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Re: [Jmol-users] How to save to JVXL both surface and structure
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From: Karl O. <obe...@me...> - 2010-08-20 14:53:09
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Bob,
I had missed the capability of writing a data file as a zip file (xxx.jmol). I suppose that after doing the compare command on two protein molecules that you could write a "xxx.jmol" file rather than a "xxx.pdb" file"? When I do this operation, I use 'load' and 'load append' putting the protein data in two different frames, but when the "xxx.pdb" file is written the data is present in one frame as two models. What is the structure of the data in the "xxx.jmol"?
Karl
Karl M. Oberholser, Ph.D. Phone:
Professor of Chemistry Voice: 717-766-0512
Chemistry & Biochemistry Dept. Fax: 717-691-6046
Messiah College e-mail: obe...@me...
P.O. Box 3049
One College Avenue
Grantham, Pa 17027
>>> Robert Hanson <ha...@st...> 08/19/10 12:39 PM >>>
(typo -- "jmol" extension is just a Jmol equivalent of "zip" the way "jar"
is for Java)
On Thu, Aug 19, 2010 at 11:37 AM, Robert Hanson <ha...@st...> wrote:
> In case that was too cryptic.
>
> 0) get the picture you want.
> 1) create the jvxl file: write "xxx.jvxl"
> 2) replace the surface with the jvxl equivalent: isosurface "xxx.jvxl"
> 3) create a manifested zip file: write "xxx.jmol"
>
> Then when you load xxx.jmol, Jmol should load the file, load the surface,
> and display it all exactly the way you had it. If it doesn't, let me know.
>
> Bob
>
>
>
> On Thu, Aug 19, 2010 at 11:30 AM, Robert Hanson <ha...@st...>wrote:
>
>> write xxx.zip
>>
>>
>>
>>
>> On Mon, Aug 16, 2010 at 4:44 AM, <jai...@we...> wrote:
>>
>>> Dear Jmol,
>>>
>>> Is there a way to save Jmol state with the pre-calculated surface?
>>>
>>> We can save the Jmol state, and render the structure with the same
>>> look, orientation, etc. However, if the state contains a surface
>>> calculation, the surface is recalculated again on load.
>>>
>>> On the other side, I can save to .jvxl the surface alone ...
>>>
>>> Can we combine both?
>>> Or the option is to reload state and then load jvxl?
>>>
>>> Thanks,
>>> Jaim
>>> --
>>> Dr Jaime Prilusky | Jai...@we...
>>> Head Bioinformatics |
>>> R&D Bioinformatics and Data Management |
>>> Department of Biological Services |
>>> Weizmann Institute of Science | fax: 972-8-9344113
>>> 76100 Rehovot - Israel | tel: 972-8-9344959
>>>
>>> OCA, http://oca.weizmann.ac.il (the protein structure/function
>>> database)
>>> Proteopedia, http://proteopedia.org (because life has more than 2D)
>>> ------------------------------------------------------------------------
>>>
>>>
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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
>>
>
>
>
> --
> 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
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