Alexander - I've checked in your patch with adjustments that make it more
efficient. Let me know if I missed something important. By the way, this is
the ONE part of the code that still exists where the underlying shape is
changed during rendering. If I can do it, I'll get that changed.
Bob
On Sun, Oct 7, 2012 at 1:07 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> nice. A few comments:
>
> you can just use
>
> monomers[i].getProteinStructure() == monomers[iNext].getProteinStructure()
>
> instead of all these:
>
> ( (isHelix(i) && isHelix(iNext)) || (isSheet(i) && isSheet(iNext)) ||
> (isTurn(i) && isTurn(iNext)) )
>
> and it's a bit more accurate, since your definition of "isTurn" as (not
> Helix and not Sheet) is not quite correct.
>
> Why the removal of the eccentricity/variable radius business?
>
> Bob
>
>
> On Sat, Oct 6, 2012 at 4:49 PM, Alexander Rose <
> alexander.r...@weirdbyte.de> wrote:
>
>> Hi,
>>
>> better images...
>>
>> https://www.dropbox.com/s/o5vdr88ebwqqf6o/1CRN_seams.jpg
>> https://www.dropbox.com/s/vcqxh6w0fh9ik7s/1CRN_noSeams.jpg
>>
>> Am 06.10.2012 um 23:44 schrieb Alexander Rose:
>>
>> Hi,
>>
>> I created an initial patch that aims to fix the seams between cartoon
>> mesh elements of consecutive residues. Attached are two images to
>> illustrate the seams. The seams occur because the (lighting) vertex normals
>> are calculated for each cartoon mesh elements individually without
>> considering the adjacent elements. The patch includes a helper function
>> that smoothes the vertex normals for the overlapping vertices two
>> consecutive cartoon meshes. I also needed to slightly change the way by
>> which the mesh of turn/loop elements is created so that the start/end
>> vertices of two turn/loop elements always overlap.
>>
>> The patch is against revision 17624.
>>
>> There are problems. I adjust the normals between two consecutive elements
>> when constructing the second element's mesh, so the first element's mesh
>> has been already created (needed to adjust the normals) and also once
>> rendered/drawn. Therefor to see the adjusted normals the meshes need to be
>> rendered/drawn again. Just interacting with Jmol, e.g. zooming, naturally
>> triggers a redraw. However its not nice initially. An idea. I could trigger
>> a redraw in Jmol after cartoon mesh constructions. How? Or do you have
>> other suggestions?
>>
>> Also I need to carefully check if the code works also when individual
>> residues are (randomly) displayed/hidden one after the other.
>>
>> Please let me know what you think!
>>
>> Best
>> Alexander
>>
>>
>> <patch_seams_r17624.txt>
>>
>> <1CRN_seams.jpeg><1CRN_noSeams.jpeg>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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