Also, if you have a lot of atoms, you might want to use a RANGE option for
the LOAD command
*RANGE x.x* Restricts the atoms loaded to those within a given range in
angstroms. If x.x is positive, then this range is relative to the entire
set of atoms that would be generated using *load "filename" {1 1 1}*, and
all atoms within the given distance from ANY atom in that set is loaded; if
x.x is negative, then the range is relative to the atoms that would be
generated using just *load* itself (the base x,y,z symmetry set), and the
atoms loaded are all those *within a box* that is the designated distance
larger than that needed to just contain the set of atoms. Then, to later
select atoms actually within a given distance from the base set, use *within
* with *select* or *display*: *load 1crn.pdb {1 1 1} range -4; display
within(4.0, symop=1555)*. (This two-step sequence is very efficient.) Note
that Jmol will expand the load box by one number in each direction in order
to find atoms that are outside of {i j k} but still within the designated
range: *load {555 555 1} range 2* actually checks all atoms within the
27-cell range 444 through 666. (Jmol 11.4)
On Thu, Oct 25, 2012 at 4:49 PM, Robert Hanson <[email protected]> wrote:
> Yes, I think that's your best bet. If no unit cell information is present,
> you will need to add that to your LOAD command as well. See the
> documentation for how to use the UNITCELL option. Then you could load {2 2
> 1}, do the connect, then either delete the atoms outside the unitcell (cell
> != 555) or just not display them.
>
>
> On Thu, Oct 25, 2012 at 2:44 AM, Angel Herráez <[email protected]>wrote:
>
>> Hello Sridhar
>>
>> I think that
>> load "filename" {i j k}
>> // Loads a block of unit cells
>>
>> may be what you need
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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