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 Post subject: Loading EM maps
PostPosted: Tue Aug 09, 2011 5:47 pm 
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Hi,

grahamj wrote to me "You can load .map files directly into Blender, adjust the isovalue, and apply color coding with our plugin ePMV" on Blender forum.

I just tried importing my EM map in MRC format into Blender by using ePMV, but looks like MRC is not a recognized format. I searched for a converter from MRC to .map to no avail. Is there such a converter, and if so, where can I find it?

Thanks.


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 Post subject: Re: Loading EM maps
PostPosted: Tue Aug 09, 2011 6:12 pm 
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Hi,

can you gave me more details:
- OS (windows, mac or linux ?)
- ePMV version (you can find it at the bottom of the plugin)

Quote:
I just tried importing my EM map in MRC format into Blender by using ePMV, but looks like MRC is not a recognized format. I searched for a converter from MRC to .map to no avail. Is there such a converter, and if so, where can I find it?


In order to load an EM map, you need to use the Browse Button from the data player. (Bottom section). MRC is generally supported, can you send me your file ?
Once the data file is loaded you can select it in the pulldown menu, and use the slider to control it. If its a map it will control the isocontour value.

After the geometry have been build you can either bind it to the molecule and apply the different color schem from the Color panel.
You can also use the value from the Map to color a geometry (color projection on surface) using the APBS extension that will take the current data, and apply the color project on the given geometry (see here http://epmv.scripps.edu/extensions/apbs)

Ludovic


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 Post subject: Re: Loading EM maps
PostPosted: Tue Aug 09, 2011 7:31 pm 
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ludo wrote:
Hi,

can you gave me more details:
- OS (windows, mac or linux ?)
- ePMV version (you can find it at the bottom of the plugin)


Win7 32bit, ePMV that comes with the Blender in the packaged version for windows (0.3.7).

Quote:
In order to load an EM map, you need to use the Browse Button from the data player. (Bottom section). MRC is generally supported, can you send me your file ?


Ah, I see. I'd suggest that it'd be more intuitive to transfer this into "Get a molecule" section, since that looks like the part where you load/import things in.

When I tried opening my MRC map, this is what I got:

Code:
('Browse', 46)
('action ', 'Browse', <bound method epmvGui.browseDATA of <ePMV.epmvGui.epmvGui
instance at 0x0B77B5F8>>)
MRC file: C:\Structures\Ref45.mrc
mode: 2
indices (1:fastest, 3:slowest) 1 2 3
nc: 180, nr: 180, ns: 180
dimensions: (180, 180, 180)
origin: -0.5, -0.5, -0.5
acell: 457.199982, bcell: 457.199982, ccell: 457.199982
alpha:  90.000000, beta:  90.000000, gamma:  90.000000
symmetry ops: 0 bytes in length
min:   -9.037665
max:     9.242389
mean:   0.000000
stdev:   1.000000

time to read file:  1.65599989891
doit addGriddoit addGriddoit addGridDoneTraceback (most recent call last):
  File "C:\Users\jacklab\epmv-blender-2.49b-windows32/MGLToolsPckgs\ePMV\epmvGui
.py", line 1205, in CreateLayout
    self._createLayout()
  File "C:\Users\jacklab\epmv-blender-2.49b-windows32/MGLToolsPckgs\pyubic\uiAda
ptor.py", line 472, in _createLayout
    self.SetTitle(self.title) #set the title #in maya this will also setup the w
indows
  File "C:\Users\jacklab\epmv-blender-2.49b-windows32/MGLToolsPckgs\pyubic\blend
er\v249\blenderUI.py", line 424, in SetTitle
    TitleColor[2]/256.0)
  File "C:\Users\jacklab\epmv-blender-2.49b-windows32/MGLToolsPckgs\ePMV\epmvGui
.py", line 2040, in loadDATA
    else : self.gridData(file=filename)
  File "C:\Users\jacklab\epmv-blender-2.49b-windows32/MGLToolsPckgs\ePMV\epmvGui
.py", line 2101, in gridData
    vname = self.COMB_BOX["mol"]["value"][val]
IndexError: list index out of range


PS: I PM'd you about sending you the map. If you don't get it, please let me know.


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 Post subject: Re: Loading EM maps
PostPosted: Tue Aug 09, 2011 9:06 pm 
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Quote:
When I tried opening my MRC map, this is what I got:


so the error you get is an error I though I correct a long time ago.
The data player is linked to the current mol selection. ePMV associate a data to a molecule. I though I add the possibility to get a Data by itself..it seems not/
Try to first load a molecule and the load your data....
if the format is recognized it should work..

Let me know

Ludovic


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 12:05 am 
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Hi,
Because the EM path is a bit circuitous, I posted a tutorial for it last month. Try to follow the steps to see if it works for the Nuclear Pore Complex (just the top 1/3 is relevant to generalEPMV- bottom third is C4D specific).
Tutorial:
http://epmv.scripps.edu/documentation/t ... -tutorials

If that works, then we can try to figure out your specific file... remember the model will be enormous and well off the viewport, so ZoomToShowAll.
Cheers,
Graham


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 3:50 pm 
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ok, once I opened a PDB first, and changed the extension of my MRC map to ccp4, it opened. It took FOREVER though. I see that it's running a single thread. Do you have any plans to get ePMV running multi-threaded? I see three of my cores idling while waiting for ePMV to do something for a looong time on a single core. Well, I got my map into Blender, and that's very nice (although I could [kind of] do this by exporting it as an X2D scene from Chimera).

But now I have problems importing my PDB. Should I start another thread with the proper title, or continue here?

Thanks.


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 6:26 pm 
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tolung wrote:
But now I have problems importing my PDB. Should I start another thread with the proper title, or continue here?

Please start a new thread for the different topic of PDB import. I'll try to post some time variations for model construction later today.

Very quickly though, I'm not sure what LONG time means in your world.
It takes <9 seconds to build the initial model after selecting emd_1097.ccp4 file with ePMV in Cinema4D on my 1st generation Intel Mac (default thread). It takes ~0.5 sec to update the model after changing the isocontour value and can be altered in almost realtime by dragging the slider around- but with a slightly noticeable lag (e.g. the quarter to half second I mentioned) on my 4 year old machine. This may be different for Blender 2.49- I'll try to test if I get time later.
G


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 9:28 pm 
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Quote:
ok, once I opened a PDB first, and changed the extension of my MRC map to ccp4, it opened. It took FOREVER though. I see that it's running a single thread. Do you have any plans to get ePMV running multi-threaded? I see three of my cores idling while waiting for ePMV to do something for a looong time on a single core. Well, I got my map into Blender, and that's very nice

Gald to here you finally get it, and you are right, processing is much much longer on windows that on Mac or Linux. The reason is that ePMv is just the interface between a host and a molecular viewer called PMV, that I had to recompile entirely for windows. Which have gave some issue on performance and stability....And I dont own a windows machine so I develop on bootcamp and sometimes wine which is not ideal...And i dont talk about multiprocessing-multithreading...

Quote:
(although I could [kind of] do this by exporting it as an X2D scene from Chimera).

Yes absolutely, and you can also used VMD with the nice tachyon rendering. You can also embed chimera or pymol in ePMV.
I think it really depend on the project situation. ePMV dont replace chimera or pymol its just a way to quiclky have molecular representation inside 3d app without importing/exporting.

Quote:
But now I have problems importing my PDB. Should I start another thread with the proper title, or continue here?


yes please open a new thread

Ludo


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 10:03 pm 
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Ok I made a quick test, and the MGL developper have produce a version for windows which is compatible with blender. Using this package instead of the one compiled using mingw improve greatly the performance for grid, and corse MS.
I will prepare the package and update the link on the web so you should be able to get this improved version.

Ludovic


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 Post subject: Re: Loading EM maps
PostPosted: Wed Aug 10, 2011 10:40 pm 
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I update the pacakge for windows, you can get it here :
https://sites.google.com/site/mgltoolse ... lender_win
or directly here :
http://mgldev.scripps.edu/projects/ePMV ... dows32.zip

You don't need to load a molecule prior to a grid.
Let me know if you encounter any other problem.

Ludo


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