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## Re: [Jmol-users] periodic boundary conditions and slabs

 Re: [Jmol-users] periodic boundary conditions and slabs From: Robert Hanson - 2010-07-31 13:13:06 Attachments: Message as HTML ```Otello, It will be fine. Just make sure you have loaded all 9 unit cells around the area you wish to see. That way you will have it. If the data is n{ot a CIF file or does not have unit cell data, that's no problem. Basically what you do is define the unit cell and symmetry (if desired) on the LOAD line after the file name, and Jmol will load the file as though it had that unit cell and symmetry. This is one of the very coolest features of Jmol and should be perfect for this if you need it. load "myfile" {3 3 1} unitcell {6.00 6.00 6.00 90 90 120} or maybe load "myfile" {445 665 1} unitcell {6.00 6.00 6.00 90 90 120} (which centers the unit cell in the set of 9) Ah, except perhaps that is not set up for slab yet.... Oh, I know. Just make that c parameter very large. Jmol will keep your coordinates in Cartesian format despite what you put in for the unit cell. Then, if you need to, you can move the unit cell into the structure using, for example: unitcell {6.0 6.0 0} or unitcell {2 2 1/} You may have to experiment, and if it doesn't work for you, let me know. I think you will find everything there for what you need. Jmol has extensive capability in exactly this area. Be sure to use isosurface LATTICE because that will save you hugely on memory. Bob On Sat, Jul 31, 2010 at 6:13 AM, Otello Maria Roscioni < roscioni@...> wrote: > Dear Bob, > > thank you for the useful suggestions. Using the command: > > isosurface ID "iso1" slab within [{0 0 -1000}, {0 0 2000}, {0 57.108 0}, > {57.108 0 0}] sasurface lattice {2 2 1} > > the isosurface looks much more correct. However, it is not computed > properly at the bounday of the unit cell, as you can see here: > > http://img696.imageshack.us/img696/9476/f1288.png > > I suppose the problem is that the probe used to compute the isosurface > does not consider periodic images for atoms at the unit cell boundaries. > Anyway, I can show just the unit cell and pretend that the corresponding > isosurface is correct ;) > no error there -- I think you just didn't have a full set of 9 unit cells. > > By the way, there is a small bug in the SLAB PLANE (or more likely in > WRITE IDTF) command: when exporting the scene in IDTF format, the > resulting object contains the whole system and not the sliced plane. > > Ah, that's interesting. Thanks. -- 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 ```

 [Jmol-users] periodic boundary conditions and slabs From: Otello Maria Roscioni - 2010-07-29 15:29:29 ```Dear Jmol users, is there a way to display isosurfaces (say, solvent accessible surface) of slabs considering periodic boundary conditions? It should be done by computing the isosurface for the top and bottom faces of the slab, ignoring the sides. Hope I made my request clear! Thank you very much for any advice I will receive. Otello. ```
 Re: [Jmol-users] periodic boundary conditions and slabs From: Robert Hanson - 2010-07-29 19:51:10 Attachments: Message as HTML ```Otello, You can do that. Jmol 12.0 includes the option LATTICE {i j k} for the isosurface command. You might want to take a look at that. In combination with isosurface SLAB UNITCELL, this works great. You basically just create the isosurface for one unit cell with SLAB -- and then use the LATTICE option to multiply it as many times as you want. Ah, now I did just fix a bug I see there. I never implemented that option for slab- and polymer-based unit cells. I think there's only one file reader -- Crystal (i.e. Crystal09) -- that can generate models with slab or polymer symmetry. So unless that's what you are using, it doesn't matter anyway. But you can "fake" that if you want. What you would do is create a SLAB based on an elongated unit cell: isosurface ID "isosurface1" slab within [{0 0 -1000}, {0 0 2000.0}, {0.0 2.9769197 0.0}, {2.9769197 0.0 0.0}] vanderWaals; That WITHIN array is [center c b a]. I don't know how I got that c b a instead of a b c, but I did. That may not even be documented, but it's what Jmol creates for it's state when you use "isosurface SLAB UNITCELL...". My point is just that you can put whatever numbers in there you want. By moving the center down in Z and making c twice that distance, we get that slabbing effect you are talking about -- slabbing along the crystallographic a and b axes and no slabbing along c. Bob On Thu, Jul 29, 2010 at 10:29 AM, Otello Maria Roscioni < roscioni@...> wrote: > Dear Jmol users, > > is there a way to display isosurfaces (say, solvent accessible surface) of > slabs considering periodic boundary conditions? It should be done by > computing the isosurface for the top and bottom faces of the slab, > ignoring the sides. > > Hope I made my request clear! > > Thank you very much for any advice I will receive. > Otello. > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of \$1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > 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 ```
 Re: [Jmol-users] periodic boundary conditions and slabs From: Otello Maria Roscioni - 2010-07-31 11:13:11 ```Dear Bob, thank you for the useful suggestions. Using the command: isosurface ID "iso1" slab within [{0 0 -1000}, {0 0 2000}, {0 57.108 0}, {57.108 0 0}] sasurface lattice {2 2 1} the isosurface looks much more correct. However, it is not computed properly at the bounday of the unit cell, as you can see here: http://img696.imageshack.us/img696/9476/f1288.png I suppose the problem is that the probe used to compute the isosurface does not consider periodic images for atoms at the unit cell boundaries. Anyway, I can show just the unit cell and pretend that the corresponding isosurface is correct ;) By the way, there is a small bug in the SLAB PLANE (or more likely in WRITE IDTF) command: when exporting the scene in IDTF format, the resulting object contains the whole system and not the sliced plane. Thank you for your help! Otello PS I am sorry for the late reply. On Thu, Jul 29, 2010, Robert Hanson ha scritto: > --0015174c11fce476a9048c8c0d5a > Content-Type: text/plain; charset=ISO-8859-1 > > Otello, > > You can do that. > > Jmol 12.0 includes the option LATTICE {i j k} for the isosurface command. > You might want to take a look at that. In combination with isosurface SLAB > UNITCELL, this works great. You basically just create the isosurface for one > unit cell with SLAB -- and then use the LATTICE option to multiply it as > many times as you want. > > Ah, now I did just fix a bug I see there. I never implemented that option > for slab- and polymer-based unit cells. I think there's only one file reader > -- Crystal (i.e. Crystal09) -- that can generate models with slab or polymer > symmetry. So unless that's what you are using, it doesn't matter anyway. > > But you can "fake" that if you want. What you would do is create a SLAB > based on an elongated unit cell: > > isosurface ID "isosurface1" slab within [{0 0 -1000}, {0 0 2000.0}, {0.0 > 2.9769197 0.0}, {2.9769197 0.0 0.0}] vanderWaals; > > That WITHIN array is [center c b a]. I don't know how I got that c b a > instead of a b c, but I did. That may not even be documented, but it's what > Jmol creates for it's state when you use "isosurface SLAB UNITCELL...". My > point is just that you can put whatever numbers in there you want. By moving > the center down in Z and making c twice that distance, we get that slabbing > effect you are talking about -- slabbing along the crystallographic a and b > axes and no slabbing along c. > > Bob > > > > On Thu, Jul 29, 2010 at 10:29 AM, Otello Maria Roscioni < > roscioni@...> wrote: > >> Dear Jmol users, >> >> is there a way to display isosurfaces (say, solvent accessible surface) of >> slabs considering periodic boundary conditions? It should be done by >> computing the isosurface for the top and bottom faces of the slab, >> ignoring the sides. >> >> Hope I made my request clear! >> >> Thank you very much for any advice I will receive. >> Otello. >> >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of \$1 Million in cash or HP Products. Visit us here for more details: >> http://p.sf.net/sfu/dev2dev-palm >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> 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 > > --0015174c11fce476a9048c8c0d5a > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Otello,

You can do that.

Jmol 12.0 includes the option LATTI= > CE {i j k} for the isosurface command. You might want to take a look at tha= > t. In combination with isosurface SLAB UNITCELL, this works great. You basi= > cally just create the isosurface for one unit cell with SLAB -- and then us= > e the LATTICE option to multiply it as many times as you want.
>
Ah, now I did just fix a bug I see there. I never implemented that opti= > on for slab- and polymer-based unit cells. I think there's only one fil= > e reader -- Crystal (i.e. Crystal09) -- that can generate models with slab = > or polymer symmetry. So unless that's what you are using, it doesn'= > t matter anyway.
>
But you can "fake" that if you want. What you would do is cre= > ate a SLAB based on an elongated unit cell:

=A0 isosurface ID "= > isosurface1" slab within [{0 0 -1000}, {0 0 2000.0}, {0.0 2.9769197 0.= > 0}, {2.9769197 0.0 0.0}] vanderWaals;=A0
>
That WITHIN array is [center c b a]. I don't know how I got that c = > b a instead of a b c, but I did. That may not even be documented, but it= > 9;s what Jmol creates for it's state when you use "isosurface SLAB= > UNITCELL...". My point is just that you can put whatever numbers in t= > here you want. By moving the center down in Z and making c twice that dista= > nce, we get that slabbing effect you are talking about -- slabbing along th= > e crystallographic a and b axes and no slabbing along c.
>
Bob

On Thu, Jul 29, 2010 at 1= > 0:29 AM, Otello Maria Roscioni < ioni@...">roscioni@...> wrote:
ockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, 204= > , 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> > Dear Jmol users,
>
> is there a way to display isosurfaces (say, solvent accessible surface) of<= > br> > slabs considering periodic boundary conditions? It should be done by
> computing the isosurface for the top and bottom faces of the slab,
> ignoring the sides.
>
> Hope I made my request clear!
>
> Otello.
>
> ---------------------------------------------------------------------------= > ---
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of \$1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.= > net/sfu/dev2dev-palm
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...= > forge.net
> =3D"_blank">https://lists.sourceforge.net/lists/listinfo/jmol-users
; >

--
Robert M. Hanson
Pro= > fessor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield= > , MN 55057
http://www.s= > tolaf.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 Gib= > bs, Lecture XXX, Monday, February 5, 1900
> > --0015174c11fce476a9048c8c0d5a-- > > -- ```
 Re: [Jmol-users] periodic boundary conditions and slabs From: Robert Hanson - 2010-07-31 13:13:06 Attachments: Message as HTML ```Otello, It will be fine. Just make sure you have loaded all 9 unit cells around the area you wish to see. That way you will have it. If the data is n{ot a CIF file or does not have unit cell data, that's no problem. Basically what you do is define the unit cell and symmetry (if desired) on the LOAD line after the file name, and Jmol will load the file as though it had that unit cell and symmetry. This is one of the very coolest features of Jmol and should be perfect for this if you need it. load "myfile" {3 3 1} unitcell {6.00 6.00 6.00 90 90 120} or maybe load "myfile" {445 665 1} unitcell {6.00 6.00 6.00 90 90 120} (which centers the unit cell in the set of 9) Ah, except perhaps that is not set up for slab yet.... Oh, I know. Just make that c parameter very large. Jmol will keep your coordinates in Cartesian format despite what you put in for the unit cell. Then, if you need to, you can move the unit cell into the structure using, for example: unitcell {6.0 6.0 0} or unitcell {2 2 1/} You may have to experiment, and if it doesn't work for you, let me know. I think you will find everything there for what you need. Jmol has extensive capability in exactly this area. Be sure to use isosurface LATTICE because that will save you hugely on memory. Bob On Sat, Jul 31, 2010 at 6:13 AM, Otello Maria Roscioni < roscioni@...> wrote: > Dear Bob, > > thank you for the useful suggestions. Using the command: > > isosurface ID "iso1" slab within [{0 0 -1000}, {0 0 2000}, {0 57.108 0}, > {57.108 0 0}] sasurface lattice {2 2 1} > > the isosurface looks much more correct. However, it is not computed > properly at the bounday of the unit cell, as you can see here: > > http://img696.imageshack.us/img696/9476/f1288.png > > I suppose the problem is that the probe used to compute the isosurface > does not consider periodic images for atoms at the unit cell boundaries. > Anyway, I can show just the unit cell and pretend that the corresponding > isosurface is correct ;) > no error there -- I think you just didn't have a full set of 9 unit cells. > > By the way, there is a small bug in the SLAB PLANE (or more likely in > WRITE IDTF) command: when exporting the scene in IDTF format, the > resulting object contains the whole system and not the sliced plane. > > Ah, that's interesting. Thanks. -- 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 ```