Nico, I'm ready to release 11.1.41. It has important fixes for Pat
Carroll and Frieda Reichsman.
Pat, if you could test out the symops, that would be great.
Frieda, 11.1.41 gets around the load append problem as follows:
1) Load append does clear out any secondary-structure rendering that
might have been in place. Partially this is because adding atoms might
change groups. Partly this is because I couldn't figure out how to do
that right (yet). This "feature" should not be considered final, though,
and in the future it would certainly be nice to have that all remain.
So, in the mean time, I've introduced a couple of new options:
save structure
Saves the state of all the secondary-structure renderings (cartoons,
traces, etc.) in the form of a "state" -- but without all the other
business, such as file loading, labels, etc. What took me all night to
get right was the fact that it also saves the detailed list of what
groups are what type -- helix, sheet, turn, or none. It looks something
like this:
select ({0:326});
Cartoon 0.3;
select ({245:252});
color Cartoon opaque [xfff000];
select ({39:46});
color Cartoon opaque [x0080ff];
select ({193:211});
color Cartoon opaque [xa0ff00];
select ({237:244});
...
color Cartoon opaque [xffa000];
structure sheet ({0:25}) # model=1 & (1 - 4);
structure none ({26:38}) # model=1 & (5 - 6);
structure helix ({39:141}) # model=1 & (7 - 19);
structure none ({142:159}) # model=1 & (20 - 22);
structure helix ({160:218}) # model=1 & (23 - 30);
structure none ({219:222}) # model=1 & (31 - 31);
structure sheet ({223:252}) # model=1 & (32 - 35);
structure none ({253:281}) # model=1 & (36 - 40);
structure turn ({282:312}) # model=1 & (41 - 44);
structure none ({313:326}) # model=1 & (45 - 46);
restore structure
This just runs the saved script. It should create the exact rendering of
cartoons and such when executed after the load append is finished. And
it should recreate helixes exactly where they were before. What took so
long was the problem that Jmol was doing a calculation after the load
append, but reading the secondary structure data from the file the first
time. If there was any mismatch, then the cartoon sizes were off.
This needs testing; I'm hoping you will give it a work out, Frieda. What
you want to do is:
...
save structure
load append ....
restore structure
and see if it works.
That structure command is new, and I don't think it's perfect yet. But
used in this way -- all the way down the line from first atom to last --
it seems to work fine. If you started playing with that, though, with
things like:
structure helix (1-3,5,8-10)
I don't know... Might work, or might not. In any case, it is kind of
interesting that now a user can set the secondary structure at will and
doesn't have to depend upon either the file contents or Jmol's
algorithm. So it might be of use to some people.
Thanks, Frieda, for spotting this problem. This might be about as good
as we can do. I'd have to think more about it and test it more before I
would suggest that it be automatic for a load append, but that would be
another possibility.
Bob
Frieda Reichsman wrote:
>
> On May 17, 2007, at May 17, 5:48 AM, Bob Hanson wrote:
>
>> 11.1.41 will have a fix; but yes, it is true, load append deletes all
>> secondary structure in the original file. It's possible that some day
>> someone will figure out a way around that, but for now that is the case.
>>
>
> OK.
>
> Just want to add that as could be expected, removing the secondary
> structures from the second file leaves those of the first intact.
>
> I'm not clear on the fix in 11.41. Does it re-calculate the structures
> after they are deleted?
>
> Frieda
>
>
>> Bob
>>
>>
>> Frieda Reichsman wrote:
>>
>>> Jmol 11.1.40 and I'm pretty sure 11.1.38_dev
>>> the command
>>> load append
>>> seems to negate the calculated secondary structure of the originally
>>> loaded file.
>>>
>>> Scripts on the way, Bob.
>>>
>>> Frieda
>>>
>>>
>>> ///////////////////////////////////////////
>>>
>>>
>>> Frieda Reichsman
>>>
>>> Molecules in Motion
>>>
>>> Interactive Molecular Structures
>>>
>>> http://www.moleculesinmotion.com
>>>
>>>
>>> ///////////////////////////////////////////
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> -------------------------------------------------------------------------
>>> This SF.net email is sponsored by DB2 Express
>>> Download DB2 Express C - the FREE version of DB2 express and take
>>> control of your XML. No limits. Just data. Click to get it now.
>>> http://sourceforge.net/powerbar/db2/
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> <mailto:[email protected]>
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by DB2 Express
>> Download DB2 Express C - the FREE version of DB2 express and take
>> control of your XML. No limits. Just data. Click to get it now.
>> http://sourceforge.net/powerbar/db2/
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> <mailto:[email protected]>
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> ///////////////////////////////////////////
>
>
> Frieda Reichsman
>
> Molecules in Motion
>
> Interactive Molecular Structures
>
> http://www.moleculesinmotion.com
>
>
> ///////////////////////////////////////////
>
>
>
>------------------------------------------------------------------------
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by DB2 Express
>Download DB2 Express C - the FREE version of DB2 express and take
>control of your XML. No limits. Just data. Click to get it now.
>http://sourceforge.net/powerbar/db2/
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Jmol-users mailing list
>[email protected]
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
