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PostPosted: Fri Jun 17, 2011 12:45 am 
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hi,

its seems that for some reason the fetch stop working recently...I need to check this feature, in the meantimes can you try to load a pdb from file.
There is nothing wrong in the following line
noModeller
noAutoFill
noARViewer
no pymol
ePMv is checking for external library such as modeller that let you do minimisation and md simulation....the other package are internal package from the lab that are currently under developpement...

Ludovic


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PostPosted: Fri Jun 17, 2011 7:36 am 
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Hi Ludovic,

Thanks for clarifying. Actually I have few PDB file as I also tried to use mMaya in Maya 2012 (not in Maya 2011) and I downloaded some PDB files for testing. These PDB files work well in mMaya. They just did not load from file into ePMV (see below lines).
I saw you have mMaya as well. What is your impression? The installation of mMaya is somehow a bit more straightforward. I would like to see ePMV in action otherwise I will not able compare them.
Thanks
Peter

WARNING: dependency check failed for command APBSVolumeRender
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5a887080>> ignored
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5aa4e210>> ignored
noModeller
noAutoFill
noARViewer
no pymol
ePMV_gui created
updateRendererUI;
updateRendererUI;
False
didn't exist try another ID
fetch None


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PostPosted: Fri Jun 17, 2011 2:31 pm 
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Hi Peter,

Did you use the fecth button to get your PDB files, or did you use the browse button?
When you have a pdb file, first of all the filename have to be short.
Then you can either use the Browse button or go through File->Load (From the ePMV top menu).
Once the molecule is load, some null object are created, and optionally camera and light. Moreover in the gui the name of the molecule appear next "Current selection"
Then check the MSMSurf check box in the surface representation you should see appear the surface of your molecule.

About mMaya, yes they did a really nice work, I particularly appreciate the use of the particule system for displaying the atoms level, which is the most difficult part in such vizualisation approach. ePMV is less performant for CPK and ball&stick representation especially in maya. But our advantage is the control over the ribbon and surface associated with the ability of changing the color schem. Moreover you can associate ePMV with modeller as I already mention you for minimizing and streching in real time...and the most important advantage is that ePMV work the same in blender and C4D as well...which is why the installation is not so easy as we have to handle the three different plugin system....

Let me know if you are able to browse and load your molecule, as the message you attach only show that you have try to fecth a PDB which is actually making a query to the PDB website and not try to load a local file.

Ludovic
PS: Could you try to fetch using a different server following theses instruction:
- in the pdb input field enter : 1h68
- next to the Fecth button click on PDB, its a pull down menu that let you select a server, choose OPM
- click the Fecth button
- click on Metaballs (which is actually a particule system) that will show you a point a cloud of a transmembranar protein
Thanks


Attachments:
Screen shot 2011-06-17 at 7.25.56 AM.png
Screen shot 2011-06-17 at 7.25.56 AM.png [ 289.46 KiB | Viewed 9720 times ]
Screen shot 2011-06-17 at 7.25.00 AM.png
Screen shot 2011-06-17 at 7.25.00 AM.png [ 72.54 KiB | Viewed 9720 times ]
Screen shot 2011-06-17 at 7.24.45 AM.png
Screen shot 2011-06-17 at 7.24.45 AM.png [ 271.36 KiB | Viewed 9720 times ]
Screen shot 2011-06-17 at 7.24.09 AM.png
Screen shot 2011-06-17 at 7.24.09 AM.png [ 153.9 KiB | Viewed 9720 times ]
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PostPosted: Fri Jun 17, 2011 6:30 pm 
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Hi Ludovic,

I followed your instructions.
Attempt A:
1. I typed 1h68 in the input field in Get a Molecule.
2. Changed the PBD format to OPM.
3. Pressed the Fetch button.
4. Nothing appeared in the Outliner. (see at bottom: Ludo requested test) No molecule loaded. No "1h68" appeared next to Current selection:

I have pretty fast internet connection and there is no problem with it. So "Fetch" seems not healthy in my installation of ePMV.

Attempt B:
1. Browsed to the folder where I downloaded some PDB files with mMaya.
2. I selected the "1AXC" PDB file.
3. Clicked on Open.
4. The molecule loaded (Peter_test_1a.jpg). 1AXC appeared next to Current selection: but the Save button did not come up like in your print screen.
5. Odd thing that "1crn" is still in the input field... while 1AXC already loaded (see at bottom: Peter test).

I can load PBD files into ePMV if I pre-download them. Anyway now I can play with it. Great news! Thank you very much your help and your script! If I have any question or problem I will let you know. Cheers, Peter
Attachment:
Ludovic_test.jpg
Ludovic_test.jpg [ 234.52 KiB | Viewed 9714 times ]

Attachment:
Peter_test_1a.jpg
Peter_test_1a.jpg [ 220.03 KiB | Viewed 9714 times ]


Ludo requested test:
WARNING: dependency check failed for command APBSVolumeRender
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5bc6f0d0>> ignored
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5b97a6e8>> ignored
noModeller
noAutoFill
noARViewer
no pymol
ePMV_gui created
False
didn't exist try another ID
fetch None
# Error: list.index(x): x not in list
# Traceback (most recent call last):
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/ePMV/epmvGui.py", line 2118, in dsMSMS
# mname,mol,sel,selection,display = self.getDsInfo("surf")
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/ePMV/epmvGui.py", line 1759, in getDsInfo
# val = self.getLong(self.COMB_BOX["mol"])
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/pyubic/autodeskmaya/mayaUI.py", line 791, in getLong
# return elem["value"].index(str) #maya combo menu is a txt + pulldown menu
# ValueError: list.index(x): x not in list #
False
didn't exist try another ID
fetch None
False
didn't exist try another ID
fetch None
createModelPanelMenu modelPanel1;
createModelPanelMenu modelPanel2;
createModelPanelMenu modelPanel3;
createModelPanelMenu modelPanel4;
createOutlinerPanelMenu outlinerPanel1;
buildPanelPopupMenu scriptEditorPanel1;
# Error: list.index(x): x not in list
# Traceback (most recent call last):
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/ePMV/epmvGui.py", line 2213, in dsMeta
# mname,mol,sel,selection,display = self.getDsInfo("meta")
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/ePMV/epmvGui.py", line 1759, in getDsInfo
# val = self.getLong(self.COMB_BOX["mol"])
# File "/Library/MGLTools/1.5.6rc1/MGLToolsPckgs/pyubic/autodeskmaya/mayaUI.py", line 791, in getLong
# return elem["value"].index(str) #maya combo menu is a txt + pulldown menu
# ValueError: list.index(x): x not in list #

Peter test:
WARNING: dependency check failed for command APBSVolumeRender
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5b6c7170>> ignored
# Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x5a1df6e8>> ignored
noModeller
noAutoFill
noARViewer
no pymol
ePMV_gui created
fileDialog2 -fm 1 -ds 2;
// /Users/peterzavorszky/Documents/Peter/mMaya/mMaya_2011-02-19_4d5fe5f15f4851/PDB/1AXC.pdb //
[(1.0, 0.5, 1.0), (1.0, 1.0, 0.5), (1.0, 0.5, 0.5), (0.25, 0.75, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0), (0.0, 0.75, 1.0), (0.0, 1.0, 0.5), (0.59999999999999998, 1.0, 0.0), (1.0, 0.5, 0.0), (1.0, 0.0, 0.5), (0.5, 0.0, 1.0), (0.5, 0.0, 0.20000000000000001), (0.0, 0.5, 0.20000000000000001), (0.75, 0, 1), (1.0, 0.75, 0), (1.0, 0.0, 0.75), (0.0, 1.0, 0.75), (1.0, 0.0, 0.25), (0.0, 0.5, 1.0)]
[(1.0, 0.5, 1.0), (1.0, 1.0, 0.5), (1.0, 0.5, 0.5), (0.25, 0.75, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0), (0.0, 0.75, 1.0), (0.0, 1.0, 0.5), (0.59999999999999998, 1.0, 0.0), (1.0, 0.5, 0.0), (1.0, 0.0, 0.5), (0.5, 0.0, 1.0), (0.5, 0.0, 0.20000000000000001), (0.0, 0.5, 0.20000000000000001), (0.75, 0, 1), (1.0, 0.75, 0), (1.0, 0.0, 0.75), (0.0, 1.0, 0.75), (1.0, 0.0, 0.25), (0.0, 0.5, 1.0)]
[(0.0, 0.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0), (0.0, 0.75, 1.0), (0.0, 1.0, 0.5), (0.59999999999999998, 1.0, 0.0), (1.0, 0.5, 0.0), (1.0, 0.0, 0.5), (0.5, 0.0, 1.0), (0.5, 0.0, 0.20000000000000001), (0.0, 0.5, 0.20000000000000001), (0.75, 0, 1), (1.0, 0.75, 0), (1.0, 0.0, 0.75), (0.0, 1.0, 0.75), (1.0, 0.0, 0.25), (0.0, 0.5, 1.0)]
# <Protein instance> 1AXC with 6 MolKit.protein.Chain
# 0
# 1
# 2
# 3
# 4
# 5
1AXC <Protein instance> 1AXC with 6 MolKit.protein.Chain
ok sel 8393
<maya.OpenMaya.MFnMesh; proxy of <Swig Object of type 'MFnMesh *' at 0x5e30e4b0> >
displaySmoothness -divisionsU 3 -divisionsV 3 -pointsWire 16 -pointsShaded 4 -polygonObject 3;
subdivDisplaySmoothness -smoothness 3;
createModelPanelMenu modelPanel1;
createModelPanelMenu modelPanel2;
createModelPanelMenu modelPanel3;
createModelPanelMenu modelPanel4;
buildPanelPopupMenu scriptEditorPanel1;


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PostPosted: Fri Jun 17, 2011 6:46 pm 
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Hi Ludovic,

I did one more test.
Attempt C:
1. Browsed to the folder where I downloaded some PDB files with mMaya.
2. I selected the "1JKR" PDB file. (DNA + Hin recombinase)
3. Clicked on Open.
4. The molecule loaded. 1JKR appeared next to Current selection: but the Save button did not come up like in your print screen.
5. Odd thing that "1crn" is still in the input field... while 1JKR already loaded.
6. When I render 1JKR where MSMSurf is on (Atoms off) with Maya renderer I have the image (Render View-2.jpg, Render_view_02 Script editor).
7. When I turned off MSMSurf and turned on Atoms (Atom Spacefill) I could see the colored spacefill balls only in the "persp window" but nothing rendred in the Render View (black image, Render View-1.jpg, Render_view_01 Script editor).
8. But when I changed the renderer to "mentalray" it started to render the colored spacefill balls but around the half of the calculating image (in Render View) Maya totally crashed. No window, no running Maya app.
I can reproduce this mentalray+Atoms turned on (Atom Spacefill) crash pretty safely.
9. Finally it turned out that I could not render 1JKR with mentalray even when just MSMSurf is on (it is not Atoms (Atom Spacefill) specific...).
Question: Is it just my special case that I could not render anything from ePMV with mentalray? Thank you.

Attachment:
Render View-2.jpg
Render View-2.jpg [ 122.13 KiB | Viewed 9714 times ]

Attachment:
Render View-1.jpg
Render View-1.jpg [ 124.75 KiB | Viewed 9714 times ]


Render View-2 Script editor:
renderWindowRender redoPreviousRender renderView;
import maya.app.stereo.stereoCameraRig as stereoCameraRig
stereoCameraRig.isRigRoot('persp')
# Result: False #
updateEditorFeedbackRenderLayer RenderLayerTab defaultRenderLayer;

Render View-1 Script editor:
renderWindowRender redoPreviousRender renderView;
import maya.app.stereo.stereoCameraRig as stereoCameraRig
stereoCameraRig.isRigRoot('persp')
# Result: False #
updateEditorFeedbackRenderLayer RenderLayerTab defaultRenderLayer;
1JKR <Protein instance> 1JKR with 3 MolKit.protein.Chain
ok sel 939
(True,)
1JKR <Protein instance> 1JKR with 3 MolKit.protein.Chain
ok sel 939
ONE COLOR
redo False
DT
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renderWindowRender redoPreviousRender renderView;
import maya.app.stereo.stereoCameraRig as stereoCameraRig
stereoCameraRig.isRigRoot('persp')
# Result: False #
updateEditorFeedbackRenderLayer RenderLayerTab defaultRenderLayer;


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PostPosted: Fri Jun 17, 2011 7:58 pm 
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Hi peter,

I will try to answer your questions...
4. The molecule loaded. 1JKR appeared next to Current selection: but the Save button did not come up like in your print screen.
The save button is on my version, which is the development version
5. Odd thing that "1crn" is still in the input field... while 1JKR already loaded.
This is normal, 1crn is in the input field for the fetch, the only purpose of this input, your molecule name should appear next to CurrentSelection (clickable as a pulldown menu for multiple molecule)

About rendering :
- when you load a molecule I automatically create a camera and a light, but these are default, and up to you to create different one, especially if the current camera is too close, or the angle is not perfect for the molecule.
- the surface color is vertex based color, thats means that it only appear in the viewport and using maya Hardware rendering. To use mental ray or software you need to back to Texture the vertex color or to link the vertex color information to a mentalray shader node (you can find a tutorial for this on our website).
- atoms rendering, to get the regular rendering you can try to apply a different color schem on the Atoms..and try render..this should fix the problem (material node connetion problem at initialisation of the geometry). I think this should also fix the mental ray crash.
About the CPK, maya is not well adapted to display thousand of spheres in real time, I am still trying to figure out how to improve the atoms representatin performances..., if you have really big molecule, prefer the metaballs (particul) representation.

Question: Is it just my special case that I could not render anything from ePMV with mentalray? Thank you. Well Its not your case, same on my laptop.
vertex color map are not render in mental as mentoned, the rest should be ok.

I will try to do some debug test and improve the plugin for maya which is not perfect currently...

Ludovic


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PostPosted: Fri Jun 17, 2011 9:32 pm 
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Hi Ludovic,

Thank you for clarifying my notes/questions.

The last couple of days my interest to be able to use ePMV was so intensive that you might feel yourself a bit stressful. You should not be.
I am simply interested in such tools like ePMV to be able to visualize scientifically correct molecular structures. I have some project plans where these kind of tools play very important role. Most probably there will be a combination of tools I will use.

I am full of enthusiasm and interested in scientific visualization. Developers like you do absolutely great job to provide useful tools which are many times clearly essential to do the work.
My major goal was on this week to be able to install and bring ePMV in Maya to work. With your essential help I managed it. Thanks a lot.
Now it is up to me to try and test ePMV what I am looking forward on the following weeks!

Thanks again for your help.

Cheers, Peter


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PostPosted: Fri Jun 17, 2011 10:46 pm 
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Hi Peter,

Thanks for you message.

Don't worry, I am always glad to give help, answer and support.

Let me know if you encounter any problem and I am sure you will, user feedback is essential for us as we can't test all situations, so don't hesitate to post comments, bugs, suggestion, rendering etc ...

Ludovic


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