My answer depends on your answer to this question:
In the end, will you want the user to be able to manipulate the protein in
any desired way, orienting it any way they desire in relation to the
surface?
Bob
On Fri, Jun 24, 2011 at 3:45 AM, Martin Hediger <[email protected]> wrote:
> **
> Thanks for the feedback Bob and Angel.
> I think I can define my problem more precise now. I added another figure to
> my blog which hopefully makes it clear what I am trying to obtain. Right
> now, I only want to make it possible for the user to figure out which side
> of the bounding box is oriented towards the wire surface.
> Here is the link to the latest post.
> http://qmviews.blogspot.com/2011/06/jmol-003-arranging-protein-on-nw.html
>
> So my question is how to add these arrows that I added to the figure and
> set it up so the rotate together with the protein
> ? Maybe I could generate separate objects within the Jmol script?
>
> Thanks again for the support here on the mailing list.
>
>
>
>
>
>
>
>
> On 23.06.11 19:25, Robert Hanson wrote:
>
> ps -- I thought you were just going to let the user manually rotate and
> translate the surface. If you do that, you don't have to worry about using
> rotateSelected. Jmol will do that for you. For that, all you need is:
>
>
> set allowrotateselected
> set picking dragSelected
> select protein
>
> then instruct the user to pick an atom on the protein and LEFT-drag to move
> the protein or ALT-LEFT-drag to rotate it.
>
> With Jmol 12.1 you can catch that motion using
>
> set atomMovedCallback "jmolScript:someFunctionNameHere()"
>
> and do whatever you want at that point in the Jmol function
>
> function someFunctionNameHere() {
> set echo top left
> echo @{"the distance is now " + distance({protein},{surface}) }
>
> }
>
> actually, now that I think of that, if all you want is an echo, you can
> even do just this:
>
>
> set allowrotateselected
> set picking dragSelected
> select protein
> set echo top left
> echo @{"the distance is now " + distance({protein},{surface}) }
>
>
> because @{} in an echo forces it to be updated upon every screen write.
>
>
>
>
>
> Bob
>
> On Thu, Jun 23, 2011 at 11:59 AM, Robert Hanson <[email protected]>wrote:
>
>> distance from center of protein to surface is just:
>>
>>
>> x = distance({protein}.xyz , {surface}.xyz)
>>
>> where "protein" and "surface" are appropriate defined.
>>
>> I don't know why you would want to rotate the boundbox. Do you really need
>> that at all?
>>
>> Rotating the protein 90 degrees about the x axis (of the stationary
>> surface), for example, would be:
>>
>> select protein
>> rotateSelected internal {protein} x 90
>>
>>
>> If you want to rotate about the axes defined by the protein, then that's a
>> bit trickier and will require some quaternions.
>>
>> Bob
>>
>>
>>
>> On Thu, Jun 23, 2011 at 11:08 AM, Martin Hediger <[email protected]>wrote:
>>
>>> Dear List
>>> I have posted a picture of the system I obtained onto my blog:
>>>
>>> http://qmviews.blogspot.com/2011/06/jmol-002-control-over-two-structures.html
>>>
>>> A protein structure is placed above a surface of atoms, this is on a
>>> website that is in development.
>>> How can I have a boundbox only around the protein?
>>> Also, assuming the protein/box could only be rotated by 90° around x,y,z
>>> (with some button), I guess I require to introduce a second coordinate
>>> system only for the box, so I know which face of the protein is oriented
>>> towards the surface (this would then be entered into the interface for
>>> further processing). How would I do this?
>>>
>>> The whole purpose of this is to find the distance of the center of
>>> bounding box from the surface, which of course is half the side length. The
>>> question is how to figure out which side length to consider.
>>>
>>> Any hints are greatly appreciated.
>>>
>>> Martin
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 15.06.11 15:32, Robert Hanson wrote:
>>>
>>> Depends how you define "surface." If you mean "some other group of atoms"
>>> then you can easily compute that at any time and even display it real time.
>>> If you mean "isosurface" that, too, might be able to be done, but I might
>>> have to add something to make that work.
>>>
>>>
>>> By "rotatable" I presume you mean independently of that surface. That's
>>> not a problem, and translation is part of it. You just use:
>>>
>>> select protein
>>> set allowRotateSelected TRUE
>>> set dragSelected TRUE
>>>
>>> Now you can use ALT-SHIFT-LEFT and ALT-LEFT to translate and rotate the
>>> protein relative to the underlying surface atoms.
>>>
>>> Now, say you want to update something as that happens. You will need to
>>> use the latest development version of Jmol, because what I describe next is
>>> not in Jmol 12.0. We have a callback called "atomMovedCallback" that can
>>> send a message either to Jmol or to your page JavaScript to do something. In
>>> this case it would report the distance of "atomX" to the nearest atom of
>>> "surfaceAtoms" where you have already defined them as, perhaps:
>>>
>>> atomX = {22.ca} # CA for residue 22
>>> surfaceAtoms = {not protein}
>>> select protein
>>> set echo top left
>>> set atomMovedCallback "jmolScript:checkDistance"
>>>
>>>
>>> function checkDistance() {
>>> Var dmin = 1e10
>>> for (Var x in {surfaceAtoms}) {
>>> Var d = x.distance(atomX)
>>> if (d < dmin) { dmin = d }
>>> }
>>> Var s = format("%3.1f Angstroms", dmin)
>>> echo @s
>>> }
>>>
>>>
>>> Something like that!
>>>
>>> Bob Hanson
>>>
>>> On Wed, Jun 15, 2011 at 7:13 AM, Martin Hediger <[email protected]>wrote:
>>>
>>>> Dear Jmol Users, I'm new to the Jmol list, I'm looking forward to a nice
>>>> community interaction.
>>>>
>>>> I would like to implement the following on a website:
>>>> A protein structure should be displayed and it should be rotatable by
>>>> the user. At the same time, the distance between a given point in the
>>>> structure (e.g. a residue alpha-C atom) and a surface "below" the
>>>> structure should be computable (once the structure is oriented the way
>>>> it should be. The background is that we want to model a binding event of
>>>> a protein on a nanowire surface, so the orientation of the molecule is
>>>> critical.
>>>>
>>>> How could I achieve this?
>>>>
>>>> Kind regards and thank you for answers.
>>>> Martin
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> EditLive Enterprise is the world's most technically advanced content
>>>> authoring tool. Experience the power of Track Changes, Inline Image
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>>>> [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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> EditLive Enterprise is the world's most technically advanced content
>>> authoring tool. Experience the power of Track Changes, Inline Image
>>> Editing and ensure content is compliant with Accessibility
>>> Checking.http://p.sf.net/sfu/ephox-dev2dev
>>>
>>>
>>> _______________________________________________
>>> Jmol-users mailing
>>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
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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
>
>
> ------------------------------------------------------------------------------
> Simplify data backup and recovery for your virtual environment with vRanger.
> Installation's a snap, and flexible recovery options mean your data is safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download
> today.http://p.sf.net/sfu/quest-sfdev2dev
>
>
> _______________________________________________
> Jmol-users mailing
> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
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> _______________________________________________
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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
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threats, fraudulent activity and more. Splunk takes this data and makes
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