Importing EM maps (MRC or other formats)

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GT-Force
Posts: 12
Joined: Sun Sep 20, 2009 10:51 pm

Importing EM maps (MRC or other formats)

Postby GT-Force » Thu Jul 28, 2011 4:35 pm

Dear all,

I've found a way to import PDBs, but not MRC files. Is there a way to import MRC maps (EM reconstruction maps) into Blender?

Thank you.

GT

GT-Force
Posts: 12
Joined: Sun Sep 20, 2009 10:51 pm

How to import EM maps into Blender

Postby GT-Force » Thu Aug 04, 2011 6:45 pm

I've found a way to do this without needing a Blender converter:

Load your MRC map into Chimera, export it as X3D, and Import it into Blender.

When Blender displays your map after opening it, it looks crappy, but that's because Blender uses flat shading by default. Select your imported map, which is now a Blender object, by right clicking it and select Smooth under Shading, and Ta da!

Now, I just need to learn how to use Blender :P

grahamj
Posts: 7
Joined: Sat Aug 06, 2011 7:07 am
Location: CA

ePMV, a Blender plugin can import MAP and PDB files directly

Postby grahamj » Sat Aug 06, 2011 7:14 am

You can load .map files directly into Blender, adjust the isovalue, and apply color coding with our plugin ePMV (embedded Python Molecular Viewer.) ePMV can load PDB files and much much more.
We have versions working for Blender 2.49b on Mac, Windows, and Linux (all 32 bit, but 64 bit available in Linux), and Blender 2.58a on Mac 10.6+ in 64 bits.
http://epmv.scripps.edu
I'll post an announcement soon, but the link will get you started with download and install instructions.

Here is a tutorial for opening an EM map downloaded from the EMDB:
http://epmv.scripps.edu/documentation/t ... -tutorials

GT-Force
Posts: 12
Joined: Sun Sep 20, 2009 10:51 pm

Re: ePMV, a Blender plugin can import MAP and PDB files dire

Postby GT-Force » Sat Aug 06, 2011 7:06 pm

grahamj wrote:You can load .map files directly into Blender, adjust the isovalue, and apply color coding with our plugin ePMV (embedded Python Molecular Viewer.) ePMV can load PDB files and much much more.
We have versions working for Blender 2.49b on Mac, Windows, and Linux (all 32 bit, but 64 bit available in Linux), and Blender 2.58a on Mac 10.6+ in 64 bits.


Great. Already underway in installation. Thanks.

GT-Force
Posts: 12
Joined: Sun Sep 20, 2009 10:51 pm

Installation problem

Postby GT-Force » Sat Aug 06, 2011 7:31 pm

Hi,

I am using Windows 64 bit, and I followed the installation instructions on here:
http://epmv.scripps.edu/installation

After I ran install_plugin.py in Blender,, this is what I get:

In the text editor window, "from ePMV.installer import Installer" line is highlighted red, and in the terminal are the following:

Code: Select all

path c:\Program Files (x86)\MGLToolsPckgs\ePMV
c:\Program Files (x86)\MGLToolsPckgs
Traceback (most recent call last):
  File "install_plugin.py", line 58, in <module>
  File "c:\Program Files (x86)\MGLToolsPckgs\ePMV\installer.py", line 789, in <m
odule>
    helperClass = pyubic.getHelperClass()
  File "c:\Program Files (x86)\MGLToolsPckgs\pyubic\__init__.py", line 153, in g
etHelperClass
    from pyubic.blender.v249.blenderHelper import blenderHelper as helper
  File "c:\Program Files (x86)\MGLToolsPckgs\pyubic\blender\v249\blenderHelper.p
y", line 31, in <module>
    import numpy
  File "c:\Program Files (x86)\MGLToolsPckgs\numpy\__init__.py", line 93, in <mo
dule>
    import add_newdocs
  File "c:\Program Files (x86)\MGLToolsPckgs\numpy\add_newdocs.py", line 9, in <
module>
    from lib import add_newdoc
  File "c:\Program Files (x86)\MGLToolsPckgs\numpy\lib\__init__.py", line 4, in
<module>
    from type_check import *
  File "c:\Program Files (x86)\MGLToolsPckgs\numpy\lib\type_check.py", line 8, i
n <module>
    import numpy.core.numeric as _nx
  File "c:\Program Files (x86)\MGLToolsPckgs\numpy\core\__init__.py", line 5, in
 <module>
    import multiarray
ImportError: DLL load failed: The specified module could not be found.


"C:\Program Files (x86)\MGLToolsPckgs" is the correct path.

In the web page it says "If the script guessed wrong, you must correct the path manually here.", but does not say how.

What should I do to fix this?

I see that you have a package for Macs, are you planning to release one for Windows, too?

Thank you.

grahamj
Posts: 7
Joined: Sat Aug 06, 2011 7:07 am
Location: CA

Re: Installation problem

Postby grahamj » Sun Aug 07, 2011 5:51 am

Hi GT,
I posted the announcement for Blender a couple days prematurely while I was excitedly posting on a Cinema4D forum.

If you want to get up and running this weekend, we can work on your problem via the ePMV forum (please visit and click to pickup where "Installation problems with bender" leaves off)- could be a python conflict or that the MGLTools patching didn't occur (our server has been acting up since Friday)...

I'd recommend waiting two days- because installation is the biggest hurdle for ePMV, Ludovic is compiling stand-alone packages (similar to the Mac 64 bit 2.58 version we've posted) for Windows and Linux as well (also for 2.49). He's working on it this weekend and says they should be ready by Monday if not sooner.

Fortunately, once you have ePMV installed, you can update it, directly from the GUI with a couple mouse clicks.

Thanks for the suggestion and for helping us iron out this β version- the Mac package is incredibly easy to run, so I hope the Windows version will keep you smiling, and sorry to send you down a tough path. The 2.49 installer for Mac is quite clean (we only have one Vista machine to test on), but the Packaging should make this comfortable for users of all levels and backgrounds.

Please let me know if I can help further here, especially once you get to the point of toying with EM maps.
Cheers,
Graham

GT-Force wrote:Hi,
After I ran install_plugin.py in Blender,, this is what I get:
...
...
What should I do to fix this?

I see that you have a package for Macs, are you planning to release one for Windows, too?

grahamj
Posts: 7
Joined: Sat Aug 06, 2011 7:07 am
Location: CA

Re: Installation problem

Postby grahamj » Sat Aug 13, 2011 3:51 am

Working with GT-Force to iron out kinks in the Windows 32-bit version, Ludovic seems to have it all working. Now you can grab fast/stable versions of ePMV-Blender 2.49 for Windows/Mac, and ePMV-Blender 2.58 for MacOX6+ and look for future updates at:

http://epmv.scripps.edu/download-install-free/perhost

Since we're still moving these pages around a bit, a longer lasting link is to just go to epmv.scripps.edu and find the installer page for Blender.


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