RMSD map, urgent help please
Hi guys, Sorry to ask you that but I urgently need to recover the matrix from an RMSD map obtained from a MD movie. Basically, that would be the same as the graphic of the map but in a file with the numbers. I only have 40 structures but doint it by hands is just painful. Could you please tell me how to catch the rmsd map, I guess we can do it from the script section of the MD movie, but can't figure it out. Sorry to bother you, Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Divendres, Juny 10, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 88, Issue 2
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Today's Topics:
1. Re: Protofibril model (Elaine Meng) 2. Re: Protofibril model (lihong huang)
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Message: 1 Date: Thu, 9 Jun 2011 13:30:22 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [chimera-dev] Protofibril model To: "Russell M. Taylor II" <taylorr@cs.unc.edu> Cc: chimera-dev@cgl.ucsf.edu, UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu>, "Susan T. Lord Ph.D." <susan@sucofa.com>, lihong huang <lihonghuang1980@gmail.com> Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii
Dear Lihong and others, The Multiscale Models tool in Chimera is meant for this purpose --- it shows low-resolution surfaces, which are often preferred for large complexes.
In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog. This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains. You can adjust the colors, surface resolution, etc. in the dialog. Click the dialog's Help button to see its manual page. There is also a copy here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul...>
I also tried it with 1m1j, which also worked fine on my computer.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote:
Dear Lihong, I am glad to hear that Chimera let you start down this path. I'm CCing the Chimera developer mailing list in case they know of a better solution. You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there.
The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this.
Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. This launched the Python Molecule Viewer. Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. Clicked to turn off the red dot under the CPK label so that we only see the surface. Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file.> I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality.
I attach the resulting coarse model (inside a Zip file) to this email. Russ
[Things below I tried that didn't work]
(Fine surface) Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified.> VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps.> NOPE:
You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. To turn off the little axes display, select Display/Axes/Off To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button.
Open Blender (available from blender.org). Press delete to get rid of the cube that is created by default. Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ"
At 10:18 AM 6/7/2011, lihong huang wrote:
Dear Dr. Taylor,
I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help.>> Lihong Huang, Postdco Pathology and lab medicine
--- Russell M. Taylor II, Ph.D. taylorr@cs.unc.edu> CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr> University of North Carolina, Voice: (919) 962-1701 Chapel Hill, NC 27599-3175 FAX: (919) 962-1799 <protofibril.zip>_______________________________________________> Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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Message: 2 Date: Fri, 10 Jun 2011 09:32:02 -0400 From: lihong huang <lihonghuang1980@gmail.com> Subject: Re: [chimera-dev] Protofibril model To: "Russell M. Taylor II" <taylorr@cs.unc.edu> Cc: meng@cgl.ucsf.edu, chimera-dev@cgl.ucsf.edu, susan@sucofa.com Message-ID: <BANLkTinJsiLgAiE9ghyTyP-0TUZT_YP_Nw@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
Hi Russ, Elaine and Tom,
Thank you very much for your help. We will try what you suggested and let you know how it works.
Best, Lihong
On Thu, Jun 9, 2011 at 3:13 PM, Russell M. Taylor II <taylorr@cs.unc.edu>wrote:
Dear Lihong, I am glad to hear that Chimera let you start down this path. I'm CCing the Chimera developer mailing list in case they know of a better solution. You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera- users/index.html and then post a query there.
The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this.
Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. This launched the Python Molecule Viewer. Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the> molecule. Clicked to turn off the red dot under the CPK label so that we only see the surface. Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file.> I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality.
I attach the resulting coarse model (inside a Zip file) to this> email. Russ
[Things below I tried that didn't work]
(Fine surface) Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb,> it crashed trying to make the surface). Compute/Molecular Surface/Compute Molecular Surface. Used the> default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified.
VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps.
NOPE:
You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing> Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. To turn off the little axes display, select Display/Axes/Off To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button.
Open Blender (available from blender.org). Press delete to get rid of the cube that is created by default. Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ"
At 10:18 AM 6/7/2011, lihong huang wrote:
Dear Dr. Taylor,
I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help.
Lihong Huang, Postdco Pathology and lab medicine
--- Russell M. Taylor II, Ph.D. taylorr@cs.unc.edu> CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr<http://www.cs.unc.edu/%7Etaylorr>> University of North Carolina, Voice: (919) 962- 1701> Chapel Hill, NC 27599-3175 FAX: (919) 962-1799
On Jun 22, 2011, at 3:51 AM, Jean Didier Pie Marechal wrote:
Hi guys,
Sorry to ask you that but I urgently need to recover the matrix from an RMSD map obtained from a MD movie. Basically, that would be the same as the graphic of the map but in a file with the numbers. I only have 40 structures but doint it by hands is just painful. Could you please tell me how to catch the rmsd map, I guess we can do it from the script section of the MD movie, but can't figure it out.
Hi JD, I guess the simplest way is just to insert a print statement where the RMSDs are being computed. In the Movie module there is a file named RmsdMap.py that you can edit. Line 232 of that file should look like this: self.rects[rect1] = (frame1, frame2, rmsd) add a print statement right after that, with the same indentation, like so: print frame1, frame2, rmsd Then all the computed RMSDs and frame numbers will be reported in the reply log, from which they could be saved. It would also be possible to write a script that fishes around to find the RMSD-map dialog and extract the RMSDs. If you really need that instead of the print-statement approach let me know and I'll whip up something. --Eric Eric Pettersen UCSF Computer Graphics Lab On Linux/Windows, the Movie module is in <your Chimera installation>/ share. On Mac, it's in Chimera.app/Contents/Resources/share.
participants (2)
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Eric Pettersen -
Jean Didier Pie Marechal