[Chimera-users] Pack molecules in Unit Cell

Elaine Meng meng at cgl.ucsf.edu
Fri May 20 13:45:13 PDT 2011

Maybe I don't understand what you are asking.  It sounds like you are using version 1.5.3 of Chimera, whereas if you get the 1.6 daily build, it will include the packing feature you mentioned.  The daily build includes the very latest changes.  Both versions are available from the download page, along with dates.

I was just trying to explain why the options shown in the manpage you were viewing might not match the software you were using.

If I still haven't answered your question, however, let me know!

On May 20, 2011, at 10:53 AM, Joe Osmundson wrote:

> Most helpful, I was wondering if there was simply a different (more
> recent) version.
> Thanks very much,
> Joe
> On Fri, May 20, 2011 at 1:52 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Joe,
>> The packing option is in version 1.6 (daily builds) but not 1.5.x.  The daily builds are also available for download, just farther down on the page:
>> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
>> The URL you gave is for "development" documentation (latest, synchronized for the most part with the daily build).  The documentation included with your download and accessible from the Chimera Help menu should be better synchronized with the features in that same version.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On May 19, 2011, at 5:17 PM, Joe Osmundson wrote:
>>> Hi everyone,
>>> I would like to transform a pdb so that it fits nicely in the unit
>>> cell, which seems to be described here:
>>> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html
>>> as "Pack molecules in unit cell".  However, this is not an option when
>>> I bring up the options in the Unit Cell tool (although literally
>>> everything else that should be there IS indeed there).
>>> Is there a glitch in the most recent version?  Is there an easy way to
>>> script this to essentially move the model (and its crystallographic
>>> mate) into the center of the unit cell?
>>> Thanks,
>>> Joe Osmundson
>>> Darst Lab
>>> Rockefeller University

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