Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Miguel]

Chris wrote:
>>That is what we will do unless someone comes up with some good
>> objections.
>
> Excellent - have logged an RFE
> 
> to track the issue.

Thank you *very* much for filing the bug report.


Miguel



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[Jmol-users] Re: "set measurements ..." to update *all* labels

[Chris Pudney]

Excellent - have logged an RFE 
 
to track the issue.
Make that 


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[Jmol-users] Re: "set measurements ..." to update *all* labels

[Chris Pudney]

G'day,
So, to clarify "set measurements ..." will update the units on all
(existing and future) measurements except those existing measurements that
span atoms that are not selected.
Is that the new behaviour?  If so, that would be great.
 
Yes, I think that is correct.
 
That is what we will do unless someone comes up with some good objections.
Excellent - have logged an RFE 
 
to track the issue.

Thanks again,
Chris.
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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Miguel]

> So, to clarify "set measurements ..." will update the units on all
> (existing and future) measurements except those existing measurements that
> span atoms that are not selected.
>
> Is that the new behaviour?  If so, that would be great.

Yes, I think that is correct.

That is what we will do unless someone comes up with some good objections.



Miguel



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[Jmol-users] Re: "set measurements ..." to update *all* labels

[Chris Pudney]

G'day,
>> Perhaps both behaviours could be supported, say, something like
>>
>> set measurements ...   affects subsequent measurement labels
>> set measurements ALL ...   affects all measurement labels
>>
>> Not all users will want to use script to do this so an "update all"
>> checkbox in the "Measurements" menu could determines which of these
>> behaviours applies.
>
>Chris,
>
>I agree ... this should be changed so that measurement units get updated
>when when the "set measurements ..." command is given.
>
>Jan,
>
>I agree with your other message ... this change should only take effect if
>the atoms in the measurements are currently selected.
So, to clarify "set measurements ..." will update the units on all 
(existing and future) measurements except those existing measurements that 
span atoms that are not selected.

Is that the new behaviour?  If so, that would be great.
Thanks,
Chris.
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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Miguel]

>>  as a user, I would say no, because this would be less flexible and not
>>  consistent with the behavior of all the other property changing
>> commands.
>>  Regards, Jan
>>
>>  > Would it be possible to have the "set measurements ..." command
>> update
>>  > the units on *all* distance labels?
>
> Perhaps both behaviours could be supported, say, something like
>
> set measurements ...  affects subsequent measurement labels
> set measurements ALL ...  affects all measurement labels
>
> Not all users will want to use script to do this so an "update all"
> checkbox in the "Measurements" menu could determines which of these
> behaviours applies.
>
> How does that sound?

Chris,

I agree ... this should be changed so that measurement units get updated
when when the 'set measurements ...' command is given.

Jan,

I agree with your other message ... this change should only take effect if
the atoms in the measurments are currently selected.


Miguel



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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Miguel]

Hens wrote:

> To add to the confusion: we are talking about different things here.
> As I understood it, Chris was talking about changing the units during
> measurements, say from the default nm to angstroms, and then updating
> the values already being displayed.
> In one particular structure.

Thanks for clarifying this :-)

I apologize for giving Chris an answer without actually reading his question.

I will split the threads and reply separately.


Miguel



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[Jmol-users] Re: 'set measurements ...' to update *all* labels

[Hens Borkent]

Hi,
To add to the confusion: we are talking about different things here.
As I understood it, Chris was talking about changing the units during 
measurements, say from the default nm to angstroms, and then updating 
the values already being displayed.
In one particular structure.
[a problem I never encountered and I have no opinion on]
Then Miguel threw in an older question, about dynamically transfering a 
measurement from one model to the next, in an animation.
This is very useful in an (XYZ or CML) animation, characterized by 
models/frames with all the same atoms in the same order (and to be 
distinguished from multi-model PDB files which can be completely 
different molecules).
In the animations the "select" command is not involved: you do not 
select a new model, you simply go to the next frame (well, maybe Jmol 
does internally?).
So Jmol could do a check which multimodel system we have, and translate 
the measurements to all frames if appropriate.
As I see it now it could be done on the basis of the file type (XYZ/CML 
vs PDB), but that is only a first order approach that will run into 
ambiguities soon.
Or we separate the two completely and reserve different commands  for 
say  'frames' and 'models' .

Hens
> Would it be possible to have the "set measurements ..." command
update
> the units on *all* distance labels?

Perhaps both behaviours could be supported, say, something like
set measurements ...affects subsequent measurement labels
set measurements ALL ...affects all measurement labels
  

Several other people have asked for this, so you are not the only one.
I think that having a 'setting' to control the behavior would be OK.
We need to specify the behavior a bit more ...
Let's talk a little bit about what the criteria would be for deciding
whether or not the measurements get replicated.
Different frames/models are can be completely different. Sometimes they
all contain exactly the same atoms in exactly the same order ... only 
the
position changes. This is what happens in many animations.

 

why not linking the set measurements command to the current selected 
set, this was consistent and flexible.
select all
select /3
regards, Jan

From one frame to the next, we need to decide whether or not the
measurements could be replicated.
I suppose that we use one or more of the following:
- the two frames have the same number and types of atoms in exactly the
same order
- the atom numbers of the elements being measured are the same
- the atom numbers and types of the elements being measured are the same
Don't know ... does anyone have any other thoughts.
Miguel
 




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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Old Address]

Miguel wrote:
G'day,
   

as a user, I would say no, because this would be less flexible and not
consistent with the behavior of all the other property changing
commands.
Regards, Jan
> Would it be possible to have the "set measurements ..." command
update
> the units on *all* distance labels?
 

Perhaps both behaviours could be supported, say, something like
set measurements ...affects subsequent measurement labels
set measurements ALL ...affects all measurement labels
Not all users will want to use script to do this so an "update all"
checkbox in the "Measurements" menu could determines which of these
behaviours applies.
   

Chris,
Several other people have asked for this, so you are not the only one.
I think that having a 'setting' to control the behavior would be OK.
We need to specify the behavior a bit more ...
Let's talk a little bit about what the criteria would be for deciding
whether or not the measurements get replicated.
Different frames/models are can be completely different. Sometimes they
all contain exactly the same atoms in exactly the same order ... only the
position changes. This is what happens in many animations.
 

why not linking the set measurements command to the current selected 
set, this was consistent and flexible.
select all
select /3
regards, Jan

From one frame to the next, we need to decide whether or not the
measurements could be replicated.
I suppose that we use one or more of the following:
- the two frames have the same number and types of atoms in exactly the
same order
- the atom numbers of the elements being measured are the same
- the atom numbers and types of the elements being measured are the same
Don't know ... does anyone have any other thoughts.
Miguel
 



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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

[Miguel]

> G'day,
>
>>  as a user, I would say no, because this would be less flexible and not
>>  consistent with the behavior of all the other property changing
>> commands.
>>  Regards, Jan
>>
>>  > Would it be possible to have the "set measurements ..." command
>> update
>>  > the units on *all* distance labels?
>
> Perhaps both behaviours could be supported, say, something like
>
> set measurements ...  affects subsequent measurement labels
> set measurements ALL ...  affects all measurement labels
>
> Not all users will want to use script to do this so an "update all"
> checkbox in the "Measurements" menu could determines which of these
> behaviours applies.
>

Chris,

Several other people have asked for this, so you are not the only one.

I think that having a 'setting' to control the behavior would be OK.

We need to specify the behavior a bit more ...

Let's talk a little bit about what the criteria would be for deciding
whether or not the measurements get replicated.

Different frames/models are can be completely different. Sometimes they
all contain exactly the same atoms in exactly the same order ... only the
position changes. This is what happens in many animations.

>From one frame to the next, we need to decide whether or not the
measurements could be replicated.

I suppose that we use one or more of the following:

 - the two frames have the same number and types of atoms in exactly the
same order

 - the atom numbers of the elements being measured are the same

 - the atom numbers and types of the elements being measured are the same

Don't know ... does anyone have any other thoughts.


Miguel



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[Jmol-users] Re: "set measurements ..." to update *all* labels

[Chris Pudney]

G'day,
 as a user, I would say no, because this would be less flexible and not 
 consistent with the behavior of all the other property changing commands.
 Regards, Jan
 
 > Would it be possible to have the "set measurements ..." command update 
 > the units on *all* distance labels?
Perhaps both behaviours could be supported, say, something like
set measurements ...affects subsequent measurement labels
set measurements ALL ...affects all measurement labels
Not all users will want to use script to do this so an "update all" 
checkbox in the "Measurements" menu could determines which of these 
behaviours applies.

How does that sound?
Regards,
Chris.


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