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 <[email protected]> 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 <
> [email protected]> 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
>> [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
>
> --0015174c11fce476a9048c8c0d5a
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
>
> Otello,<br><br>You can do that. <br><br>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. <br>
> <br>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.<br>
> <br>But you can "fake" that if you want. What you would do is cre=
> ate a SLAB based on an elongated unit cell:<br><br>=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 <br>
> <br>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.<br>
> <br>Bob<br><br><br><br><div class=3D"gmail_quote">On Thu, Jul 29, 2010 at 1=
> 0:29 AM, Otello Maria Roscioni <span dir=3D"ltr"><<a href=3D"mailto:rosc=
> [email protected]">[email protected]</a>></span> wrote:<br><bl=
> 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,<br>
> <br>
> is there a way to display isosurfaces (say, solvent accessible surface) of<=
> br>
> slabs considering periodic boundary conditions? It should be done by<br>
> computing the isosurface for the top and bottom faces of the slab,<br>
> ignoring the sides.<br>
> <br>
> Hope I made my request clear!<br>
> <br>
> Thank you very much for any advice I will receive.<br>
> Otello.<br>
> <br>
> ---------------------------------------------------------------------------=
> ---<br>
> The Palm PDK Hot Apps Program offers developers who use the<br>
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share<br>
> of $1 Million in cash or HP Products. Visit us here for more details:<br>
> <a href=3D"http://p.sf.net/sfu/dev2dev-palm"; target=3D"_blank">http://p.sf.=
> net/sfu/dev2dev-palm</a><br>
> _______________________________________________<br>
> Jmol-users mailing list<br>
> <a href=3D"mailto:[email protected]";>[email protected]=
> forge.net</a><br>
> <a href=3D"https://lists.sourceforge.net/lists/listinfo/jmol-users"; target=
> =3D"_blank">https://lists.sourceforge.net/lists/listinfo/jmol-users</a><br>
> </blockquote></div><br><br clear=3D"all"><br>-- <br>Robert M. Hanson<br>Pro=
> fessor of Chemistry<br>St. Olaf College<br>1520 St. Olaf Ave.<br>Northfield=
> , MN 55057<br><a href=3D"http://www.stolaf.edu/people/hansonr";>http://www.s=
> tolaf.edu/people/hansonr</a><br>
> phone: 507-786-3107<br><br><br>If nature does not answer first what we want=
> ,<br>it is better to take what answer we get. <br><br>-- Josiah Willard Gib=
> bs, Lecture XXX, Monday, February 5, 1900<br>
>
> --0015174c11fce476a9048c8c0d5a--
>
>
--
------------------------------------------------------------------------------
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
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