Hans,
Congratulations on achieving all this on just your second day. Many good
days to come, I think.
Right, we refer to cell 555 as all atoms that are within or on the
edges/faces/vertices of cell 555. Same with 556. so some atoms are, for
example "cell 555 and cell 556". Hope that sounds reasonable.
So where do these PDB/crystal files come from?
Bob
On Wed, Nov 30, 2011 at 7:37 PM, Hans Horn <[email protected]> wrote:
> Bob,
>
> thx for the clarifications about "REMARK 290".
>
> Btw., I'm able to hide the atom at (0,0,17.59) (which is equivalent by
> translational symmetry to the atom at (0,0,0)) by issuing:
>
> $ display remove cell=556 (or cell={1 1 2})
> (1 atoms hidden)
>
> but *NOT* by issuing:
>
> $ display cell=555
> (0 atoms hidden)
>
> I guess there're still things I don't get!
>
> Thx.,
> Hans
>
> P.S. btw, it's my 2nd day using jmol - so bear with me if I'm asking
> seemingly stupid questions.
>
>
> On 11/30/2011 3:15 PM, Robert Hanson wrote:
>
> On Wed, Nov 30, 2011 at 2:09 PM, Hans Horn <[email protected]> wrote:
>
>> Bob,
>>
>> $ display cell=555
>> 0 atoms hidden
>> (all 10 atoms shown)
>>
>> $ display cell=556
>> 9 atoms hidden
>>
>>
> exactly. So you would use
>
> display cell=555 and not cell=556
>
> if you want to remove that particular atom.
>
>
>
>>
>> Would you mind reiterating about what I should do about "REMARK 290".
>>
>> thx,
>> H.
>>
>>
> REMARK 290 allows you to specify the specific Jones-Faithful operators
> that define a space group. CIF files generally provide these, and PDB files
> do as well. I don't know what access you have to that. Check that message I
> sent for the format. If you can't provide that, that's OK, but realize that
> some space groups can have different settings, or different origins, so the
> space group name itself (unless it is a Hall name) is not always sufficient.
>
> Bob
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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contains a definitive record of customers, application performance,
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