Hi Bob,
sorry to come back to this (only once), but would it make sense to
change the default? Usually when someone asks for an Hbond, they
would want it there, whether it exists or not ...
(feel free to dismiss, you may have your reasons; I know now, and
very much appreciate jmol as a whole. Just felt that that change
might help others in the future.)
best wishes & thanks again
Volker
On Sep 21, 2008, at 8:11 PM, Robert Hanson wrote:
From the documentation:
[radius option] Addition of the keyword "radius" followed by a
distance in angstroms allows definition of the radius of a modified
or newly created bond. If the modify/create option is absent, then
"modify" is assumed; if the bond type is absent, then bonds of any
type are set, but their bond type is not changed.
Key there is that MODIFY is assumed. So you need:
connect (atomno=70) (atomno=111) hbond orange radius 0.05 CREATE
instead.
Bob
On Sun, Sep 21, 2008 at 6:56 AM, Volker Blum <[EMAIL PROTECTED]
berlin.mpg.de> wrote:
Dear all,
using the latest prerelease version of jmol, prerelease
11.6.RC15, I have
questions on two issues that I've found difficult for a while:
1) (minor) For two initially unconnected atoms,
connect (atomno=70) (atomno=111) hbond orange radius 0.05
does not work.
Doing first
connect (atomno=70) (atomno=111) hbond
and then
connect (atomno=70) (atomno=111) hbond orange radius 0.05
produces the desired result. Any reason why the original command
does not work
out of the box?
2) Regarding cartoons (ribbons etc) - I have found it excessively
tedious to
get a ribbon into what is obviously a helix in a structure of mine.
Doing
this based on an xyz file is obviously impossible. Converting first
to a .pdb
file, then hand-editing the pdb file to get CA's and CB's right
gets the
ribbon for me correctly in one structure, but not in another
(exactly same
procedure).
Questions:
What exact information does jmol even require to safely produce a
ribbon? For
me, this was a rather frustrating "guessing in the dark experience.
Empirically, it's
- a pdb file
- numbered residues, perhaps their names
- correctly specified CA's and CB's
- ??? what else?
Is there any reason why a ribbon should not be producable by "simply"
specifying the atoms to be connected from within jmol itself?
Having such a
feature available would be a great help ....
thanks & best wishes
V. Blum
----------------------------------------------------------------------
---
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
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
----------------------------------------------------------------------
---
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
