[chimera-dev] RMSD map, urgent help please
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Wed Jun 22 03:51:37 PDT 2011
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 at uab.es
www: http://asklipio.qf.uab.es
----- Missatge original -----
De: chimera-dev-request at 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:
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> 1. Re: Protofibril model (Elaine Meng)
> 2. Re: Protofibril model (lihong huang)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Thu, 9 Jun 2011 13:30:22 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Protofibril model
> To: "Russell M. Taylor II" <taylorr at cs.unc.edu>
> Cc: chimera-dev at cgl.ucsf.edu, UCSF Chimera Mailing List
> <chimera-users at cgl.ucsf.edu>, "Susan T. Lord Ph.D."
> <susan at sucofa.com>, lihong huang <lihonghuang1980 at gmail.com>
> Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A at 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/framemulti.html>
>
> 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://www.rbvi.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 at 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 at cgl.ucsf.edu
> > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 Jun 2011 09:32:02 -0400
> From: lihong huang <lihonghuang1980 at gmail.com>
> Subject: Re: [chimera-dev] Protofibril model
> To: "Russell M. Taylor II" <taylorr at cs.unc.edu>
> Cc: meng at cgl.ucsf.edu, chimera-dev at cgl.ucsf.edu, susan at sucofa.com
> Message-ID: <BANLkTinJsiLgAiE9ghyTyP-0TUZT_YP_Nw at 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 at 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://www.rbvi.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 at 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
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