PDA

View Full Version : Protein Data Bank / Conversion



Joey_C
07-12-2018, 03:15 AM
Protein Data Bank / Conversion
Is there a tutorial to show me teach me how to put skin on these proteins I down load from the Protein Data Bank? It has been so long I have forgotten what the steps to do next with all these metaballs. See image attached. THANK YOU for your help thank you for your time.

Sensei
07-12-2018, 03:45 AM
Are they really metaballs? They look like regular polygons to me..
If they're metaballs, you could try freezing them to regular geometry (Construct > Freeze).
If they're polygons, you can click single polygon from each "atom", then press ']' (Select Connected), and then one ball at a time will be selected (if you're lucky, and they are not the all connected), and then press 'q' (Change Surface)..

50one
07-12-2018, 04:18 AM
epmv in Blender has plenty of meshing options for the proteins.
That's what I used in the past.

Joey_C
07-12-2018, 05:29 AM
Thank you. What does "epmy in Blender" mean?

Joey_C
07-12-2018, 05:33 AM
It's imbarrassing to tell you how many times I have done this in the past but I have forgotten. The steps you mentioned don't ring a bell. I kind of remember with one click delete what makes the metaballs leaving only the points and then making triangles with one click of the mouse and then delete the points left over. I forget it all. THANKS for your help.

50one
07-12-2018, 06:26 AM
Thank you. What does "epmy in Blender" mean?

http://epmv.scripps.edu/

LW lacks importer and mesher, but luckily there's one for Blender with easy options to follow (if Blender is not your thing))

Sensei
07-12-2018, 06:31 AM
It's imbarrassing to tell you how many times I have done this in the past but I have forgotten. The steps you mentioned don't ring a bell. I kind of remember with one click delete what makes the metaballs leaving only the points and then making triangles with one click of the mouse and then delete the points left over. I forget it all. THANKS for your help.

Metaballs editing tools are in
Create > Polygons > More > Draw metaballs,
and
Construct > Convert > Meta > .... (couple of them).

Joey_C
07-12-2018, 06:35 AM
Where do I find this "Blender"?

- - - Updated - - -

Thank you I will fish around there. TKS!!

daforum
07-12-2018, 07:01 AM
Have a look at this script. It reads .pdb files into LW
https://www.lightwave3d.com/assets/plugins/entry/pdb-reader/

Hope it helps :)

Joey_C
07-12-2018, 07:08 AM
THANK YOU! I will download it now.

Joey_C
07-12-2018, 07:15 AM
Oh this is the plugin YES I used to end up with the Metaballs. Now I am trying to remember what to do next how to put skin around this shape.

mummyman
07-12-2018, 07:21 AM
From Pymol, you can export the .pdb as a "surface" / .obj

142208142207

Joey_C
07-12-2018, 07:23 AM
Thank you!

Sensei
07-12-2018, 07:23 AM
Oh this is the plugin YES I used to end up with the Metaballs. Now I am trying to remember what to do next how to put skin around this shape.

You can freeze them, like I said in 2nd post of this thread..
Freezing converts them to regular polygons, which can have assigned surfaces with 'q' key.

mummyman
07-12-2018, 07:30 AM
FYI... that PDB importer for modeler, I use too all the time. It actually flips the model in the Z upon import. No one would know unless you have to match the PDB from Pymol to the imported sticks / spheres in modeler. Wonky, but it works great!

Joey_C
07-12-2018, 10:29 AM
Ok I downloaded "Pymol" and I got the surface on like your instrusted in the photo. Now how do I save that to a LW object? THANK YOU

mummyman
07-12-2018, 11:49 AM
In the 2nd image I posted... there is a command prompt in the window above your model.. You can just type in "save D: blobbyobject.obj and then it will kick out an obj on your hard drive. There are methods to increase the surface quality as well, but that is in a menu somehwere. That should work for you.

You may have to mirror your first "sphere" object in the z axis to match / fit this new skinned .obj from Pymol. But it works like a charm.

Joey_C
07-12-2018, 12:06 PM
Thank you very much. I will go look at that second image.

mummyman
07-12-2018, 12:09 PM
Sure.. it's very fast! Good luck!

Joey_C
07-12-2018, 12:26 PM
I guess I must pay for this Pymol before it will save the .obj? I have not license and just downloaded the Evaluation version.

mummyman
07-12-2018, 12:31 PM
I thought it was always free... unless they changed it up.

Joey_C
07-12-2018, 12:47 PM
I have tried to save it where you said with all kinds of commands and keep getting "Invalid Syntax". Do I skip a space after the "save"? Does the "D" need to be caps?

mummyman
07-12-2018, 12:57 PM
Well, in my case "D" is my hard drive letter. You can type save C: blobby.obj or save D: blobby.obj which will should save the object out to your local drive. Or a specific folder would be save D:\convert\blobby.obj Just make a folder if you need one.

Joey_C
07-12-2018, 01:01 PM
I see. Does it take a long time for Pymol to save it? Can I just push my enter key to save it or do I need to drop down the "File/Save Session? Thank you for all your help, I am sure you are busy right now. THANK YOU.

- - - Updated - - -

Does your version say "No License File" "For Evaluation Only" (30 days remaining)

Joey_C
07-12-2018, 01:13 PM
Here is a screen grab TKS!

mummyman
07-12-2018, 01:22 PM
Looks like mine is an old version. No.. I don't have that message. I private messaged you. Looks like you almost have it correct, or did... your image says it saved to your desktop the .obj. did that not work? It usually saves out pretty quickly.

Joey_C
07-12-2018, 01:26 PM
What version are you using?

Joey_C
07-12-2018, 01:35 PM
Not on my desk top :(:(:(:( Maybe I can find your version and download it? What version are you using? I REALLY like this Pymol. In the past I had to do a lot of steps to get here in LW. This will be great when I can save it. THANK YOU again for all your time.

mummyman
07-12-2018, 01:51 PM
Joey, I sent you a private message..if you want to send me your email. gotta run for now!! Chat soon. Glad you like it. It's pretty powerful. I think there is also other ones out there..

lertola2
07-12-2018, 08:52 PM
Whenever I have to create a molecule I use the workflow in this post: https://forums.newtek.com/showthread.php?131095-Poll-How-many-users-would-like-an-embedded-molecular-modeller-for-LW&p=1278185&viewfull=1#post1278185. You can make nice ribbon type molecules as well as balls or balls and sticks.

lertola2
07-12-2018, 09:01 PM
I should have checked the links before I posted. The dspovtols script link is broken. It is available from this link: http://www.kombyonyx.com/utilities/

Joey_C
07-13-2018, 07:38 AM
Last time I will bug you. Can you tell me which version of Pymol you are using. THANKS FOR ALL YOUR HELP!!!

mummyman
07-13-2018, 07:44 AM
I think I'm on an old eval copy at home.. maybe 1.2??? but work has a paid version. Maybe it limits the export? if you email me, I could export something.. unless it's a ton of stuff. Good luck!

Joey_C
07-13-2018, 08:23 AM
Thank you so much. I do have a TON of Stuff. I am going to try and find your version. This is so much easier the way you do it with Pymol. THANK YOU again for all your help!

mummyman
07-13-2018, 08:58 AM
Good luck!