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View Full Version : Ball, stick, and ribbon molecule models?



Nangleator
08-08-2016, 09:38 AM
I've had some success using the .PDB importer plugin, but for more complex molecules, you'll often see not just the ball-and-stick representations, but also ribbons. The .PDB importer doesn't seem to create those.

Is there some plugin or app for decoding those from common downloadable molecule model formats?

Thanks.

prometheus
08-08-2016, 12:35 PM
image sample of ribbons please?

Nangleator
08-08-2016, 12:42 PM
Here's (https://www.researchgate.net/profile/Leila_Mahdavian/publication/266595678/figure/fig2/AS:[email protected]/Figure-2-Structure-of-Troponin-C-in-muscle-contraction-a-View-Ribbon-Crystal-structure.png) an example. I believe it's short hand for complex molecules, proteins, etc.

lertola2
08-08-2016, 01:06 PM
I have had good success using the work flow described in post 19 of this thread: http://forums.newtek.com/showthread.php?131095-Poll-How-many-users-would-like-an-embedded-molecular-modeller-for-LW&p=1278185&viewfull=1#post1278185

-Joe

prometheus
08-08-2016, 01:13 PM
Here's (https://www.researchgate.net/profile/Leila_Mahdavian/publication/266595678/figure/fig2/AS:[email protected]/Figure-2-Structure-of-Troponin-C-in-muscle-contraction-a-View-Ribbon-Crystal-structure.png) an example. I believe it's short hand for complex molecules, proteins, etc.

I know the DNA plugin makes bonds, but you got to know the sequence or copy the human genome sequence and feed it in the base line of that plugin,
but the pdb I am not sure, I think I have seen it produce bonds, but maybe it has to do with what you have in the pdb library and if such bonds exists or not?

EDITED....
I think the pdb v3 reader is old...try this one; https://www.lightwave3d.com/assets/plugins/entry/pdb-reader/

I just installed it and it works, by default it is set to stick none, check generate.
I will check the stuff you posted later...
also I fiddled with the dna plugin and compiled it with ls commander to work direcly in layout, it may be possible to do the same with pdb reader, if I got the time.
It actually opens up some possibilites to use for other stuff than just molycular viz, you could use it to create cloud formation structures and add hypervoxels to them, either by adding particles to them, or directly on the vertices then adjust random size, or fill the structures with points in modeler with fill solid, It would be great if the new volumetrics in upcoming lightwave can use just item, wich means whatever geoshape there is can be converted to a volume.






https://www.youtube.com/watch?v=BpbUhXqiO9M

Nangleator
08-08-2016, 01:45 PM
Thanks, guys. A lot to digest. I'll be reviewing this stuff.

prometheus
08-08-2016, 02:09 PM
Thanks, guys. A lot to digest. I'll be reviewing this stuff.

go for installing the refered plugin link ..and your set for initial needs..https://www.lightwave3d.com/assets/p...ry/pdb-reader/

Nangleator
08-08-2016, 02:14 PM
Oh, I've got PDB reader. It's great for small stick-and-ball molecules, but not really big ones. I never had it output ribbons for me, so maybe I'm missing an option in the settings.

prometheus
08-08-2016, 02:47 PM
Oh, I've got PDB reader. It's great for small stick-and-ball molecules, but not really big ones. I never had it output ribbons for me, so maybe I'm missing an option in the settings.

Ah..I see now, I was assuming wrong...as for the image posted, I see now it was the twirled hellix ribbons or the curved ribbons in red as shown in the a labels, and I think you are right there, I havenīt seen anything there to get that representation, but I think that is just another way of displaying it all? maybe there is some software that can display it as such and perhaps export it as such.
Otherwise I donīt know if it is the bonds that is represented as ribbons or if it is parts of the molucule cluster itself? and if you knew that could build helix twirls around that manually? but it would be a painstakingly process I guess.

Nangleator
08-08-2016, 02:54 PM
This software: http://mgltools.scripps.edu/packages/pmv Seems to work. It exports to .STL, which Modeler can open. You've got to name surfaces yourself, which might be an insurmountable problem for some.

It's not, unfortunately, free for commercial use. If it comes down to it, I'll definitely look into it further.

prometheus
08-08-2016, 04:12 PM
This software: http://mgltools.scripps.edu/packages/pmv Seems to work. It exports to .STL, which Modeler can open. You've got to name surfaces yourself, which might be an insurmountable problem for some.

It's not, unfortunately, free for commercial use. If it comes down to it, I'll definitely look into it further.

Thanks for the research, interesting and looks good, however...I guess Itīs not an option unless I would really need it if someone would pay me to do something for a case like that, until then..not.
Maybe there is a free one out there? seems it shouldnīt be impossible...considering itīs scientific purpose.

this might be of interest if you care to open blender, thereīs no option in the import settings though, but it gives different colors already assigned, as opposed to lightwave just surfaces which you need to color adjust manually.

The description is a bit too overly informational about some other things though..but useful if you are complete newbie in blender.


https://www.youtube.com/watch?v=RUiFgI1Vbh4

Michael

prometheus
08-08-2016, 04:18 PM
Export of blender pdb imported objects..to lightwave.
fbx will maintain color information of the structure, obj doesnīt, so that is one way to get it in with proper colors without manually adjusting it.