[Jmol-developers] [ jmol-Feature Requests-2025831 ] Pass Jmol start/end residue #'s as well as PDB/Chain ID's

[SourceForge.net <no...@so...>]

Feature Requests item #2025831, was opened at 2008-07-23 16:53
Message generated for change (Comment added) made by aherraez
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2025831&group_id=23629

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Interface Improvements
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: David  Halitsky (davidhalitsky)
Assigned to: Nobody/Anonymous (nobody)
Summary: Pass Jmol start/end residue #'s as well as PDB/Chain ID's

Initial Comment:
I am working with a few members of the SAP community:

https://forums.sdn.sap.com/thread.jspa?threadID=972132&tstart=0

to automate production of the "cases":

http://strucclue.ornl.gov/cases/index.html

accumulating here:

http://strucclue.ornl.gov

As you can see from examining any "case" in the case library, a critical piece of each case is currently provided by presenting two RasMol snaphots of partial PDB structures, i.e. structures delimited by a PDB ID, chain ID, start residue number, and end residue number.

Rolf Huehne of JenaLib has told me that Jmol doesn't currently support start/end residue numbers as input parameters, and he suggested that I make it a "feature request" here.

Thanks for any time you can afford to spend considering this matter.



----------------------------------------------------------------------

Comment By: Angel Herraez (aherraez)
Date: 2008-07-23 18:20

Message:
Logged In: YES 
user_id=1065324
Originator: NO

Let's move this to the jmol-users list. 
Discussion will be more manageable.


----------------------------------------------------------------------

Comment By: David  Halitsky (davidhalitsky)
Date: 2008-07-23 18:11

Message:
Logged In: YES 
user_id=2156323
Originator: YES

Sorry!  In my last comment, I meant Frame1, not FrameA in item (2).  Item
(2) should have read:

2) A query in Frame1 against a certain database brings back two sets of
specifications for Jmol, say:


----------------------------------------------------------------------

Comment By: David  Halitsky (davidhalitsky)
Date: 2008-07-23 18:09

Message:
Logged In: YES 
user_id=2156323
Originator: YES

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

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 FrameA 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?

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.

Thanks very much again for your time.

Best regards.
djh



----------------------------------------------------------------------

Comment By: Angel Herraez (aherraez)
Date: 2008-07-23 17:44

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 17:23

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 17:10

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?



----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2025831&group_id=23629