bonding patterns at the
designated atoms or, if no atoms are specified, at all atoms. Note that
this command is not intended to be used for the assignment of hydrogen
atoms in standard PDB files. All atoms must have any formal charges already
designated, and all multiple bonds must be in place. If you want to add
hydogen atoms to a standard PDB structure, use set pdbAddHydrogens prior to
loading the file. Jmol will then do a proper hydrogen atom addition, to
proteins, nucleic acids, carbohydrates, and all ligands. See set
pdbAddHydrogens, below.*
*
*
Bob
> Thanks! Eric
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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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