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PostPosted: Wed Feb 06, 2013 11:34 pm 
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Backbone Representations; Armature

I'm using the most recent Blender all-in-one installer pack; 2.32bit- uPy-aP-eP_blender2.62_win32_1_0_app.zip

The default armature that gets built is the "Trace" armature. The trace armature roughly follows the path of the cartoon representation of the 1CRN.pdb structure. But no matter how hard i try, i can't get the Bones to follow any of the other paths. Beside the Armature tick box, there is a drop down menu called "Bones" with lots of options for the type of armature. When i try select a different set of Bones, like "Full Atoms" or "Backbone", it doesn't work. It still draws the same set bones.

Is there some trick to get this to work? It would be a great advantage if it would draw the "Full atoms" type of bones for the armature.

Thank you,
John.


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PostPosted: Mon Mar 11, 2013 5:56 pm 
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Hi,

trace (follow the CA) and backbone (follow CA,C,O,N) should work fine. The other option are still to be done. But the selection should work fine too.
you need to delete the armature and then recheck the checkbox to see a change.

I will double check the code, and see what is possible.

The problem of the full atoms is the branching of the side chains bones to the backbone, as well as cyclic residues.

L


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PostPosted: Tue Mar 12, 2013 3:01 am 
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ludo wrote:
Hi,

trace (follow the CA) and backbone (follow CA,C,O,N) should work fine. The other option are still to be done. But the selection should work fine too.
you need to delete the armature and then recheck the checkbox to see a change.

I will double check the code, and see what is possible.

The problem of the full atoms is the branching of the side chains bones to the backbone, as well as cyclic residues.

L

Hi Ludo,
Your software is very good. Thank you for the work you have done!

Ok yes, the trace (follow the CA) and backbone (follow CA,C,O,N) do seem to work. But it doesn't help with what i want to do.

Let me explain;
In the following Youtube video, you have animated the ribbon structure by building the "trace" armature and parenting the two together -
ePMV; Blender Ribbon Armature .
http://www.youtube.com/watch?v=ScknbDYRZbg

I want to do the same thing as in that video, but i want to do it with the "sticks" structure. The same as you do in that video, i want to drag the protein structure around, but i want to do it with the sticks model, not the ribbons. The ribbons look very pretty, but they are not real. Inside PyMOL, i can go into "sculpting" mode and drag the protein structure around to simulate a type of protein folding. I would like to do this with ePMV inside Blender. See this; http://www.pymolwiki.org/index.php/Molecular_Sculpting

To drag the actually atomic structure around, the bones of the armature need to follow the complete protein structure, including the side chains. But with just the "trace" armature, i can only parent the backbone of the protein. It won't pick up the side chains because they are too far from the bones of the armature. I use;
The "object" menu, and Object->Parent->Set->With automatic weights
But it won't parent the side chains, they are too far from the nearest bone.

The only way to do this is to build the armature bones of the complete molecular structure, with side chains too.

Is this possible? It would be a big help to my research if i can get this to work.

Thank you Ludo,
John.


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PostPosted: Tue Mar 12, 2013 6:02 am 
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The way I do it is to use Modeller minimization and do some steering molecular dynamics, that I can record and then play back.
I am not sure I got it working in Blender but it is in C4D and Maya, but it sure feasible in Blender, you can try by installing modeller and see if you can import it in blender,then the option should be available in ePMV.

The problem with the stick in blender and other software is the time of building them, and then display them. I am planning to move to the vertex instance system which seems faster.

If you want to do the full armature for every atoms, I can look into it. But I am worried that it may not be real-time.
Also if you have some knowledge in python programming language we can look into together.

Ludo


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PostPosted: Wed Mar 13, 2013 1:29 am 
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ludo wrote:
The way I do it is to use Modeller minimization and do some steering molecular dynamics, that I can record and then play back.
I am not sure I got it working in Blender but it is in C4D and Maya, but it sure feasible in Blender, you can try by installing modeller and see if you can import it in blender,then the option should be available in ePMV.

I'm not exactly sure how to do that. I have UCSF Chimera, and it comes with Modeller pre-installed. But i haven't used it yet.

ludo wrote:
The problem with the stick in blender and other software is the time of building them, and then display them. I am planning to move to the vertex instance system which seems faster.

If you want to do the full armature for every atoms, I can look into it. But I am worried that it may not be real-time.
Also if you have some knowledge in python programming language we can look into together.

Ludo

As i said, all i'm looking for is some way to drag the protein structure around inside blender. Currently i can do this inside PyMOL and UCSF Chimera, but PyMOL and UCSF Chimera are no good for making movies. I don't have C4D or Maya and i don't have a budget to pay for them. I'm just trying out Blender because its free and its easy to experiment with.

I have not learned python programming language. I have some skills in php and html, but thats it.

The molecular models i need to work with are the stick type, and the MSMSurf. The ribbons and beaded ribbons are no good to me because i need the amino acid side chains to move when i drag the structure around, i need the real atomic and molecular data.

Look if its possible for you to get the armature working so it plots the "full atoms" model of the structure, that would be great, it would be a big help to me in my research. If its too much work, then thats ok, don't worry about it. I will just have to find some other way.

Thanks Ludo,
John.


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PostPosted: Wed Mar 13, 2013 6:54 am 
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Ok I will look into the armature when I got a minute, and I will let you know.
Meanwhile check this page : http://epmv.scripps.edu/extensions/modeller and see if its what you are looking for.
Last time I check if wasnt working properly with Blender but I will look into it again
Also Maya is free for academic, so you could give it a try.

L


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PostPosted: Thu Mar 14, 2013 8:16 am 
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Ok, i installed modeller, i got my licence key and modeller does work inside UCSF Chimera. But i didn't succeed in getting modeller to work as an extension in Blender. I tried to follow the instructions on this page, http://epmv.scripps.edu/extensions/modeller , but i just could not get it to add modeller as an extension, or i could not get it to find modeller by editing the patho_ePMV/extension/liste.txt.
But the Youtube video on that page does look good! Thats exactly what i need to be able to do!

On a better note, as you suggested, i went and registered on the Autodesk Maya website as an academic user. Yipeee :D ... they let me download the Maya software! So now i have Maya 2013, the latest version!!

But there was a problem with that too. So i start following the instructions on the all-in-one ePMV Autodesk Maya Installation; http://www.autopack.org/install/maya-installation

So the version of Maya i installed is Autodesk Maya 2013. Then i was following "Option 1" for windows xp. I downloaded this installer; http://upy.googlecode.com/files/uPy-aP- ... -Setup.zip

But here is the problem; That installer for ePMV on Maya 2013 is only for windows 64 bit. Both of my computers are 32 bit, so i had to stop in the installation.

So here is my question;
With my windows 32 bit computer, i could uninstall the Maya 2013 version and install Maya 2012 version instead. Then i could use the older version of ePMV; http://upy.googlecode.com/files/uPy-aP- ... _0_man.zip

Is that what i should do? Should i go with the Maya 2012 and the ePMV windows 32 bit version because i don't see any link for a 32 bit ePMV that i can install with the Maya 2013? This installer is only for windows 64 bit; http://upy.googlecode.com/files/uPy-aP- ... -Setup.zip

Thanks Ludo,
John.


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PostPosted: Thu Mar 14, 2013 8:37 pm 
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I will look into modeller and blender and let you know.
for Maya, yes your options are maya2013 64bits or maya2012 32bits.

L


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PostPosted: Fri Mar 15, 2013 7:02 am 
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Ok, i'm making progress here!

So now i have Maya 2012 installed, and working. And i installed the autopack/ePMV plugin, and its working. It opens the ePMV plugin in Maya and i can go and get the 1CRN.pdb file from the net. And as a bonus, Maya also recognised that i have the modeller extension installed, so modeller is available and when i select modeller, it opens the modeller window. All good so far!

But!!! Modeller is not working. This is what happens;

1. I go and get the 1CRN protein from the PDB
2. I display the "sticks" model of the protein
3. I build the "trace" model armature
4. I select the Modeller extension and it opens the modeller window
5. Nothing happens??? The modeller window is open, but no molecular dynamics?
6. If i tick the "real-time" tick box in Modeller, i get this error;
# Error: AttributeError: Protein instance has no attribute 'pmvaction' #
7. If i click the "Molecular dynamics options" button in Modeller, i get this error;
# Error: AttributeError: Protein instance has no attribute 'mdl' #

Note: Its my first time using Maya and i'm just a beginner at this animation stuff. So it could be some simple setting in Maya that i have to select, or something like that? I'm not familiar with Maya yet.

Any idea what might be wrong?

Thanks Ludo,
John.


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PostPosted: Fri Mar 15, 2013 5:10 pm 
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Nice,
to activate and use modeller you have to tell ePMV through the preferences as mention here http://epmv.scripps.edu/extensions/modeller
that mean that before loading any molecule go to ePMV preference, check use modeller, then load your molecule.

I will try to find if I have a better tutorial for that and will send to you,

L


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