BTW -- to remove that atom, use display cell=555 and not cell=556
On Wed, Nov 30, 2011 at 12:31 PM, Robert Hanson <[email protected]> wrote: > {1 1 1} replicates the symmetry operations, and some of those might bring > an atom into another unit cell. Particularly with molecular compounds, we > see this all the time, and it is what people want. > > You can specify PACKED to get only atoms within one unit cell, although > then atoms that are at vertices or on faces of the unit cell are > duplicated. You could try that. PACKED by itself implies {1 1 1} PACKED: > > load t.pdb PACKED > > load t.pdb {2 2 2} PACKED > > But I'm guessing you will not like that! > > Would you say the same about the atoms on the edges? They are in other > unit cells as well. > > There's probably no adequate solution I can offer you. > > Bob > > > On Wed, Nov 30, 2011 at 11:35 AM, Hans Horn <[email protected]> wrote: > >> Bob, >> >> whatever magic you did - it fixed the atom duplication. >> However, I think the unit cell should have only 9 atoms, not 10. >> >> >> >> The Mg atom (0.0 0.0 17.59) pointed to by the arrow should be in the >> next cell, shouldn't it?. >> >> I'm afraid that I did not catch the meaning of what I should do about >> "REMARK 290". >> >> Anyhow, thank you very much for this incredibly fast turn around. >> >> Are you going to release your fix soon? >> >> Greets, >> Hans >> >> >> On 11/29/2011 8:09 PM, Robert Hanson wrote: >> >> Hans, >> >> OK, I got it. Very simple fix. See >> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip >> >> By the way, Jmol is guessing at the origin and setting of that unit cell. >> Jmol can read the Jones-Faithful data in the PDB record REMARK 290: >> >> REMARK 290 CRYSTALLOGRAPHIC >> SYMMETRY >> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 >> 1 >> REMARK >> 290 >> REMARK 290 SYMOP >> SYMMETRY >> REMARK 290 NNNMMM >> OPERATOR >> REMARK 290 1555 >> X,Y,Z >> REMARK 290 2555 >> -X,Y+1/2,-Z >> REMARK >> 290 >> >> That's guaranteed to work. >> >> Bob Hanson >> >> >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > 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 > -- 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
<<ebgcbibi.png>>
------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d
_______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
