Feature Requests item #1827837, was opened at 2007-11-07 12:14
Message generated for change (Comment added) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1827837&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: New IO Format
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Write capability in various formats
Initial Comment:
Greetings:
JMol understands many formats. Wouldn't it be nice to be able to write in these
formats also! This would give the ability to translate from one format to
another. For crystals, it might mean loading in a unit cell and getting atomic
xyz locations in a different format.
Regards,
Assadullah
a s s a d u l l a h at y a h o o . c o m
----------------------------------------------------------------------
Comment By: Nobody/Anonymous (nobody)
Date: 2007-11-11 06:23
Message:
Logged In: NO
Greetings:
Thank you very much and please forgive me for being ignorant about this
feature.
Regards,
Assadullah
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2007-11-09 10:01
Message:
Logged In: YES
user_id=1082841
Originator: NO
yes, that's right. And I believe it only writes the selected atoms. So
first select the atoms you want to put into an XYZ file or MOL file (if you
want the bonding) and then execute the WRITE command.
This is from the Jmol application. If you are using the applet, the WRITE
command returns the string that was written, so you can do something like
this:
(JavaScript)
var xyzdata = jmolEvaluate('script("select within(molecule,atomno=1);print
script(\\"write coord\\")")')
I see there is a bug there that doesn't let you choose the file type with
the applet....
----------------------------------------------------------------------
Comment By: Nobody/Anonymous (nobody)
Date: 2007-11-09 08:06
Message:
Logged In: NO
Thanks! That is what I was looking for.
I understand that for crystals, it would expand the unit cell depending
upon the space group and then write the entire structure in xyz. Right?
Regards,
Assadullah
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2007-11-09 06:16
Message:
Logged In: YES
user_id=1082841
Originator: NO
Yes, that would be great.
http://chemapps.stolaf.edu/jmol/docs?command=write
write coords SPT|XYZ|MOL|PDB "fileName"
Writes molecular data to a file determined by the extension (SPT, XYZ,
MOL, or PDB). "coords" and the type may be omitted if the filename has a
three-letter extension matching one of these types. In the case of XYZ,
MOL, and PDB, only selected atoms are saved. In the case of SPT, a script
file containing the coordinates of the model. This is useful in the case
that one or more of the atoms have been moved using invertSelected,
rotateSelected, or translateSelected. This format is also suitable for
loading back into Jmol, but only in a simple XYZ-like format, using the
load command. However, if the file is read using the script command, then
atoms should appear in their new positions.
Or were you thinking of something different?
Bob Hanson
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1827837&group_id=23629
-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
