June 2011 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

4 3

RMSD map, urgent help please
by Jean Didier Pie Marechal 22 Jun '11

22 Jun '11

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(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Juny 10, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 88, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 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(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, UCSF Chimera Mailing List > <chimera-users(a)cgl.ucsf.edu>, "Susan T. Lord Ph.D." > <susan(a)sucofa.com>, lihong huang <lihonghuang1980(a)gmail.com> > Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A(a)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/framemu…> > > 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(a)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(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Jun 2011 09:32:02 -0400 > From: lihong huang <lihonghuang1980(a)gmail.com> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: meng(a)cgl.ucsf.edu, chimera-dev(a)cgl.ucsf.edu, susan(a)sucofa.com > Message-ID: <BANLkTinJsiLgAiE9ghyTyP-0TUZT_YP_Nw(a)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(a)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(a)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 >

2 1

Re: [chimera-dev] Protofibril model
by Russell M. Taylor II 10 Jun '11

10 Jun '11

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(a)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

3 2