From: Hans H. <ha...@2h...> - 2011-11-29 21:38:46
|
Folks, I have a pdb file : ############# HEADER 09-NOV-11 TITLE Structure 1 REVDAT 1 09-NOV-11 0 REMARK 4 REMARK 4 COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996 HET UNK A 1 2 FORMUL 1 UNK Mg3 Cl6 CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 m -1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.278087 0.160553 -0.000000 0.00000 SCALE2 0.000000 0.321107 -0.000000 0.00000 SCALE3 0.000000 0.000000 0.056850 0.00000 HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00 0.00 Mg2+ HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00 0.00 Cl1- END ############ I'd like to see the unit cell displayed, as well as the atoms in the unit cell generated and displayed. Is this possible using jmol? Thx., H. |
From: Robert H. <ha...@st...> - 2011-11-29 21:46:07
|
sure. load xxx.pdb {1 1 1} gives you a full unit cell. unitcell on gets you the unit cell axes on gets you a,b,c axes for the unit cell. On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn <ha...@2h...> wrote: > Folks, > > I have a pdb file : > > ############# > HEADER > 09-NOV-11 > TITLE Structure > 1 > REVDAT 1 09-NOV-11 > 0 > REMARK > 4 > REMARK 4 COMPLIES WITH FORMAT V. 2.1, > 25-OCT-1996 > HET UNK A 1 > 2 > FORMUL 1 UNK Mg3 > Cl6 > CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 m > -1 > ORIGX1 1.000000 0.000000 0.000000 > 0.00000 > ORIGX2 0.000000 1.000000 0.000000 > 0.00000 > ORIGX3 0.000000 0.000000 1.000000 > 0.00000 > SCALE1 0.278087 0.160553 -0.000000 > 0.00000 > SCALE2 0.000000 0.321107 -0.000000 > 0.00000 > SCALE3 0.000000 0.000000 0.056850 > 0.00000 > HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00 > 0.00 Mg2+ > HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00 > 0.00 Cl1- > END > > ############ > > I'd like to see the unit cell displayed, as well as the atoms in the unit > cell generated and displayed. > Is this possible using jmol? > > Thx., > H. > > > ------------------------------------------------------------------------------ > 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 > Jmo...@li... > 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 |
From: Hans H. <ha...@2h...> - 2011-11-29 22:59:33
|
Robert, neat! when I do that with the pdb file posted, I see 10 atoms in the unit cell. However, when I write it out (e.g. as xyz) I get 72 atoms. Why's that? Is there a way to save the unit cell as 3*3 matrix? thx, H. On 11/29/2011 1:45 PM, Robert Hanson wrote: > sure. > > load xxx.pdb {1 1 1} > > gives you a full unit cell. > > unitcell on > > gets you the unit cell > > axes on > > gets you a,b,c axes for the unit cell. > > > > On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn <ha...@2h... > <mailto:ha...@2h...>> wrote: > > Folks, > > I have a pdb file : > > ############# > HEADER 09-NOV-11 > TITLE Structure 1 > REVDAT 1 09-NOV-11 0 > REMARK 4 > REMARK 4 COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996 > HET UNK A 1 2 > FORMUL 1 UNK Mg3 Cl6 > CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 > m -1 > ORIGX1 1.000000 0.000000 0.000000 0.00000 > ORIGX2 0.000000 1.000000 0.000000 0.00000 > ORIGX3 0.000000 0.000000 1.000000 0.00000 > SCALE1 0.278087 0.160553 -0.000000 0.00000 > SCALE2 0.000000 0.321107 -0.000000 0.00000 > SCALE3 0.000000 0.000000 0.056850 0.00000 > HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00 > 0.00 Mg2+ > HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00 > 0.00 Cl1- > END > ############ > > I'd like to see the unit cell displayed, as well as the atoms in > the unit cell generated and displayed. > Is this possible using jmol? > > Thx., > H. > > ------------------------------------------------------------------------------ > 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 > Jmo...@li... > <mailto:Jmo...@li...> > 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 > > > ------------------------------------------------------------------------------ > 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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2011-11-30 03:49:10
|
Oh, I guess I did not actually try it with your file. I didn't realize it was a complete model! Ah, that's a problem! Well, I can tell you why that is. Jmol presumes that a PDB file is a protein and saves hugely on processing by assuming that there are no special positions. Therefore it does not check to see if atoms are on top of each other after symmetry transformations. But in your case this isn't really a PDB file, it's an inorganic crystal file. You sure you don't want to use CIF format -- like everyone else ;) ? I have an idea, though. Let me think about this.... Bob On Tue, Nov 29, 2011 at 4:59 PM, Hans Horn <ha...@2h...> wrote: > Robert, > > neat! > > when I do that with the pdb file posted, I see 10 atoms in the unit cell. > However, when I write it out (e.g. as xyz) I get 72 atoms. > Why's that? > > Is there a way to save the unit cell as 3*3 matrix? > > thx, > H. > On 11/29/2011 1:45 PM, Robert Hanson wrote: > > sure. > > load xxx.pdb {1 1 1} > > gives you a full unit cell. > > unitcell on > > gets you the unit cell > > axes on > > gets you a,b,c axes for the unit cell. > > > > On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn <ha...@2h...> wrote: > >> Folks, >> >> I have a pdb file : >> >> ############# >> HEADER >> 09-NOV-11 >> TITLE Structure >> 1 >> REVDAT 1 09-NOV-11 >> 0 >> REMARK >> 4 >> REMARK 4 COMPLIES WITH FORMAT V. 2.1, >> 25-OCT-1996 >> HET UNK A 1 >> 2 >> FORMUL 1 UNK Mg3 >> Cl6 >> CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 m >> -1 >> ORIGX1 1.000000 0.000000 0.000000 >> 0.00000 >> ORIGX2 0.000000 1.000000 0.000000 >> 0.00000 >> ORIGX3 0.000000 0.000000 1.000000 >> 0.00000 >> SCALE1 0.278087 0.160553 -0.000000 >> 0.00000 >> SCALE2 0.000000 0.321107 -0.000000 >> 0.00000 >> SCALE3 0.000000 0.000000 0.056850 >> 0.00000 >> HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00 >> 0.00 Mg2+ >> HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00 >> 0.00 Cl1- >> END >> >> ############ >> >> I'd like to see the unit cell displayed, as well as the atoms in the unit >> cell generated and displayed. >> Is this possible using jmol? >> >> Thx., >> H. >> >> >> ------------------------------------------------------------------------------ >> 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 >> Jmo...@li... >> 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 > > > ------------------------------------------------------------------------------ > 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > 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 > Jmo...@li... > 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 |
From: Robert H. <ha...@st...> - 2011-11-30 04:09:54
|
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 On Tue, Nov 29, 2011 at 9:49 PM, Robert Hanson <ha...@st...> wrote: > Oh, I guess I did not actually try it with your file. I didn't realize it > was a complete model! > > Ah, that's a problem! Well, I can tell you why that is. Jmol presumes that > a PDB file is a protein and saves hugely on processing by assuming that > there are no special positions. Therefore it does not check to see if atoms > are on top of each other after symmetry transformations. But in your case > this isn't really a PDB file, it's an inorganic crystal file. > > You sure you don't want to use CIF format -- like everyone else ;) ? > > I have an idea, though. Let me think about this.... > > Bob > > > > > On Tue, Nov 29, 2011 at 4:59 PM, Hans Horn <ha...@2h...> wrote: > >> Robert, >> >> neat! >> >> when I do that with the pdb file posted, I see 10 atoms in the unit cell. >> However, when I write it out (e.g. as xyz) I get 72 atoms. >> Why's that? >> >> Is there a way to save the unit cell as 3*3 matrix? >> >> thx, >> H. >> On 11/29/2011 1:45 PM, Robert Hanson wrote: >> >> sure. >> >> load xxx.pdb {1 1 1} >> >> gives you a full unit cell. >> >> unitcell on >> >> gets you the unit cell >> >> axes on >> >> gets you a,b,c axes for the unit cell. >> >> >> >> On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn <ha...@2h...> wrote: >> >>> Folks, >>> >>> I have a pdb file : >>> >>> ############# >>> HEADER >>> 09-NOV-11 >>> TITLE Structure >>> 1 >>> REVDAT 1 09-NOV-11 >>> 0 >>> REMARK >>> 4 >>> REMARK 4 COMPLIES WITH FORMAT V. 2.1, >>> 25-OCT-1996 >>> HET UNK A 1 >>> 2 >>> FORMUL 1 UNK Mg3 >>> Cl6 >>> CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 m >>> -1 >>> ORIGX1 1.000000 0.000000 0.000000 >>> 0.00000 >>> ORIGX2 0.000000 1.000000 0.000000 >>> 0.00000 >>> ORIGX3 0.000000 0.000000 1.000000 >>> 0.00000 >>> SCALE1 0.278087 0.160553 -0.000000 >>> 0.00000 >>> SCALE2 0.000000 0.321107 -0.000000 >>> 0.00000 >>> SCALE3 0.000000 0.000000 0.056850 >>> 0.00000 >>> HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00 >>> 0.00 Mg2+ >>> HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00 >>> 0.00 Cl1- >>> END >>> >>> ############ >>> >>> I'd like to see the unit cell displayed, as well as the atoms in the >>> unit cell generated and displayed. >>> Is this possible using jmol? >>> >>> Thx., >>> H. >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> Jmo...@li... >>> 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 >> >> >> ------------------------------------------------------------------------------ >> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> Jmo...@li... >> 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 |
From: Hans H. <ha...@2h...> - 2011-11-30 17:35:36
|
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 |