Re: [Jmol-users] Pass Jmol start/end residue #'s as well as PDB/Chain ID's

[Angel H. <ang...@ua...>]

(I'm bringing into this list the discussion started in the SF feature 
request site as this is more flexible. Although quite verbose, it may 
be of help to other users)


> >Comment By: David  Halitsky (davidhalitsky)
> 
> Hi Angel - 
> 
> Thanks again for replying so promptly.
> 
> I think I should have made the context clearer: input parameters on the
> applet "command line".
> As per discussion in this thread at SAP:
> https://forums.sdn.sap.com/thread.jspa?threadID=972132&tstart=0

Sorry, the discussion there is quite confusing to me, with all the 
jargon about portals and so on. I tried to find specific Jmol-related 
comments there and I couldn't.


> here's what we want to do:
> 
> 1) we're in Frame1 of a portal that has two other frames in it: FrameA and
> FrameB.
> 
> 2) A query in Frame1 against a certain database brings back two sets of
> specifications for Jmol, say:
> 
> a 1hru, A, 123-145
> b) 2eqa, A, 144-167
> 
> 3) Via "client-side eventing" at the portal level , the portal passes the
> parameters in (a) to JMol and Jmol runs in FrameA to display the "partial"
> structure view requested (with rotate capability, same as in interactive
> JMol;
> 
> 4) At the same time , the portal passes the parameters in (b) to JMol and
> Jmol runs in FrameB to display the "partial" structure view requested (with
> rotate capability, same as in interactive JMol;
> 
> Is this scenario currently possible as JMol is currently written?

As long as you have already set the means to communicate with the 
Jmol applets in your portal system, I think it is indeed.

This is what I'd pass to Jmol in FrameA:
	load "1hru.pdb"; display *:A and 123-145;
and this to jmol in FrameB:
	load "2eqa.pdb"; display *:A and 144-167;

(you will have to adjust the loading of the pdb file depending on 
where it is located)

"display" is a better choice than the alternative, "restrict", for 
reason I won't discuss now (but we can separately, if you need it)


Depending on your ways of inserting Jmol into your frames, there may 
be some details to solve, but on the Jmol scripting side that's all 
needed.


> Or would I have to settle for the portal simply invoking Jmol in FrameB
> and again in FrameC and letting the user manipulate settings in the
> console, as you suggest.

No, I won't suggest so, you can indeed preprogram what you want.


> Thanks very much again for your time.

A pleasure to help.

> ----------------------------------------------------------------------
> 
> Comment By: Angel Herraez (aherraez)
> Date: 2008-07-23 11:44
> 
> Message:
> Logged In: YES 
> user_id=1065324
> Originator: NO
> 
> Hi again
> 
> I thought that your would be programming the selection in the page. Users
> will also be able to do those as long as they can and know how to use the
> console. All my comments will apply based on that assumption.
> 
>    select 12-14,45-60,123-165
> is something that you can already do
> 
>    select 12-14(A), 45-60(B), 123-165(B)
> is not possible as such, only if converted to
>    select 12-14 and *:A, 45-60 and *:B, 123-165 and *:B
> which, by the way, is the same as RasMol syntax, except that maybe the
> comma is not allowed in RasMol and you need to use "or". 
> 
> 
> 
> ----------------------------------------------------------------------
> 
> Comment By: David  Halitsky (davidhalitsky)
> Date: 2008-07-23 11:23
> 
> Message:
> Logged In: YES 
> user_id=2156323
> Originator: YES
> 
> Hello aherraez - 
> 
> Thanks for taking the time to respond.  
> 
> As I mentioned in the request, Rolf Huehne of Jena thought that users
> couldn't currently select residues.  If users currently can select residues
> the way you indicate, that's great.  (I guess I should have looked at the
> documentation first, before making the feature request.  )
> 
> But as long as the feature request is open, it would be very nice to have
> a standard "list" version of this parameter, e.g. instead of just 123-145,
> you could have:
> 
> 12-14,45-60,123-165
> 
> and also a version of this that crosses chains, e.g.
> 
> 12-14(A), 45-60(B), 123-165(B)
> 
> 
> Reason why this would be nice is that in certain cases documented at
> StrucClues (http://strucclue.ornl.gov), non-contiguous areas of a chain are
> of interest, and also non-contiguous areas across chains.  (I mean
> non-contiguous in the primary structure sequence, of course.)
> 
>  .  I won't be offended.
> 
> ----------------------------------------------------------------------
> 
> Comment By: Angel Herraez (aherraez)
> Date: 2008-07-23 11:10
> 
> Message:
> Logged In: YES 
> user_id=1065324
> Originator: NO
> 
> David, I'm not sure if I understand fully your request.
> If you could specify waht your input parameters are, if would help.
> For example, if you want to select residues 123 to 145 of chain B, you do
>    select 123-145 and *:B
> that's all there is to it. What else do you need?
> 
> 
> 
> ----------------------------------------------------------------------