From glennm at chemistry.ucsc.edu Sun Jun 1 20:13:31 2008 From: glennm at chemistry.ucsc.edu (Glenn Millhauser) Date: Sun, 1 Jun 2008 20:13:31 -0700 Subject: [Chimera-users] OS X aqua version Message-ID: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> Hi Folks, I just saw the mac aqua version at the download site and decided to give it a try. Layout looks terrific. However, it seems to move molecules much more slowly than the X windows version. I'm running on a macbook (intel) with inherent limited graphics capabilities, so perhaps that's the problem. Any comments? thanks, g Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell glennm at chemistry.ucsc.edu http://chemistry.ucsc.edu/~glennm From ibdeno at gmail.com Mon Jun 2 02:28:14 2008 From: ibdeno at gmail.com (=?ISO-8859-1?Q?Miguel_Ortiz-Lombard=EDa?=) Date: Mon, 2 Jun 2008 11:28:14 +0200 Subject: [Chimera-users] Volume viewer negative isosurface Message-ID: Hi, I'm using Chimera 1.2509 for X11 on a G4 iBook running OSX.4.11 I have a problem with Volume Viewer to visualize an electrostatic potential map calculated with APBS. The same potential map can be used without trouble to color a molecular surface. The problem is that when I try to set a negative isosurface to a negative value, the box that contains map also gets colored, making the scene unclear. I'm attaching a picture to illustrate this effect. I have tried to change several settings but so far unsuccessfully... Thanking you in advance for your help, Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en libert? Dans les jardins mal fr?quent?s! Georges Brassens -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VV.png Type: image/png Size: 22238 bytes Desc: not available URL: From cardoneg at mail.nih.gov Mon Jun 2 09:18:25 2008 From: cardoneg at mail.nih.gov (Giovanni Cardone) Date: Mon, 2 Jun 2008 12:18:25 -0400 Subject: [Chimera-users] How to define a center of rotation when applying a symmetry Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13@mail.nih.gov> Hi, I would like to apply a rotation to a pdb model, in order to place copies of it in equivalent symmetry points (icosahedral symmetry). I am not sure I understand all the different coordinate systems in chimera, but digging into the program code, I was able to write the following script. I am not sure it is the best way to do it, and obviously at the moment it does not work properly, because I am not specifying the center of rotation. With respect to the coordinates of the pdb model, I know the center of symmetry, let's say (161,161,161), but I don't know how to impose it. I tried to assign these coordinates to the parameter 'cofr', but the result does not change. Does anyone know how to apply, inside a script, a rotation matrix around a given point? Any other feedback on the correctness of the script is very welcome. Thank you. Giovanni ############################################### from chimera import openModels, Point from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') for rmat in icomats: xf = chimera_xform(rmat) m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = xf # set rotation ############################################### ============================================= Giovanni Cardone Laboratory of Structural Biology Research National Institutes of Health 50 South Drive (Building 50), Room 1511 Bethesda, MD 20892-8025 USA Tel: (301) 451-8247 FAX: (301) 480-7629 Giovanni_Cardone at nih.gov ============================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jun 2 09:28:02 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Jun 2008 09:28:02 -0700 Subject: [Chimera-users] Volume viewer negative isosurface In-Reply-To: References: Message-ID: Hi Miguel, In the Volume Viewer menu, choose "Features... Surface and Mesh options" to show several additional options on the main dialog. Turn off the one at the bottom, "Cap high values at box faces" - that will get rid of the red box. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From fglaser at technion.ac.il Mon Jun 2 03:38:02 2008 From: fglaser at technion.ac.il (Fabian Glaser) Date: Mon, 02 Jun 2008 13:38:02 +0300 Subject: [Chimera-users] problem with opengl glx kubuntu Message-ID: <4843CD8A.6090904@technion.ac.il> Hi, I installed a new version of chimera in kubuntu,and after a while, I started to get the following error when I click chimera: "Missing opengl windowing protocol (glx)" I am using kubuntu version: Linux 2.6.24-16-generic #1 SMP UTC 2008 i686 GNU/Linux nvidia and nvidia-glx are updated and installed. Any help will be highly appreciated. Best, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser at tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396 From goddard at cgl.ucsf.edu Mon Jun 2 11:29:32 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 11:29:32 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> Message-ID: <48443C0C.1010304@cgl.ucsf.edu> Hi Glenn, I compared the molecule rendering speed with Mac X11 and Mac Aqua Chimera snapshots (version 1.2524) and found them to be the same on an Intel Mac PowerBook with Radeon X1600 graphics and on a Power Mac G5 with Radeon ATI 9800 pro graphics. Here are scores for the G5 system Aqua Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 59.8 59.8 3.4 3.7 11.1 6.0 13.4 X11 Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 70.8 86.3 3.4 3.7 9.4 5.9 14.9 (The aqua values are clamped to my display refresh of 60 Hz.) You could try this on your system using Tools / Utilities / Benchmark. You can click the "Show individual test controls" checkbutton and press the "Molecule" button to just run the molecule tests. If the numbers do come out much different for X11 versus Aqua could you use Help / Report A Bug... to send us the numbers? Using that dialog will send us the technical specs for your graphics. Tom From pett at cgl.ucsf.edu Mon Jun 2 11:52:55 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 2 Jun 2008 11:52:55 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> Message-ID: Hi Glenn, Did you have the Model Panel open while moving the molecule? We have found that due to an underlying bug in the Aqua versions of some windowing libraries, performance can be heavily impacted if the Model Panel is being displayed (as well as other tools that use the same kind of table as the Model Panel, namely: Axes, ModBase, ViewDock, Rotamers, and CASTp). --Eric On Jun 1, 2008, at 8:13 PM, Glenn Millhauser wrote: > Hi Folks, > I just saw the mac aqua version at the download site and decided > to give it a try. Layout looks terrific. However, it seems to move > molecules much more slowly than the X windows version. I'm running on > a macbook (intel) with inherent limited graphics capabilities, so > perhaps that's the problem. Any comments? > thanks, > g > > > Glenn Millhauser > Department of Chemistry & Biochemistry > UC Santa Cruz > Santa Cruz, CA 95064 > > 831 459 2176 voice > 831 459 2935 fax > 831 566 3337 cell > > glennm at chemistry.ucsc.edu > http://chemistry.ucsc.edu/~glennm > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From gregc at cgl.ucsf.edu Mon Jun 2 11:58:10 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 2 Jun 2008 11:58:10 -0700 (PDT) Subject: [Chimera-users] problem with opengl glx kubuntu In-Reply-To: <4843CD8A.6090904@technion.ac.il> References: <4843CD8A.6090904@technion.ac.il> Message-ID: On Mon, 2 Jun 2008, Fabian Glaser wrote: > Hi, > > I installed a new version of chimera in kubuntu,and after a while, I > started to get the following error when I click chimera: > > "Missing opengl windowing protocol (glx)" > > I am using kubuntu version: > Linux 2.6.24-16-generic #1 SMP UTC 2008 i686 GNU/Linux > > nvidia and nvidia-glx are updated and installed. > > Any help will be highly appreciated. > > Best, > > Fabian This is probably due to a missing OpenGL package. Make sure that the libgl1-mesa-dri and libgl1-mesa-glx packages are installed. There's a chance that you will then need to reinstall the nvidia packages. - Greg From jkhilmer at gmail.com Mon Jun 2 13:23:22 2008 From: jkhilmer at gmail.com (Jonathan Hilmer) Date: Mon, 2 Jun 2008 14:23:22 -0600 Subject: [Chimera-users] rotation matrices around a given center (Chimera-users Digest, Vol 62, Issue 3) Message-ID: <81277ce10806021323l29ccff4cted0525b423764bb@mail.gmail.com> I haven't tried it out, but it looks like all you have to do is apply a transformation to your model before you apply the set of rotations. You could create a set of matrices to do it all in one step, but that's more trouble than it's worth. Something like this should work: Jonathan ############################################### from chimera import openModels from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') centerRot = (161.,161.,161.) tMat = ((1.0,0.0,0.0,-centerRot[0]), (0.0,1.0,0.0,-centerRot[1]), (0.0,0.0,1.0,-centerRot[2])) for rmat in icomats: m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = chimera_xform(tMat) # set translation to for center of rotation offset m.openState.xform = chimera_xform(rmat) # set rotation ############################################### On Mon, Jun 2, 2008 at 1:00 PM, wrote: > 1. How to define a center of rotation when applying a symmetry > (Giovanni Cardone) > 2. Re: Volume viewer negative isosurface (Elaine Meng) > 3. problem with opengl glx kubuntu (Fabian Glaser) > 4. Re: OS X aqua version (Thomas Goddard) > 5. Re: OS X aqua version (Eric Pettersen) > 6. Re: problem with opengl glx kubuntu (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Jun 2008 12:18:25 -0400 > From: Giovanni Cardone > Subject: [Chimera-users] How to define a center of rotation when > applying a symmetry > To: chimera-users at cgl.ucsf.edu > Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13 at mail.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I would like to apply a rotation to a pdb model, in order to place > copies of it in equivalent symmetry points (icosahedral symmetry). > I am not sure I understand all the different coordinate systems in > chimera, but digging into the program code, I was able to write the > following script. > I am not sure it is the best way to do it, and obviously at the > moment it does not work properly, because I am not specifying the > center of rotation. > With respect to the coordinates of the pdb model, I know the center > of symmetry, let's say (161,161,161), but I don't know how to impose it. > I tried to assign these coordinates to the parameter 'cofr', but the > result does not change. > Does anyone know how to apply, inside a script, a rotation matrix > around a given point? > Any other feedback on the correctness of the script is very welcome. > > Thank you. > > Giovanni > > > > ############################################### > > from chimera import openModels, Point > > from PDBmatrices import chimera_xform > > from Icosahedron import icosahedral_symmetry_matrices > > > icomats = icosahedral_symmetry_matrices(orientation = '222r') > > > for rmat in icomats: > > xf = chimera_xform(rmat) > > m, = openModels.open('/dummy/dummy.pdb') # open a copy of the > model > > m.openState.xform = xf # set rotation > > ############################################### > > > > > ============================================= > Giovanni Cardone > Laboratory of Structural Biology Research > National Institutes of Health > 50 South Drive (Building 50), Room 1511 > Bethesda, MD 20892-8025 USA > > Tel: (301) 451-8247 > FAX: (301) 480-7629 > Giovanni_Cardone at nih.gov > ============================================= From e.orlova at mail.cryst.bbk.ac.uk Mon Jun 2 13:16:34 2008 From: e.orlova at mail.cryst.bbk.ac.uk (Elena Orlova) Date: Mon, 02 Jun 2008 21:16:34 +0100 Subject: [Chimera-users] fit correlation Message-ID: <48445522.8040002@mail.cryst.bbk.ac.uk> Dear Chimera team, I have some troubles in getting numbers of the quality of the atomic structure fit into EM map. I wonder if you can give me directions where I can find the quantitative assessment of such fit? Do you have something like Cross Correlation Coeficient or R factor, or any other statistical test ? many thanks in advance. Elena -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Elena Orlova Dept. of Crystallography Tel: (+44) (0)20 7631 6845 Birkbeck College Fax: (+44) (0)20 7631 6803 University of London Malet Street London WC1E 7HX UK e-mail: e.orlova at mail.cryst.bbk.ac.uk From glennm at chemistry.ucsc.edu Mon Jun 2 13:44:14 2008 From: glennm at chemistry.ucsc.edu (glenn millhauser) Date: Mon, 2 Jun 2008 13:44:14 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <48443C0C.1010304@cgl.ucsf.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> Message-ID: <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> Hi Tom and Eric, I ran the benchmarks on my macbook and sent the results to Help (and included below). From my untrained eye, it looks as though there are performance differences. From the user perspective, as I noted in the previous email, rotating the molecule in the aqua version using the laptop feels jerky. However, I also did benchmarks on my imac, fairly new one with intel dual 2.8 GHz processors, and they are much closer to each other. These were also forwarded through Help. I did not have the Model Panel open. Hope this helps. all the best, g macbook dual intel gma950 graphics aqua Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 32.5 14.0 3.0 2.8 9.8 1.5 27.8 X11 1F4H (33805): 141.0 56.0 5.0 5.0 73.0 3.0 31.0 iMac dual intel ATI,RadeonHD2600 graphics aqua Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 60.5 60.2 5.5 5.5 15.4 8.6 36.3 X11 1F4H (33805): 8.0 102.0 3.0 3.0 8.0 4.0 39.0 On Jun 2, 2008, at 11:29 AM, Thomas Goddard wrote: > Hi Glenn, > > I compared the molecule rendering speed with Mac X11 and Mac Aqua > Chimera snapshots (version 1.2524) and found them to be the same on > an Intel Mac PowerBook with Radeon X1600 graphics and on a Power Mac > G5 with Radeon ATI 9800 pro graphics. Here are scores for the G5 > system > > Aqua > Molecule 1f4h (33805 atoms): > Null Wire Stick BStick Ribbon Sphere Ops > 59.8 59.8 3.4 3.7 11.1 6.0 13.4 > > X11 > Molecule 1f4h (33805 atoms): > Null Wire Stick BStick Ribbon Sphere Ops > 70.8 86.3 3.4 3.7 9.4 5.9 14.9 > > (The aqua values are clamped to my display refresh of 60 Hz.) You > could try this on your system using Tools / Utilities / Benchmark. > You can click the "Show individual test controls" checkbutton and > press the "Molecule" button to just run the molecule tests. > > If the numbers do come out much different for X11 versus Aqua could > you use Help / Report A Bug... to send us the numbers? Using that > dialog will send us the technical specs for your graphics. > > Tom > > Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jun 2 13:51:04 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 13:51:04 -0700 Subject: [Chimera-users] How to define a center of rotation when applying a symmetry In-Reply-To: <919BC0E8-98BD-4F1A-97DD-13F048B71C13@mail.nih.gov> References: <919BC0E8-98BD-4F1A-97DD-13F048B71C13@mail.nih.gov> Message-ID: <48445D38.2010507@cgl.ucsf.edu> Hi Giovanni, To convert icosahedron rotation matrices that act about origin 0,0,0 to instead use a different center of rotation (cx,cy,cz) you would first shift by -cx,-cy,-cz then apply the rotation then shift by cx,cy,cz. I've attached an example script. Note that "a.premultiply(b)" means to multiply b to the left of "a" which means that b acts after a. Note that the Chimera Multiscale dialog (Tools / Higher-Order Structure / Multiscale) will apply icosahedral symmetry and load the coordinates (use select all, then style show wire). It doesn't allow you to change the icosahedron origin to something different from 0,0,0 but you could modify your PDB coordinates to make that the origin. Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: icospdb.py URL: From goddard at cgl.ucsf.edu Mon Jun 2 14:20:16 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 14:20:16 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> Message-ID: <48446410.9030002@cgl.ucsf.edu> Hi Glenn, Your benchmark numbers on the MacBook with Intel GMA950 graphics suggest molecule display is 2-3x slower with Aqua Chimera vs X11 Chimera. But it appears you are using an older X11 Chimera because the ribbon benchmark frame rate is 73 which is too high to be right and older X11 Chimera versions gave incorrect high ribbon frame rates. I changed the benchmark code recently because the older Chimera versions gave inflated frame rates because they did not actually draw to the screen. If you tested the current X11 snapshot you will get smaller frame rates reported although actual performance has not changed. On your iMac with Radeon HD2600 graphics the Aqua version appears to be about 2x faster than the X11 version. That is unexpected too. I don't know why the Aqua and X11 OpenGL performance is so different on the machines you tested. Tom glenn millhauser wrote: > Hi Tom and Eric, > I ran the benchmarks on my macbook and sent the results to Help (and > included below). From my untrained eye, it looks as though there are > performance differences. From the user perspective, as I noted in the > previous email, rotating the molecule in the aqua version using the > laptop feels jerky. However, I also did benchmarks on my imac, fairly > new one with intel dual 2.8 GHz processors, and they are much closer to > each other. These were also forwarded through Help. > I did not have the Model Panel open. > Hope this helps. > all the best, > g > > > > macbook dual intel gma950 graphics > > aqua > Molecule 1f4h (33805 atoms): > Null Wire Stick BStick Ribbon Sphere Ops > 32.5 14.0 3.0 2.8 9.8 1.5 27.8 > > X11 > 1F4H (33805): > 141.0 56.0 5.0 5.0 73.0 3.0 31.0 > > > > iMac dual intel ATI,RadeonHD2600 graphics > > aqua > Molecule 1f4h (33805 atoms): > Null Wire Stick BStick Ribbon Sphere Ops > 60.5 60.2 5.5 5.5 15.4 8.6 36.3 > > X11 > 1F4H (33805): > 8.0 102.0 3.0 3.0 8.0 4.0 39.0 > > > > On Jun 2, 2008, at 11:29 AM, Thomas Goddard wrote: > >> Hi Glenn, >> >> I compared the molecule rendering speed with Mac X11 and Mac Aqua >> Chimera snapshots (version 1.2524) and found them to be the same on an >> Intel Mac PowerBook with Radeon X1600 graphics and on a Power Mac G5 >> with Radeon ATI 9800 pro graphics. Here are scores for the G5 system >> >> Aqua >> Molecule 1f4h (33805 atoms): >> Null Wire Stick BStick Ribbon Sphere Ops >> 59.8 59.8 3.4 3.7 11.1 6.0 13.4 >> >> X11 >> Molecule 1f4h (33805 atoms): >> Null Wire Stick BStick Ribbon Sphere Ops >> 70.8 86.3 3.4 3.7 9.4 5.9 14.9 >> >> (The aqua values are clamped to my display refresh of 60 Hz.) You >> could try this on your system using Tools / Utilities / Benchmark. >> You can click the "Show individual test controls" checkbutton and >> press the "Molecule" button to just run the molecule tests. >> >> If the numbers do come out much different for X11 versus Aqua could >> you use Help / Report A Bug... to send us the numbers? Using that >> dialog will send us the technical specs for your graphics. >> >> Tom >> >> > > > > Glenn L. Millhauser > > Department of Chemistry & Biochemistry > > UC Santa Cruz > > Santa Cruz, CA 95064 From goddard at cgl.ucsf.edu Mon Jun 2 14:23:59 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 14:23:59 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> Message-ID: <484464EF.6010307@cgl.ucsf.edu> Having the model panel open did not effect frame rate much (down about 10% on aqua with 1f4h stick) on Radeon 9800 pro graphics. Model panel is using CPU while the rendering should be mostly on the GPU. Tom From goddard at cgl.ucsf.edu Mon Jun 2 14:47:07 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 14:47:07 -0700 Subject: [Chimera-users] fit correlation In-Reply-To: <48445522.8040002@mail.cryst.bbk.ac.uk> References: <48445522.8040002@mail.cryst.bbk.ac.uk> Message-ID: <48446A5B.3050302@cgl.ucsf.edu> Hi Elena, Cross correlation coefficients are frequently used to describe the quality of fit of an atomic model in an EM map. Other measures such as the number of atoms at positions with density above 1 sigma are also used. The Chimera fit in map tool in recent Chimera versions (snapshot or daily build since Feb 20, 2008) can report correlation coefficient. Correlation measures the agreement between a simulated map at a specified resolution with the experimental map. You enter that resolution in the fit map dialog in the options panel. Also turn on "use map simulated from atoms". Then press the "Update" button on the line of the dialog that says "correlation" and "average map value". The fitting also reports the number of atoms lying outside the displayed map contour surface. You can set that to 1 sigma or 2 sigma or a value of your choosing. To figure out the standard deviation of the map values use volume dialog menu Tools / Volume Mean, SD, RMS. More fit map documentation is in the manual http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html The volume guide also has info but is not up to date with the latest Chimera features: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmap Tom From jparmache at lmb.uni-muenchen.de Mon Jun 2 14:03:24 2008 From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache) Date: Mon, 02 Jun 2008 23:03:24 +0200 Subject: [Chimera-users] OS X aqua version In-Reply-To: <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> Message-ID: <4844601C.7010003@lmb.uni-muenchen.de> Hello, I used Chimera Aqua some time ago, I tried it for two-three days on a Macbook Pro with Leopard (at that time 10.5.2). I have to say that it worked for five minutes at maximum before it crashed. The same situation with a new Mac Pro. Then I used a X11 version, which is more stable, but also has a tendency to crash (sporadically). The biggest trouble was to load more than 8 volumes. On a Mac it was extremely slow and usually crashing. On a similarly configured, but Linux-based machine there were no problems encountered and it was clearly much faster. Good luck with it, thanks for all the effort! Best regards, Jean-Paul Armache From goddard at cgl.ucsf.edu Mon Jun 2 15:16:21 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 15:16:21 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <4844601C.7010003@lmb.uni-muenchen.de> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> <4844601C.7010003@lmb.uni-muenchen.de> Message-ID: <48447135.40303@cgl.ucsf.edu> Hi Jean-Paul, Thanks for the info. Chimera crashes that occur just on specific machines (mac, linux, windows) are almost always graphics driver problems and there is little the Chimera developers can do about those. Some crashes may also be related to loading large volume data sets (totaling > 1 Gbyte) using 32-bit versions of Chimera. There simply isn't enough addressable memory in the 32-bit address space (only 4 Gbytes used by libraries, os, stack, ...). We try to catch large memory allocation failures so they do not cause a crash but many allocations are done by the >30 third-party libraries we use. We plan on making a 64-bit Mac Chimera but it is not ready yet. A 64-bit version is available for Linux. The most common Chimera crash scenario is calculating solvent excluded molecular surfaces (menu entry Actions / Surface / show) which occurs on all platforms (mac, linux, windows) in Chimera production release 1.2470 (Nov 2007) but not in recent snapshots and daily builds. Tom From gregc at cgl.ucsf.edu Mon Jun 2 15:30:00 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 2 Jun 2008 15:30:00 -0700 (PDT) Subject: [Chimera-users] OS X aqua version In-Reply-To: <4844601C.7010003@lmb.uni-muenchen.de> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> <4844601C.7010003@lmb.uni-muenchen.de> Message-ID: The current Chimera Aqua daily builds are much better and more stable than the older Aqua builds. We are getting reports that the new Aqua version is slower than the X11 version on Macs with Intel graphics, and comparable speeds on Macs with ATI or NVidia graphics. We are spending more time on the Aqua builds and hope to resolve that and other issues soon. With a little bit of luck, we will replace the Mac X11 version with the Aqua version by the next production release. And if not the next one, the one after that. So please try out a daily build at , I think you will be pleasantly suprised. Greg Couch UCSF Computer Graphics Lab On Mon, 2 Jun 2008, Jean-Paul Armache wrote: > Hello, > > I used Chimera Aqua some time ago, I tried it for two-three days on a > Macbook Pro with Leopard (at that time 10.5.2). I have to say that it > worked for five minutes at maximum before it crashed. The same situation > with a new Mac Pro. Then I used a X11 version, which is more stable, but > also has a tendency to crash (sporadically). The biggest trouble was to > load more than 8 volumes. On a Mac it was extremely slow and usually > crashing. On a similarly configured, but Linux-based machine there were > no problems encountered and it was clearly much faster. > > Good luck with it, thanks for all the effort! > > Best regards, > > Jean-Paul Armache > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jparmache at lmb.uni-muenchen.de Mon Jun 2 15:37:25 2008 From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache) Date: Tue, 03 Jun 2008 00:37:25 +0200 Subject: [Chimera-users] OS X aqua version In-Reply-To: References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> <4844601C.7010003@lmb.uni-muenchen.de> Message-ID: <48447625.7060306@lmb.uni-muenchen.de> Thank you very much, I'll give it a go! I have a question in addition - is it somehow possible to make a difference map of two volumes using Chimera ? Best regards, Jean-Paul Armache From I.moustafa at psu.edu Mon Jun 2 15:42:09 2008 From: I.moustafa at psu.edu (Ibrahim Moustafa) Date: Mon, 02 Jun 2008 18:42:09 -0400 Subject: [Chimera-users] Chimera-users Digest, Vol 61, Issue 29 In-Reply-To: Message-ID: Dear Chimera developers, Many many thanks for your great help. The script provided by Eric Peterson did the job very easily. Many thanks, Ibrahim On 5/31/08 12:54 PM, "chimera-users-request at cgl.ucsf.edu" wrote: > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Plotting modes from PCA onto the structure (Eric Pettersen) > 2. Re: add atom type in MMTK (Elaine Meng) > 3. Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008 > (Bruce D. Ray) > 4. Re: Import error with chimera-1.2509-osx_x11.dmg, May 01, > 2008 (Randy Heiland) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 May 2008 15:15:02 -0700 > From: Eric Pettersen > Subject: Re: [Chimera-users] Plotting modes from PCA onto the > structure > To: Ibrahim Moustafa > Cc: "chimera-users at cgl.ucsf.edu" > Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02 at cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Ibrahim, > As Bala pointed out, IED in VMD may well be the way to go for now. > Also, the "porcupine needles" can be accomplished with BILD, as > Elaine mentioned. I've attached a script that reads a file of > displacements and applies them to the CAs of a structure. Obviously, > there should be as many lines in the file as there are CAs in the > structure. Each line should consist of 3 numbers, the X, Y, and Z > displacements. Since the script only modifies the CAs, you should > probably only be displaying the CAs -- the rest of the structure will > be out of position. You may need to edit the script to put in the > name of the file with the displacements, otherwise it will use a file > named "displacements" in the same directory as the script. You run > the script by simply opening it with File...Open or the "open" command. > We are working on closer coordination between Amber and Chimera, > with the help of Wei Zhang. He has already contributed one tool, > Solvate, which uses sleap to solvate a system. Solvate is available > in daily builds. In the short term he hopes to write tools to add > ions and write parmtop files. Longer term goals are to include the > minimization and MD functionality of NAB, and ptraj trajectory analysis. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > ? > On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote: > >> Dear Chimera support, >> >> I hope Chimera (with supporting scripts) can be used to make the >> figures described below: >> >> I want to make a figure to display the different modes >> obtained from PCA analysis (on MD trajectory obtained from AMBER) >> as different snapshots of the structure under study. >> >> To explain it more, I have a file containing the displacement in >> X, Y, Z for each C-alpha in a column format. Is there a simple >> script that can add the displacement vectors to the x, y, z >> coordinates of the original structure? So the new structure with >> modified C-alpha can be plotted representing a particular mode in >> Chimera. >> >> Also, related to the same point, is it possible to represent the >> vectors at each C-alpha as arrows/porcupine needle in Chimera? >> >> P.S. It would be great if Chimera can add features to represent >> these kind of figures from PTRAJ output or similar analysis >> programs used in MD simulation. Especially, Chimera support >> analysis of AMBER trajectory. >> >> Thanks in advance for your great support, >> Ibrahim >> >> >> -- >> Ibrahim M. Moustafa, Ph.D. >> Biochemistry and Molecular Biology Dept. >> 201 Althouse Lab., University Park, >> Pennsylvania State University >> PA 16802 >> >> Tel. (814) 863-8703 >> Fax (814) 865-7927 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/ > attachment-0002.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: pca.py > Type: text/x-python-script > Size: 682 bytes > Desc: not available > Url : > http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/ > pca-0001.bin > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/ > attachment-0003.html > > ------------------------------ > > Message: 2 > Date: Fri, 30 May 2008 17:34:49 -0700 > From: Elaine Meng > Subject: Re: [Chimera-users] add atom type in MMTK > To: Lionel Nauton > Cc: chimera-users at cgl.ucsf.edu > Message-ID: <7F83CFB3-19E1-4C36-9C28-5BE5B55DB005 at cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hello Lionel, > Are you trying to run "addcharge" or "minimize"? > > If "addcharge" to calculate partial charges on some Pt complex (e.g. > cisplatin or carboplatin): > > Nonstandard residues are sent to Antechamber, but that program is > only meant to be used on organic molecules (C,H,O,N,S,P,F,Cl,Br,I), > not metal complexes or inorganic species. See the antechamber site: > http://amber.scripps.edu/antechamber/tips.html > I think you have to use some other program that can handle metal > complexes to derive partial charges. I don't think it is possible to > simply edit some antechamber data files to get it to work on such > compounds. > > If "minimize" and you just wanted to treat the Pt as a monatomic ion > with integer charge: > > I had thought it possible to add a metal ion type by editing a > parameter file. However, I have not been successful at minimizing a > structure with the "new" type even when the file appears to include > the necessary parameters. Maybe there is an additional step that I > don't know about. So currently my best answer is that it is not > possible, but if we find a way, we will send another message. (I may > be wrong given my lack of success, but I think the relevant parameter > file within the Chimera installation is lib/python2.5/site-packages/ > MMTK/ForceFields/amber/amber_parm99 ) > > Sorry about that, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > On May 30, 2008, at 5:52 AM, Lionel Nauton wrote: > >> hello everybody >> this is my first question since I use chimera, more than 3 years ago, >> and I would like to know >> if is it possible to add atom type in the MMTK basis set ? >> I actually work on a molecule containing platinium, and I can't run >> mopac >> because there is no description. >> I'm looking for some description files , and I found this : >> /antechamber/dat/antechamber/*****.DAT >> which is the good one and which is the way to modify it ? >> thank's for your answer and excuse me for my english..... >> best regards >> > > > ------------------------------ > > Message: 3 > Date: Sat, 31 May 2008 08:50:53 -0700 (PDT) > From: "Bruce D. Ray" > Subject: [Chimera-users] Import error with > chimera-1.2509-osx_x11.dmg, May 01, 2008 > To: chimera-users at cgl.ucsf.edu > Message-ID: <640107.47762.qm at web35804.mail.mud.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > I have a Mac G4 PPC running OS X 10.3.9 on which > previous versions of chimera have run without > incident. > I installed chimera-1.2509 of May 01, 2008 after > removing the chimera-1.2492 of Feb 11, 2008 I had been > using. However, when I attempted to run > chimera-1.2509 > it did not start and the following error messages were > written to the console.log file accessible by > console.app rather than to the X-terminal: > > Traceback (most recent call last): > > File > "/Applications/Chimera.app/Contents/Resources/share/__main__.py", > line 65, in > > value = chimeraInit.init(sys.argv) > > File > "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", > line 279, in init > > import chimera > > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 15, in > > from _chimera import * > > ImportError: dynamic module does not define init > function (init_chimera) > > > > This appears to be specific to the Mac OS X version > as the Windows version of chimera-1.2509 works. > Obviously, I removed chimera-1.2509 from the Mac and > reinstalled chimera-1.2492 of Feb 11, 2008 which does > work on this Mac. > > > Sincerely, > > > From goddard at cgl.ucsf.edu Mon Jun 2 15:45:48 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jun 2008 15:45:48 -0700 Subject: [Chimera-users] OS X aqua version In-Reply-To: <48447625.7060306@lmb.uni-muenchen.de> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> <4844601C.7010003@lmb.uni-muenchen.de> <48447625.7060306@lmb.uni-muenchen.de> Message-ID: <4844781C.6040103@cgl.ucsf.edu> Hi Jean-Paul, Chimera cannot subtract two maps. Is that what you had in mind? or is it more complicated requiring determining equivalent normalizations for the maps? Do you have in mind that the maps have identical grids, or would one map need to be interpolated? There's underlying Python code to do all this in Chimera but no user interface. Tom From jparmache at lmb.uni-muenchen.de Mon Jun 2 15:53:47 2008 From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache) Date: Tue, 03 Jun 2008 00:53:47 +0200 Subject: [Chimera-users] OS X aqua version In-Reply-To: <4844781C.6040103@cgl.ucsf.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> <48443C0C.1010304@cgl.ucsf.edu> <9B49ABFB-40BC-4372-9964-046356209D27@hydrogen.ucsc.edu> <4844601C.7010003@lmb.uni-muenchen.de> <48447625.7060306@lmb.uni-muenchen.de> <4844781C.6040103@cgl.ucsf.edu> Message-ID: <484479FB.1040008@lmb.uni-muenchen.de> Actually I had in mind a simple subtraction of two aligned maps - there is no need for interpolation. However, if it is still inexistant, maybe in some time I will try to figure out how to do it. Best regards, Jean-Paul Armache From dchen at caltech.edu Mon Jun 2 21:02:07 2008 From: dchen at caltech.edu (David Chenoweth) Date: Mon, 2 Jun 2008 21:02:07 -0700 Subject: [Chimera-users] making a plane through the atoms of a ring and Distance measurements Message-ID: <8DF0A196-EE94-4FDE-9226-42D959D44ACA@caltech.edu> Dear Chimera team, I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen at caltech.edu ********************************************** From hsosa at aecom.yu.edu Tue Jun 3 06:34:13 2008 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Tue, 03 Jun 2008 09:34:13 -0400 Subject: [Chimera-users] fit correlation In-Reply-To: <48446A5B.3050302@cgl.ucsf.edu> References: <48445522.8040002@mail.cryst.bbk.ac.uk> <48446A5B.3050302@cgl.ucsf.edu> Message-ID: <48454855.6000806@aecom.yu.edu> One thing I am curious about it, when calculating correlation values, is how to deal with cases in which the pdb atomic structure of only one asymmetric unit is fitted into an electron density corresponding to more than one asymmetric unit. Is there an easy way to exclude from the calculation the densities corresponding to the extra asymmetric units. Thanks Hernando Thomas Goddard wrote: > Hi Elena, > > Cross correlation coefficients are frequently used to describe the > quality of fit of an atomic model in an EM map. Other measures such as > the number of atoms at positions with density above 1 sigma are also used. > > The Chimera fit in map tool in recent Chimera versions (snapshot or > daily build since Feb 20, 2008) can report correlation coefficient. > Correlation measures the agreement between a simulated map at a > specified resolution with the experimental map. You enter that > resolution in the fit map dialog in the options panel. Also turn on > "use map simulated from atoms". Then press the "Update" button on the > line of the dialog that says "correlation" and "average map value". > > The fitting also reports the number of atoms lying outside the > displayed map contour surface. You can set that to 1 sigma or 2 sigma > or a value of your choosing. To figure out the standard deviation of > the map values use volume dialog menu Tools / Volume Mean, SD, RMS. > > More fit map documentation is in the manual > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html > > The volume guide also has info but is not up to date with the latest > Chimera features: > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmap > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From gregc at cgl.ucsf.edu Tue Jun 3 12:54:15 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 3 Jun 2008 12:54:15 -0700 (PDT) Subject: [Chimera-users] making a plane through the atoms of a ring and Distance measurements In-Reply-To: <8DF0A196-EE94-4FDE-9226-42D959D44ACA@caltech.edu> References: <8DF0A196-EE94-4FDE-9226-42D959D44ACA@caltech.edu> Message-ID: On Mon, 2 Jun 2008, David Chenoweth wrote: > Dear Chimera team, > > I would like to make a plane through the atoms of an aromatic ring and > then measure a distance from an atom to the ring centroid. I would > also like to measure the angle between the normal to the ring plane > and the line joining the centroid and the atom I am measuring from. It > would also be nice if I could specify the dimensions, color, and > transparency of the plane. In addition it would be great to be able to > make multiple planes through atoms, select and color them separately, > and measure the angles at the intersection of the planes. Just > wondering if there is a way to do this with Chimera. > > Thanks in advance, > Dave This sort of thing currently requires writing Python code. For example, if you selected a ring by hand, the following code computes the plane. The plane's origin is the centroid of the atoms: from chimera import selection, Plane atoms = selection.currentAtoms() plane = Plane([a.coord() for a in atoms]) To calculate the plane equation, chimera uses Newell's method, so points should be given in ring order, but the ring doesn't have to be convex. If you computed a least-squared fit plane, the answer would be slightly different. To measure the angle between two planes, just calculate the angle between their normals (arccos of the (normalized) dot product). To visualize the results, I'd recommend creating a SurfaceModel from the _surface module. Since much of chimera is implemented in Python, "example" code that uses chimera Planes and SurfaceModels can be found the Python modules in the CHIMERA/share directory. Specifically, the NucleicAcids and GraspSurface modules. To get started programming chimera with Python, please look at the tutorials in the Chimera Programmer's Guide, . And if you have any programming questions, please ask them on the chimera developer's mailing list, chimera-dev at cgl.ucsf.edu. Good luck, Greg Couch UCSF Computer Graphics Lab From goddard at cgl.ucsf.edu Tue Jun 3 13:19:51 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 03 Jun 2008 13:19:51 -0700 Subject: [Chimera-users] fit correlation In-Reply-To: <48454855.6000806@aecom.yu.edu> References: <48445522.8040002@mail.cryst.bbk.ac.uk> <48446A5B.3050302@cgl.ucsf.edu> <48454855.6000806@aecom.yu.edu> Message-ID: <4845A767.1090502@cgl.ucsf.edu> Hi Hernando, If the fit in map option to "Use only data above contour level from first map" is enabled (it is by default) then the correlation is calculated using only grid points within the displayed contour level of the first map. If you turn that option off, then the correlation uses all grid points of the first map. If the second map contains other structures (e.g. other asymmetric units) within the bounds of the first map box, then using all grid points will give a lower correlation due to the mismatch between the maps in those regions. So it is usually best to use the default setting and set the contour level of the first map low enough to include all grid points where the correlation is desired. Tom hsosa at aecom.yu.edu wrote: > One thing I am curious about it, when calculating correlation values, > is how to deal with cases in which the pdb atomic structure of only > one asymmetric unit is fitted into an electron density corresponding > to more than one asymmetric unit. Is there an easy way to exclude > from the calculation the densities corresponding to the extra > asymmetric units. > > Thanks > > Hernando > > > > > > Thomas Goddard wrote: >> Hi Elena, >> >> Cross correlation coefficients are frequently used to describe the >> quality of fit of an atomic model in an EM map. Other measures such >> as the number of atoms at positions with density above 1 sigma are >> also used. >> >> The Chimera fit in map tool in recent Chimera versions (snapshot >> or daily build since Feb 20, 2008) can report correlation >> coefficient. Correlation measures the agreement between a simulated >> map at a specified resolution with the experimental map. You enter >> that resolution in the fit map dialog in the options panel. Also >> turn on "use map simulated from atoms". Then press the "Update" >> button on the line of the dialog that says "correlation" and "average >> map value". >> >> The fitting also reports the number of atoms lying outside the >> displayed map contour surface. You can set that to 1 sigma or 2 >> sigma or a value of your choosing. To figure out the standard >> deviation of the map values use volume dialog menu Tools / Volume >> Mean, SD, RMS. >> >> More fit map documentation is in the manual >> >> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html >> >> >> The volume guide also has info but is not up to date with the latest >> Chimera features: >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmap >> >> >> Tom >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> > From pett at cgl.ucsf.edu Tue Jun 3 17:55:42 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Jun 2008 17:55:42 -0700 Subject: [Chimera-users] making a plane through the atoms of a ring and Distance measurements In-Reply-To: <8DF0A196-EE94-4FDE-9226-42D959D44ACA@caltech.edu> References: <8DF0A196-EE94-4FDE-9226-42D959D44ACA@caltech.edu> Message-ID: <74FD6418-9210-4F88-A6B0-E679A75A851B@cgl.ucsf.edu> Hi Dave, We want to make measurements of axes, centroids, and planes possible, and as the first step of that we have been working on axes. So planes/centroids will be coming, but I can't really guarantee when (there's still plenty of work left for axes!). So as Greg says, measuring planes/centroids has to be done using Python for now. Now, the fact that the Chimera Plane constructor requires the points in "ring order" (for now) is kind of a major PITA, so my suggestion is to do a singular value decomposition and take as the plane normal the cross product of the two largest eigenvectors. This is actually really easy. If you look at the axis() function of StructureMeasure/ __init__.py, it finds the centroid and does an SVD on a set of coordinates. The single largest eigenvector is the "axis" of those coordinates. You would use numpy.argsort to find the two eigenvectors with the largest eigenvalues, and numpy.cross to get the cross product. Some useful numpy docs are here: http://www.scipy.org/ Numpy_Example_List_With_Doc . The other thing to know is that to get a bunch of atoms (say from chimera.selection.currentAtoms()) into an Nx3 numpy array, you use the function chimera.numpyArrayFromAtoms. With the centroid and the normal, you would construct a chimera.Point and chimera.Vector. Then there is a chimera.Plane constructor that takes a Point and a Vector. There are a bunch of methods of Point, Vector, and Plane for measuring distances and angles, etc. You can see documentation for them by typing e.g. help (chimera.Vector) in the IDLE tool. So for instance, the distance from an atom to the centroid is atom.coord().distance(centroid). Some measurements, such as angle(), are only available as functions in the chimera module (so help(chimera) to see them). So the angle atom-centroid-normal is: chimera.angle(atom.coord() - centroid, normal) [the subtraction of two Points produced a Vector]. To show planes, you might want to construct BILD files/strings and open those: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 2, 2008, at 9:02 PM, David Chenoweth wrote: > Dear Chimera team, > > I would like to make a plane through the atoms of an aromatic ring and > then measure a distance from an atom to the ring centroid. I would > also like to measure the angle between the normal to the ring plane > and the line joining the centroid and the atom I am measuring from. It > would also be nice if I could specify the dimensions, color, and > transparency of the plane. In addition it would be great to be able to > make multiple planes through atoms, select and color them separately, > and measure the angles at the intersection of the planes. Just > wondering if there is a way to do this with Chimera. > > Thanks in advance, > Dave > > ********************************************** > David M. Chenoweth > California Institute of Technology > Division of Chemistry and Chemical Engineering > Mail Code: 164-30 > 1200 California Boulevard, 91125 Pasadena > California, USA > > Phone: 626-395-6074 > Email: dchen at caltech.edu > ********************************************** > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Jun 3 23:01:26 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 3 Jun 2008 23:01:26 -0700 (PDT) Subject: [Chimera-users] OS X aqua version In-Reply-To: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> References: <8ECF1F65-EA8C-4416-9265-F0D5F5C57589@chemistry.ucsc.edu> Message-ID: On Sun, 1 Jun 2008, Glenn Millhauser wrote: > Hi Folks, > I just saw the mac aqua version at the download site and decided > to give it a try. Layout looks terrific. However, it seems to move > molecules much more slowly than the X windows version. I'm running on > a macbook (intel) with inherent limited graphics capabilities, so > perhaps that's the problem. Any comments? So it turns out this is due to chimera asking the graphics to multisample each pixel to improve the image quality (it reduces the jagged edge effect, especially noticable on ribbons and surfaces). This was not implemented in Apple's X11 OpenGL, so we didn't have this problem before. Here are Chimera Aqua benchmark results for a MacBook 2Ghz Core Duo with Intel GMA 650 graphics running OS X 10.4.11: Volume benchmark scores surface mesh contour solid recolor 1 16 157 1 3 Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 29.8 7.5 1.6 1.4 4.3 0.3 26.3 And without multisampling: Volume benchmark scores surface mesh contour solid recolor 128 139 156 138 88 Molecule 1f4h (33805 atoms): Null Wire Stick BStick Ribbon Sphere Ops 72.2 41.8 14.1 14.1 26.5 10.2 26.7 So without multisampling, it's 6-100 times faster! Unfortunately, there's no way to give command line arguments when clicking on the chimera icon, so to turn off multisampling for now, you would need to start up a Terminal and type: ./Desktop/Chimera.app/Contents/Resources/bin/chimera --nomultisample That's assuming the Chimera.app is on your personal desktop. Or you could edit the Chimera.app/Contents/Resources/share/chimeraInit.py file so that nomultisample defaults to True instead of False on line 52. We will figure out an alternative solution that by default doesn't ask for multisampling for Intel motherboard graphics (same issue exists with Microsoft Windows). Greg Couch UCSF Computer Graphics Lab From bokcmho at ust.hk Thu Jun 5 02:17:25 2008 From: bokcmho at ust.hk (Maurice Ho) Date: Thu, 05 Jun 2008 17:17:25 +0800 Subject: [Chimera-users] coloring residues according to electrostatic force Message-ID: <4847AF25.6050806@ust.hk> How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho -------------- next part -------------- A non-text attachment was scrubbed... Name: bokcmho.vcf Type: text/x-vcard Size: 417 bytes Desc: not available URL: From mgochin at touro.edu Thu Jun 5 09:21:43 2008 From: mgochin at touro.edu (mgochin at touro.edu) Date: Thu, 5 Jun 2008 12:21:43 -0400 (EDT) Subject: [Chimera-users] Chimera - quantitative possibilities using surfnet? Message-ID: <20080605122143.APD59009@mail.touro.edu> I am wondering if it is possible to get numerical values for areas / volumes of molecular cavities and indentations drawn by surfnet in either the Interface or Selected Atoms mode. Any help is appreciated. - Miriam Gochin From meng at cgl.ucsf.edu Thu Jun 5 09:34:20 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Jun 2008 09:34:20 -0700 Subject: [Chimera-users] coloring residues according to electrostatic force In-Reply-To: <4847AF25.6050806@ust.hk> References: <4847AF25.6050806@ust.hk> Message-ID: <1D55729E-D282-4657-B0CC-EF28292760D4@cgl.ucsf.edu> On Jun 5, 2008, at 2:17 AM, Maurice Ho wrote: > How to color residues of a protein according to the electrostatic > potential map generated by APBS? I could only color the molecular > surface by loading the potential map. Please kindly advice. > Thanks and regards, > Maurice Ho Hi Maurice, First, map the potential values to the atoms (assign them as attributes). Then you can color the atoms by those attribute values. After you have opened the protein structure and APBS map, start "Values at Atom Positions" (under Tools... Volume Data). In that tool: - Choose the protein as the "Molecule" and the APBS map as the "Volume data." If you didn't open the map yet, you can open it now using the Browse button. - Click the Histogram button to assign the atom values, which also automatically starts the "Render by Attribute" tool. The new attribute will be named based on the APBS map file name but with "value_" stuck on the front. There will be a histogram of values with vertical colored bars. These bars or thresholds can be moved around, added or deleted with Ctrl-click, and their colors changed to control the color mapping. You can click Apply to perform the coloring but keep the dialog up for further adjustments. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#colors It is also possible to color by attribute value with the command "rangecolor" instead of the graphical interface. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html I hope this helps, Elaine From goddard at cgl.ucsf.edu Thu Jun 5 09:37:20 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 05 Jun 2008 09:37:20 -0700 Subject: [Chimera-users] Chimera - quantitative possibilities using surfnet? In-Reply-To: <20080605122143.APD59009@mail.touro.edu> References: <20080605122143.APD59009@mail.touro.edu> Message-ID: <48481640.7070604@cgl.ucsf.edu> Hi Miriam, You can use the Measure and Color Blobs tools to get areas and volumes of connected surface blobs produced by Surfnet. It is found under Tools / Surface&Binding Analysis. You'll need a newer version of Chimera than the production release. Get a daily build or snapshot: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html http://www.cgl.ucsf.edu/chimera/download.html#snapshots Tom From meng at cgl.ucsf.edu Thu Jun 5 09:52:37 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Jun 2008 09:52:37 -0700 Subject: [Chimera-users] Chimera - quantitative possibilities using surfnet? In-Reply-To: <48481640.7070604@cgl.ucsf.edu> References: <20080605122143.APD59009@mail.touro.edu> <48481640.7070604@cgl.ucsf.edu> Message-ID: <78D974F6-3F1D-4403-80B0-FB92C4489936@cgl.ucsf.edu> Tom already answered the question perfectly... I just wanted to mention a related feature: If your structure is in the CASTp database, you can get pre-computed pocket surface areas, volumes, etc. in a very convenient form within Chimera. This also requires a recent version of Chimera. The drawback is that not all structures are in the CASTp database. CASTp fetch is one of the options in File... Fetch by ID, or you can do it with the "open" command, e.g.: open castp:4enl or open castp:2gbp http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html Elaine On Jun 5, 2008, at 9:37 AM, Tom Goddard wrote: > Hi Miriam, > > You can use the Measure and Color Blobs tools to get areas and > volumes > of connected surface blobs produced by Surfnet. It is found under > Tools > / Surface&Binding Analysis. You'll need a newer version of Chimera > than > the production release. Get a daily build or snapshot: > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > http://www.cgl.ucsf.edu/chimera/download.html#snapshots > > > Tom > From pett at cgl.ucsf.edu Thu Jun 5 11:34:50 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 5 Jun 2008 11:34:50 -0700 Subject: [Chimera-users] Installing Chimera in Ubunty Hardy In-Reply-To: <1212130421.9096.6.camel@david-radiosun> References: <1212130421.9096.6.camel@david-radiosun> Message-ID: Hi David, In the terminal, go to the directory where the Chimera installer you downloaded is. Type "ls -l". You should see a list of the files in the directory. One of them (the installer) should be something like: -rwxr-xr-x 1 chimera staff 103907447 Jun 5 00:36 chimera-alpha- linux.exe This would be if you had downloaded today's daily build. If you had gotten the production release, the name would be chimera-1.2470- linux.exe instead of chimera-alpha-linux.exe. The big number in the middle of the line is the file size. Make sure it's the same as the size listed on the download page. The string of letters on the left is the "permissions" for the file. The last letter needs to be 'x' for it to be executable. If it's not, type "chmod +x ", then do "ls -l" again and check that it's executable. Now type "./". The installation should either start up or you get some kind of error message. If you get an error, let me know what it is. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 29, 2008, at 11:53 PM, David wrote: > Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu > for > 6 gb of ram that couldn't be used in XP 32 bits. I need help > installing > Linux version of Chimera, I have read and goggled web for > instructions, > and none of them seems to work, I run .exe in terminal (knowing linux > doesn't use .exe i find this confusing) and nothing happens, I try > that > Chmod command and running again and nothing too... Im a really > beginner > here in linux, also browsed Ubuntu forums for help and at least till > today have got no answer. All help would be greatly appreciated. > > sincerely, > David Bulnes Abundis > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From bokcmho at ust.hk Fri Jun 6 01:20:16 2008 From: bokcmho at ust.hk (Maurice Ho) Date: Fri, 06 Jun 2008 16:20:16 +0800 Subject: [Chimera-users] smoothening the edge of molecular surface Message-ID: <4848F340.6070700@ust.hk> Is there any way to smoothen the edge of molecular surface when only part of it would be displayed? It's quite often that a couple of triangles sticking out from the edges which makes the image a bit absurd. Please kindly advice. rgds, Maurice Ho -------------- next part -------------- A non-text attachment was scrubbed... Name: bokcmho.vcf Type: text/x-vcard Size: 417 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Jun 6 10:59:26 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 6 Jun 2008 10:59:26 -0700 Subject: [Chimera-users] smoothening the edge of molecular surface In-Reply-To: <4848F340.6070700@ust.hk> References: <4848F340.6070700@ust.hk> Message-ID: <85697B2C-5574-46C8-AA2F-165C6730C53B@cgl.ucsf.edu> Hi Maurice, There is not complete control of the edges when you show part of a molecular surface, but there are ways to try to improve the appearance: Which triangles are shown: (A) Hiding or showing the surface with the Actions menu and/or the "surface" command only sets the surface per atom; you either get all the surface that comes from that atom or none of it. However, you can carefully choose which atoms' surface patches are shown (admittedly this can be difficult). (B) The Surface Zone tool (under Tools... Surface/Binding Analysis) allows independent control of triangles even if they come from the same atom. It turns triangle display on/off based on distance from a selected set of atoms. The advantage is that the edge will not be as rough as if you were restricted to per-atom patches. Disadvantages are that you need to have some atoms that are suitable for defining the zone, and the zone is spherical for each selected atom. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfzone/ surfzone.html Clipping: Even if you have the best set of triangles possible, the edge will still show the triangle shapes. However, the surface can be sliced cleanly with a clipping plane. The limitation is that planes are planar! (A) global clipping planes as shown in the Side View - these clip everything, and are always normal to the line of sight (B) per-model clipping (under Tools... Depiction) - can clip the surface only, and can face in any direction http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Change the triangles by changing surface parameters: If you select the surface with Ctrl-click and open the Selection Inspector, you can then change various parameters of "MSMS surface": (A) turning off "show disjoint surfaces" will omit additional surface bubbles within the structure that may be making the view more complicated. (B) increasing "vertex density" will make the triangles smaller etc. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 6, 2008, at 1:20 AM, Maurice Ho wrote: > Is there any way to smoothen the edge of molecular surface when > only part of it would be displayed? It's quite often that a couple > of triangles sticking out from the edges which makes the image a > bit absurd. Please kindly advice. > rgds, > Maurice Ho From goddard at cgl.ucsf.edu Fri Jun 6 12:16:47 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 06 Jun 2008 12:16:47 -0700 Subject: [Chimera-users] smoothening the edge of molecular surface In-Reply-To: <4848F340.6070700@ust.hk> References: <4848F340.6070700@ust.hk> Message-ID: <48498D1F.8000505@cgl.ucsf.edu> Hi Maurice, As Elaine pointed out there is no way to flexibly smooth a surface edge in Chimera right now. I wrote a little Python code that creates a new mouse mode in Chimera that allows you to hide individual triangles of a surface by clicking on them. It is attached to this email. You open it in Chimera (File / Open) then hold the ctrl key and click with the right mouse button (of a 3 button mouse) and it will hide the triangle. I tested this with the June 4 Chimera daily build. It definitely will not work in the Chimera 1.2470 production release (Nov 2007). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html This has lots of limitations to beware of. Saving a Chimera session will not remember the hidden triangles. So basically all you can do is trim triangles, save an image, then lose your trimming when you quit Chimera. Also there is no way to reshow specific hidden triangles. Using Actions / Surface / show or hide will undo the effect of all your hiding though. Enjoy, Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: hidetriangles.py URL: From goddard at cgl.ucsf.edu Fri Jun 6 12:39:23 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 06 Jun 2008 12:39:23 -0700 Subject: [Chimera-users] Molecular voodoo Message-ID: <4849926B.4070308@cgl.ucsf.edu> While debugging a bit of Chimera code I stumbled upon molecular voodoo. Stick pins in any evil molecule. Ask your doctor if this treatment may be right for you. A snake toxin (PDB 1a0m) has been fully cursed in the attached image. I attach the voodoo doll Chimera script for your amusement. You open voodoodoll.py in Chimera and then ctrl-right-mouse-button lets you place pins. Works in Chimera production release 1.2470 and newer. Tom -------------- next part -------------- A non-text attachment was scrubbed... Name: voodoo.png Type: image/png Size: 48698 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: voodoodoll.py URL: From hatuey.hack at gmail.com Mon Jun 9 06:24:29 2008 From: hatuey.hack at gmail.com (Hatuey Hack) Date: Mon, 9 Jun 2008 10:24:29 -0300 Subject: [Chimera-users] << Plotting Gaussian MO >> In-Reply-To: <612c95fa0806090608m206099c1lb682ace46442c912@mail.gmail.com> References: <612c95fa0806090608m206099c1lb682ace46442c912@mail.gmail.com> Message-ID: <612c95fa0806090624l5395ab11k6c9b235379e1a4fe@mail.gmail.com> Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey From goddard at cgl.ucsf.edu Mon Jun 9 12:05:59 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Jun 2008 12:05:59 -0700 Subject: [Chimera-users] << Plotting Gaussian MO >> In-Reply-To: <612c95fa0806090624l5395ab11k6c9b235379e1a4fe@mail.gmail.com> References: <612c95fa0806090608m206099c1lb682ace46442c912@mail.gmail.com> <612c95fa0806090624l5395ab11k6c9b235379e1a4fe@mail.gmail.com> Message-ID: <484D7F17.1080803@cgl.ucsf.edu> Hi Hatuey, If you open a Gaussian cube file containing more than one orbital Chimera should open a separate volume for each orbital. Chimera determines whether the file contains multiple orbitals by looking for a negative atom count in the first field of the third line (weird format) then after the lines that list the atom coordinates there is a single line that names each of the orbitals. Below is a single orbital example. You can look at your cub file in a text editor and see if it matches this format. If it does but doesn't display correctly then I can look at the file if you can put it on the web. Tom Example cube file: azurin 1JZF SCF Molecular Orbitals -141 -22.336829 -16.222711 -12.353810 95 0.436104 0.000000 0.000000 83 0.000000 0.436104 0.000000 65 0.000000 0.000000 0.436104 1 1.000000 12.122777 -2.902144 -5.146283 6 6.000000 12.104072 -2.113008 -3.229603 ... (removed additional 138 atom lines) 1 1.000000 12.112141 -5.890766 -0.172029 1 1515 -1.84745E-19 -2.68150E-19 -3.85426E-19 -5.51630E-19 -7.94108E-19 -1.16861E-18 -1.79519E-18 -2.93148E-18 -5.10836E-18 -9.35382E-18 -1.75136E-17 -3.26273E-17 ... (removed 86734 additional lines containing density values) From jkhilmer at gmail.com Mon Jun 9 12:57:50 2008 From: jkhilmer at gmail.com (Jonathan Hilmer) Date: Mon, 9 Jun 2008 13:57:50 -0600 Subject: [Chimera-users] gaussian orbitals, Chimera-users Digest, Vol 62, Issue 11 Message-ID: <81277ce10806091257m7a865832v9bef5ed07494746c@mail.gmail.com> Hatuey, If I remember correctly, you need to open the density map twice, then contour at the same level for both maps: one at the positive value and the other negative. Each map is colored independently, so they can be depicted however you want. Jonathan On Mon, Jun 9, 2008 at 1:00 PM, wrote: > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. << Plotting Gaussian MO >> (Hatuey Hack) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Jun 2008 10:24:29 -0300 > From: "Hatuey Hack" > Subject: [Chimera-users] << Plotting Gaussian MO >> > To: chimera-users at cgl.ucsf.edu > Message-ID: > <612c95fa0806090624l5395ab11k6c9b235379e1a4fe at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a cube file with the Molecular Orbitals calculated with Gaussian. > > When I load the cub file into Chimera, I am only seen half of the > orbital surface. > > I would like to know what should I do to get the whole molecular > orbital surface colored (as usually) with only to colors (each on for > one half). > > Regards, > > Hatuey > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 11 > ********************************************* > From proteus.support at gmail.com Mon Jun 9 13:14:07 2008 From: proteus.support at gmail.com (ProtEUS) Date: Mon, 9 Jun 2008 23:14:07 +0300 Subject: [Chimera-users] Swapaa from Java Runtime.exec Message-ID: <521DBEBD6429470B87F3A7A64922249C@stealth> Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hatuey.hack at gmail.com Mon Jun 9 14:35:43 2008 From: hatuey.hack at gmail.com (Hatuey Hack) Date: Mon, 9 Jun 2008 18:35:43 -0300 Subject: [Chimera-users] << Plotting Gaussian MO >> In-Reply-To: <484D7F17.1080803@cgl.ucsf.edu> References: <612c95fa0806090608m206099c1lb682ace46442c912@mail.gmail.com> <612c95fa0806090624l5395ab11k6c9b235379e1a4fe@mail.gmail.com> <484D7F17.1080803@cgl.ucsf.edu> Message-ID: <612c95fa0806091435j3467fc9dx33e8772d04b8e328@mail.gmail.com> Hi Tom and Jonathan. Thanks by your answers. Tom, my cube file begins as you said (see below). As it has 30MB (I compacted with ZIP and RAR but get a 7MB file!) I could not send to you. Opt-Freq mo=67 Alpha MO coefficients -34 -19.025542 -8.992895 -7.648475 234 0.166667 0.000000 0.000000 ...... Jonathan, I load the map twice. In the first control window, I stay at the left (negative value) of the histogram and in the second, I stay at the right (positive). Now, I can see both part of the orbital but I also see a box (from the negative value) that make the surface difficult to see. Also, I did not see any atoms Regards, Hatuey On Mon, Jun 9, 2008 at 4:05 PM, Thomas Goddard wrote: > Hi Hatuey, > > If you open a Gaussian cube file containing more than one orbital Chimera > should open a separate volume for each orbital. Chimera determines whether > the file contains multiple orbitals by looking for a negative atom count in > the first field of the third line (weird format) then after the lines that > list the atom coordinates there is a single line that names each of the > orbitals. Below is a single orbital example. You can look at your cub file > in a text editor and see if it matches this format. If it does but doesn't > display correctly then I can look at the file if you can put it on the web. > > Tom > > Example cube file: > > > azurin 1JZF > SCF Molecular Orbitals > -141 -22.336829 -16.222711 -12.353810 > 95 0.436104 0.000000 0.000000 > 83 0.000000 0.436104 0.000000 > 65 0.000000 0.000000 0.436104 > 1 1.000000 12.122777 -2.902144 -5.146283 > 6 6.000000 12.104072 -2.113008 -3.229603 > ... (removed additional 138 atom lines) > 1 1.000000 12.112141 -5.890766 -0.172029 > 1 1515 > -1.84745E-19 -2.68150E-19 -3.85426E-19 -5.51630E-19 -7.94108E-19 > -1.16861E-18 > -1.79519E-18 -2.93148E-18 -5.10836E-18 -9.35382E-18 -1.75136E-17 > -3.26273E-17 > ... (removed 86734 additional lines containing density values) > > From meng at cgl.ucsf.edu Mon Jun 9 14:41:55 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Jun 2008 14:41:55 -0700 Subject: [Chimera-users] << Plotting Gaussian MO >> In-Reply-To: <612c95fa0806091435j3467fc9dx33e8772d04b8e328@mail.gmail.com> References: <612c95fa0806090608m206099c1lb682ace46442c912@mail.gmail.com> <612c95fa0806090624l5395ab11k6c9b235379e1a4fe@mail.gmail.com> <484D7F17.1080803@cgl.ucsf.edu> <612c95fa0806091435j3467fc9dx33e8772d04b8e328@mail.gmail.com> Message-ID: <4F22A995-5811-4BCC-8E39-F8C8572C59AA@cgl.ucsf.edu> Hatuey and Jonathan, It sounds like you can just open the cube file one time and Ctrl- click on the histogram so that there are two contour levels. You can color each isosurface differently even though you just have one copy of the data open. This recent message explains how to undisplay the box that appears when you have negative contour levels: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-June/002688.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 9, 2008, at 2:35 PM, Hatuey Hack wrote: > Hi Tom and Jonathan. > > Thanks by your answers. > > Tom, my cube file begins as you said (see below). As it has 30MB (I > compacted with ZIP and RAR but get a 7MB file!) I could not send to > you. > > Opt-Freq mo=67 > Alpha MO coefficients > -34 -19.025542 -8.992895 -7.648475 > 234 0.166667 0.000000 0.000000 > ...... > > > Jonathan, > > I load the map twice. In the first control window, I stay at the left > (negative value) of the histogram and in the second, I stay at the > right (positive). Now, I can see both part of the orbital but I also > see a box (from the negative value) that make the surface difficult to > see. > > Also, I did not see any atoms > > Regards, > > Hatuey From glander at scripps.edu Mon Jun 9 15:29:08 2008 From: glander at scripps.edu (Gabriel Lander) Date: Mon, 9 Jun 2008 15:29:08 -0700 Subject: [Chimera-users] saving 2 maps for difference Message-ID: I have 2 density maps, and use the "fit in map" function to best align the 2 of them. I'd like to use this fitting to create a difference map, but the original maps are not the same size. Does anyone know how to save both maps to the same grid in Chimera? For now I've been using the "subregion selection" tool in combination with "resampling voxel size", but if someone has a more direct method it'd be much appreciated. Thanks, -gabe From pett at cgl.ucsf.edu Mon Jun 9 15:31:04 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 9 Jun 2008 15:31:04 -0700 Subject: [Chimera-users] Swapaa from Java Runtime.exec In-Reply-To: <521DBEBD6429470B87F3A7A64922249C@stealth> References: <521DBEBD6429470B87F3A7A64922249C@stealth> Message-ID: <1EAF7B67-6A1F-46BE-918C-E409985DE6A7@cgl.ucsf.edu> If you run Chimera in nogui mode (i.e. with the command-line flag "-- nogui") with no script file argument then standard input would be interpreted as Chimera commands. Alternatively, you could supply a script file (Chimera commands or Python) as an argument. This is basically described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui You could use a series of commands like: open input.pdb swapaa TYR :15.a write output.pdb to do the swapaa. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 9, 2008, at 1:14 PM, ProtEUS wrote: > Hello all! > > I am sorry if this is a dump question, but is it possible for > swapaa to run fromJava server with Runtime.exec()? > > Thank you very much!! > > Andreas, Greece. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jun 9 15:44:09 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Jun 2008 15:44:09 -0700 Subject: [Chimera-users] saving 2 maps for difference In-Reply-To: References: Message-ID: <484DB239.8080404@cgl.ucsf.edu> Hi Gabe, If you would like to just get one map calculated on the grid of a second map you can use the "vop" command with the "resample" operation. Something like: vop #1 resample onGrid #0 It makes a new map which you could save with the "volume" command or the volume dialog "File / Save map as..." menu entry. Here's the vop documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html That was added January 24, 2008 (Chimera 1.2485) for Bridget Carragher. I've been meaning to also add a subtract map operation to the "vop" command but that is not in yet. Tom From proteus.support at gmail.com Tue Jun 10 10:25:28 2008 From: proteus.support at gmail.com (ProtEUS) Date: Tue, 10 Jun 2008 20:25:28 +0300 Subject: [Chimera-users] Swapaa from Java Runtime.exec References: <521DBEBD6429470B87F3A7A64922249C@stealth> <1EAF7B67-6A1F-46BE-918C-E409985DE6A7@cgl.ucsf.edu> Message-ID: Hello again! I tried the way you explained me, but it doesn't seem to work. I also tried to use the script mode with simple commands, but i am getting back error like: cannot execute 'gzip'... and a series of other errors of python. Could you please help me with this situation? Thank you so much in advance... Andreas. ----- Original Message ----- From: Eric Pettersen To: ProtEUS Cc: chimera-users at cgl.ucsf.edu Sent: Tuesday, June 10, 2008 1:31 AM Subject: Re: [Chimera-users] Swapaa from Java Runtime.exec If you run Chimera in nogui mode (i.e. with the command-line flag "--nogui") with no script file argument then standard input would be interpreted as Chimera commands. Alternatively, you could supply a script file (Chimera commands or Python) as an argument. This is basically described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui You could use a series of commands like: open input.pdb swapaa TYR :15.a write output.pdb to do the swapaa. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 9, 2008, at 1:14 PM, ProtEUS wrote: Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece. _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nils.becker at ens-lyon.fr Tue Jun 10 10:32:12 2008 From: nils.becker at ens-lyon.fr (Nils Becker) Date: Tue, 10 Jun 2008 19:32:12 +0200 Subject: [Chimera-users] translation + rotation of a whole scene Message-ID: <484EBA9C.8080701@ens-lyon.fr> Hi list, I have a question about rotating and translating a bunch of models together while preserving their spatial relations. In particular, I would like to apply a matrix almost as in the matrixset command. THe difference is that I do not want to apply it individually to each model, but to one chosen models, while having the rest move together with the chosen model. Is that feasible in chimera? cheers, Nils From meng at cgl.ucsf.edu Tue Jun 10 15:14:05 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Jun 2008 15:14:05 -0700 Subject: [Chimera-users] translation + rotation of a whole scene In-Reply-To: <484EBA9C.8080701@ens-lyon.fr> References: <484EBA9C.8080701@ens-lyon.fr> Message-ID: <851B5FB9-4493-4642-BE14-3FF6A64DCD59@cgl.ucsf.edu> Hi Nils, Perhaps I am misunderstanding your question, but the movement commands such as move, turn, roll, ... move all the models together. Normally all models are movable ("activated for motion") but the activation status of each can be toggled using select/~select commands, or the Model Panel "Active" checkboxes, or the checkboxes under the Command Line. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ movies.html#moviecommands http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef You can combine various motion commands with the select command to sequentially manipulate different subsets of the models. Here is a tiny example (commands): open 1zik open 1gcn open 6bna preset apply int 1 roll y 2 45 move x -1 25 move x 10; move y -10 ~select 0,1 move x 2 10 turn z 45 select 0,1 move y 1 25 Semicolon (;) is for stringing commands together when you don't want to see intermediate states. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 10, 2008, at 10:32 AM, Nils Becker wrote: > Hi list, > I have a question about rotating and translating a bunch of models > together while preserving their spatial relations. In particular, I > would like to apply a matrix almost as in the matrixset command. THe > difference is that I do not want to apply it individually to each > model, > but to one chosen models, while having the rest move together with the > chosen model. Is that feasible in chimera? > cheers, Nils > From nils.becker at ens-lyon.fr Wed Jun 11 01:55:29 2008 From: nils.becker at ens-lyon.fr (Nils Becker) Date: Wed, 11 Jun 2008 10:55:29 +0200 Subject: [Chimera-users] translation + rotation of a whole scene In-Reply-To: <851B5FB9-4493-4642-BE14-3FF6A64DCD59@cgl.ucsf.edu> References: <484EBA9C.8080701@ens-lyon.fr> <851B5FB9-4493-4642-BE14-3FF6A64DCD59@cgl.ucsf.edu> Message-ID: <484F9301.7020809@ens-lyon.fr> Hi Elaine, thanks for your answer. Sorry that I did not make my question clearer. I know that move, turn , roll etc. do move models together. However, this is not what I need. I need to specify a precise orientation and position of one of the molecule models, say #0, so that the view direction is exactly along a symmetry axis of that model. This orientation and position was generated externally and I have it available as a rotation matrix and translation vector, in the same format as that used by matrixset/matrixget. I could write the same matrix into a matrixset file N times for N models in the session. This however does not rotate the molecules together, but sets each one individually to the orientation and position needed only for model 1. is it possible to do that? Thanks! Nils Elaine Meng wrote: > Hi Nils, > Perhaps I am misunderstanding your question, but the movement commands > such as move, turn, roll, ... > move all the models together. Normally all models are movable > ("activated for motion") but the activation status of each can be > toggled using select/~select commands, or the Model Panel "Active" > checkboxes, or the checkboxes under the Command Line. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef > > You can combine various motion commands with the select command to > sequentially manipulate different subsets of the models. > > Here is a tiny example (commands): > open 1zik > open 1gcn > open 6bna > preset apply int 1 > roll y 2 45 > move x -1 25 > move x 10; move y -10 > ~select 0,1 > move x 2 10 > turn z 45 > select 0,1 > move y 1 25 > > Semicolon (;) is for stringing commands together when you don't want to > see intermediate states. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Jun 10, 2008, at 10:32 AM, Nils Becker wrote: > >> Hi list, >> I have a question about rotating and translating a bunch of models >> together while preserving their spatial relations. In particular, I >> would like to apply a matrix almost as in the matrixset command. THe >> difference is that I do not want to apply it individually to each model, >> but to one chosen models, while having the rest move together with the >> chosen model. Is that feasible in chimera? >> cheers, Nils >> From meng at cgl.ucsf.edu Wed Jun 11 07:30:10 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Jun 2008 07:30:10 -0700 Subject: [Chimera-users] translation + rotation of a whole scene In-Reply-To: <484F9301.7020809@ens-lyon.fr> References: <484EBA9C.8080701@ens-lyon.fr> <851B5FB9-4493-4642-BE14-3FF6A64DCD59@cgl.ucsf.edu> <484F9301.7020809@ens-lyon.fr> Message-ID: Hi Nils, Perhaps it is the "matrixcopy" command that you need ... if "matrixset" was used to position your first model, say #0, then you could apply the same transformation to the others with commands like: matrixcopy #0 #1 matrixcopy 0 2 (the pound signs # are optional) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html This command does not require a matrix to be in a file. It simply applies the transformation of one model to another. Again you can combine all the commands with semicolons to avoid seeing the intermediate stages. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 11, 2008, at 1:55 AM, Nils Becker wrote: > Hi Elaine, > > thanks for your answer. Sorry that I did not make my question > clearer. I know that move, turn , roll etc. do move models > together. However, this is not what I need. > > I need to specify a precise orientation and position of one of the > molecule models, say #0, so that the view direction is exactly > along a symmetry axis of that model. This orientation and position > was generated externally and I have it available as a rotation > matrix and translation vector, in the same format as that used by > matrixset/matrixget. > > I could write the same matrix into a matrixset file N times for N > models in the session. This however does not rotate the molecules > together, but sets each one individually to the orientation and > position needed only for model 1. > > is it possible to do that? > > Thanks! Nils From goddard at cgl.ucsf.edu Wed Jun 11 08:28:19 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 11 Jun 2008 08:28:19 -0700 Subject: [Chimera-users] translation + rotation of a whole scene In-Reply-To: <484F9301.7020809@ens-lyon.fr> References: <484EBA9C.8080701@ens-lyon.fr> <851B5FB9-4493-4642-BE14-3FF6A64DCD59@cgl.ucsf.edu> <484F9301.7020809@ens-lyon.fr> Message-ID: <484FEF13.30507@cgl.ucsf.edu> Hi Nils, I don't think there is a Chimera command to achieve what you want. Attached is a Python script that will do it. You edit the transform at the top of the script then open the file in Chimera. Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: place.py URL: From pett at cgl.ucsf.edu Wed Jun 11 10:51:09 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 11 Jun 2008 10:51:09 -0700 Subject: [Chimera-users] Swapaa from Java Runtime.exec In-Reply-To: References: <521DBEBD6429470B87F3A7A64922249C@stealth> <1EAF7B67-6A1F-46BE-918C-E409985DE6A7@cgl.ucsf.edu> Message-ID: <19AF452D-7609-4A40-AE5F-BC26F4225777@cgl.ucsf.edu> On Jun 10, 2008, at 10:25 AM, ProtEUS wrote: > Hello again! > > I tried the way you explained me, but it doesn't seem to work. I think I need more detail than "doesn't seem to work". Did you get an error message? Was the output wrong? What specifically happened? > I also tried to use the script mode with simple commands, but i am > getting back error like: > > cannot execute 'gzip'... That's just a warning that files compressed with 'compress' (i.e. ending in '.Z') won't be openable in Chimera because no gzip executable could be found. You can ignore it assuming that none of the files you're using are compressed that way. > > and a series of other errors of python. The text of the script you used and the contents of the error messages would be helpful. --Eric > > Could you please help me with this situation? > > Thank you so much in advance... > > Andreas. > ----- Original Message ----- > From: Eric Pettersen > To: ProtEUS > Cc: chimera-users at cgl.ucsf.edu > Sent: Tuesday, June 10, 2008 1:31 AM > Subject: Re: [Chimera-users] Swapaa from Java Runtime.exec > > If you run Chimera in nogui mode (i.e. with the command-line flag > "--nogui") with no script file argument then standard input would > be interpreted as Chimera commands. Alternatively, you could > supply a script file (Chimera commands or Python) as an argument. > This is basically described here: > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui > > You could use a series of commands like: > > open input.pdb > swapaa TYR :15.a > write output.pdb > > to do the swapaa. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jun 9, 2008, at 1:14 PM, ProtEUS wrote: > >> Hello all! >> >> I am sorry if this is a dump question, but is it possible for >> swapaa to run fromJava server with Runtime.exec()? >> >> Thank you very much!! >> >> Andreas, Greece. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From dchen at caltech.edu Fri Jun 13 11:57:18 2008 From: dchen at caltech.edu (David Chenoweth) Date: Fri, 13 Jun 2008 11:57:18 -0700 Subject: [Chimera-users] 3D surfaces from MacMolPlt or Gamess Message-ID: Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below and I can send you example files if you need. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen at caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values) -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Jun 13 12:37:27 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Jun 2008 12:37:27 -0700 Subject: [Chimera-users] 3D surfaces from MacMolPlt or Gamess In-Reply-To: References: Message-ID: <4852CC77.9040701@cgl.ucsf.edu> Hi David, What is the format of the grid data from the Gamess DFT calculation? It seems like it would be better to read the Gamess file instead of the grid file produced by MacMolPlt. The MacMolPlt 3D surface export would be simple to read in Chimera using a modified version of the Gaussian cube file reader (Python code chimera/share/VolumeData/gaussian/gaussian_format.py). I would need an example file to test with. Tom From goddard at cgl.ucsf.edu Fri Jun 13 15:59:17 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Jun 2008 15:59:17 -0700 Subject: [Chimera-users] 3D surfaces from MacMolPlt or Gamess In-Reply-To: References: Message-ID: <4852FBC5.3040909@cgl.ucsf.edu> Hi Dave, I added a MacMolPlt grid file reader to Chimera. Works with the example files you sent. It will be in tonight's daily builds if they succeed. I made the automatically recognized file suffix ".mmp". Tell me if there is a standard file suffix for these files and I will make Chimera recognize it. Otherwise you have to choose the file type each time you open such a file in Chimera. Tom David Chenoweth wrote: > Hi Tom, > I agree that it would be better to just read from the Gamess file > directly but I think MacMolPlt3D is calculating the electron density > map and electrostatic potential map from the Gamess file not just > reading it in. I am sending you the Gamess file Imidazole_321g_jag.log > that I open in MacMolPlt3D to create the surfaces. I am also sending > you two exported surface files for imidazole that were made from > MacMolPlt3d and they are called Im_Dens_Gamess and Im_EPot_Gamess > (they are zipped into Example_Gemess_file.zip). Maybe the modified > Gaussian cube file reader will work with these files. > > Thanks for all the help, > Dave Chenoweth Tom Goddard wrote: > Hi David, > > What is the format of the grid data from the Gamess DFT calculation? > It seems like it would be better to read the Gamess file instead of the > grid file produced by MacMolPlt. > > The MacMolPlt 3D surface export would be simple to read in Chimera > using a modified version of the Gaussian cube file reader (Python code > chimera/share/VolumeData/gaussian/gaussian_format.py). I would need an > example file to test with. > > Tom > David Chenoweth wrote: > Dear Chimera team, > > I am having a bit of trouble reading a file into Chimera. Currently I > am using Gamess to run DFT calculations and I can open these files in > MacMolPlt which allows me to display orbitals or plot electrostatic > potential surfaces. I can export the 3D surface data however I can't > get Chimera to read the 3D grid files. Can you help me? I attached > the file format info below and I can send you example files if you > need. I am really trying to use Chimera for all my graphics needs > wether it be viewing surfaces or orbitals from DFT calculations or > looking at electron density maps from crystal structure data. If I > could convert the 3D surface data files below into ccp4 or cns > formated files that should also work for Chimera I just haven't found > a way to do this yet. > > Thanks in advance, > Dave From dchen at caltech.edu Thu Jun 12 19:08:07 2008 From: dchen at caltech.edu (David Chenoweth) Date: Thu, 12 Jun 2008 19:08:07 -0700 Subject: [Chimera-users] 3D surfaces from MacMolPlt or Gamess Message-ID: <3041E517-28BA-4A16-953A-1ECA11DCFC9F@caltech.edu> Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below with an exported density file and electrostatic potential map. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen at caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Im_Dens_Gamess Type: application/octet-stream Size: 3050533 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Im_EPot_Gamess Type: application/octet-stream Size: 3153161 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Tue Jun 17 15:44:57 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 17 Jun 2008 15:44:57 -0700 Subject: [Chimera-users] Find contour level to enclose a specified volume Message-ID: <48583E69.5090608@cgl.ucsf.edu> Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: findlevel.py URL: From goddard at cgl.ucsf.edu Wed Jun 18 11:02:46 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 18 Jun 2008 11:02:46 -0700 Subject: [Chimera-users] Find contour level to enclose a specified volume In-Reply-To: <48583E69.5090608@cgl.ucsf.edu> References: <48583E69.5090608@cgl.ucsf.edu> Message-ID: <48594DC6.3000801@cgl.ucsf.edu> The script I posted calculates the contour level but does not show it. To set the contour level and display the new surface use Python code: v.set_parameters(surface_levels = [level]) v.show() Tom From JeanDidier.Marechal at uab.cat Wed Jun 18 15:50:41 2008 From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal) Date: Thu, 19 Jun 2008 00:50:41 +0200 Subject: [Chimera-users] connectivity Message-ID: Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, JD Dr. Jean-Didier Mar?chal Professor Lector Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es ----- Missatge original ----- De: chimera-users-request at cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18 > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Find contour level to enclose a specified volume (Thomas > Goddard) 2. Re: Find contour level to enclose a specified volume > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 17 Jun 2008 15:44:57 -0700 > From: Thomas Goddard > Subject: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" > Message-ID: <48583E69.5090608 at cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Ed Brignole asked about setting a volume contouring level so that > the > resulting surface encloses a desired volume (cubic Angstroms). > Attached > is a Python script that does this in two ways. The first way is > fast > but approximate finding the level such that the number of enclosed > grid > points times the voxel volume equals the requested volume. > Estimating > the enclosed volume of the surface this way can give a much > different > result than actually computing analytically the volume within the > surface. The second approach computes surfaces at different > contour > levels and calculates analytically the volume. It uses bisection > to > find the correct contour level. This approach can be slow, about > 30 > seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface > triangles. Most of that time (80%) is actually computing the > enclosed > volume. That should be very fast but the code is checking for > holes in > the surface in a rather slow way. Both methods use the step size > (subsampling) set in the volume dialog. > > Tom > -------------- next part -------------- > An embedded and charset-unspecified text was scrubbed... > Name: findlevel.py > Url: http://www.cgl.ucsf.edu/pipermail/chimera- > users/attachments/20080617/d7aef5ee/findlevel-0001.ksh > > ------------------------------ > > Message: 2 > Date: Wed, 18 Jun 2008 11:02:46 -0700 > From: Tom Goddard > Subject: Re: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" > Message-ID: <48594DC6.3000801 at cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The script I posted calculates the contour level but does not show > it. > To set the contour level and display the new surface use Python code: > > v.set_parameters(surface_levels = [level]) > v.show() > > Tom > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 18 > ********************************************* > From pett at cgl.ucsf.edu Wed Jun 18 17:14:31 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 18 Jun 2008 17:14:31 -0700 Subject: [Chimera-users] connectivity In-Reply-To: References: Message-ID: Hi JD, For a Molecule model "m", m.bonds is the list of bonds. Each Bond "b" has the bonded atoms in b.atoms. Conversely each Atom "a" lists its bonded neighbor atoms in a.neighbors. Is this basically what you wanted? --Eric On Jun 18, 2008, at 3:50 PM, Jean Didier Pie Marechal wrote: > Dear all, > > I would like to use chimera to generate inputs for gaussian QM/MM > calculations (ONIOM). > One of the element I need is the connectivity of the atoms. I > looked around the programmer's guide but couldn't find the right > module that takes this in charge. > > what is the way to have access the connectivity of a given molecule? > > All the best, > JD > > > > > Dr. Jean-Didier Mar?chal > Professor Lector > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal at uab.es > > ----- Missatge original ----- > De: chimera-users-request at cgl.ucsf.edu > Data: Dimecres, Juny 18, 2008 9:00 pm > Assumpte: Chimera-users Digest, Vol 62, Issue 18 > >> Send Chimera-users mailing list submissions to >> chimera-users at cgl.ucsf.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> or, via email, send a message with subject or body 'help' to >> chimera-users-request at cgl.ucsf.edu >> >> You can reach the person managing the list at >> chimera-users-owner at cgl.ucsf.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Chimera-users digest..." >> >> >> Today's Topics: >> >> 1. Find contour level to enclose a specified volume (Thomas >> Goddard) 2. Re: Find contour level to enclose a specified volume >> (Tom Goddard) >> >> >> -------------------------------------------------------------------- >> -- >> >> Message: 1 >> Date: Tue, 17 Jun 2008 15:44:57 -0700 >> From: Thomas Goddard >> Subject: [Chimera-users] Find contour level to enclose a specified >> volume >> To: "'Chimera BB'" >> Message-ID: <48583E69.5090608 at cgl.ucsf.edu> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Ed Brignole asked about setting a volume contouring level so that >> the >> resulting surface encloses a desired volume (cubic Angstroms). >> Attached >> is a Python script that does this in two ways. The first way is >> fast >> but approximate finding the level such that the number of enclosed >> grid >> points times the voxel volume equals the requested volume. >> Estimating >> the enclosed volume of the surface this way can give a much >> different >> result than actually computing analytically the volume within the >> surface. The second approach computes surfaces at different >> contour >> levels and calculates analytically the volume. It uses bisection >> to >> find the correct contour level. This approach can be slow, about >> 30 >> seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface >> triangles. Most of that time (80%) is actually computing the >> enclosed >> volume. That should be very fast but the code is checking for >> holes in >> the surface in a rather slow way. Both methods use the step size >> (subsampling) set in the volume dialog. >> >> Tom >> -------------- next part -------------- >> An embedded and charset-unspecified text was scrubbed... >> Name: findlevel.py >> Url: http://www.cgl.ucsf.edu/pipermail/chimera- >> users/attachments/20080617/d7aef5ee/findlevel-0001.ksh >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 18 Jun 2008 11:02:46 -0700 >> From: Tom Goddard >> Subject: Re: [Chimera-users] Find contour level to enclose a >> specified >> volume >> To: "'Chimera BB'" >> Message-ID: <48594DC6.3000801 at cgl.ucsf.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> The script I posted calculates the contour level but does not show >> it. >> To set the contour level and display the new surface use Python code: >> >> v.set_parameters(surface_levels = [level]) >> v.show() >> >> Tom >> >> >> ------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> End of Chimera-users Digest, Vol 62, Issue 18 >> ********************************************* >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Thu Jun 19 11:07:35 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 19 Jun 2008 11:07:35 -0700 Subject: [Chimera-users] find levels and morph conformations In-Reply-To: <558F6B7F5360E046B597A008686EAFBF51A0DF@EXCHV1.lj.ad.scripps.edu> References: <200806161851.m5GIp0OW1832725@guanine.cgl.ucsf.edu> <4856DE12.7030700@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0D8@EXCHV1.lj.ad.scripps.edu> <48575B36.1000402@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DB@EXCHV1.lj.ad.scripps.edu> <48583B57.9050904@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DF@EXCHV1.lj.ad.scripps.edu> Message-ID: <485AA067.5070202@cgl.ucsf.edu> Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed From k_alnasr at yahoo.com Thu Jun 19 10:08:45 2008 From: k_alnasr at yahoo.com (Kamal Al Nasr) Date: Thu, 19 Jun 2008 10:08:45 -0700 (PDT) Subject: [Chimera-users] how could u know the order of atoms? Message-ID: <354699.26543.qm@web51304.mail.re2.yahoo.com> Dear Sir/Madam, I am using Chimera viewer..and it is a great viewer ever... I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that? I appreciate your time.... Kamal -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Jun 23 14:22:31 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 23 Jun 2008 14:22:31 -0700 Subject: [Chimera-users] how could u know the order of atoms? In-Reply-To: <354699.26543.qm@web51304.mail.re2.yahoo.com> References: <354699.26543.qm@web51304.mail.re2.yahoo.com> Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4@cgl.ucsf.edu> On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > Dear Sir/Madam, > > I am using Chimera viewer..and it is a great viewer ever... Thanks! I'm glad you like it. > I kindly have a question... how could you know (from PDB file) the > coorect bonding between atoms? I mean that how could you know that > this atom is connected with CA not N nor C.....do u have all these > bonds stored already in a database? or you use atom positions to > determine that? For standard amino and nucleic acids, Chimera has templates containing the correct connectivity. For non-standard residues it bases the connectivity on inter-atomic distances, with a few added heuristics (e.g. hydrogens can only have one bond). The templates are accessible in the Python layer with the chimera.restmplFindResidue() function. You can look in the Rotamers extension for examples of its use. The distance-based connectivity function is also available for an entire molecule as chimera.connectMolecule(). It takes the molecule as its only argument and adds bonds to it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jun 24 13:24:58 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Jun 2008 13:24:58 -0700 Subject: [Chimera-users] selecting/displaying zones In-Reply-To: References: <047E2934-FDD1-496C-A784-EF7A126301E4@cgl.ucsf.edu> <4BB15CDD-B67E-4A78-9697-25725E06352F@imp.univie.ac.at> <261B7E9C-A29E-4C63-A127-0B39F26CAC01@cgl.ucsf.edu> Message-ID: On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote: > > Am using Chimera and would like to do the following: > - would first like to focus on specific side chain residues (for > example lysines) > - at a specific atom of either one or all lysines present in my > sample, I would like to draw a region of interest (which should be > a sphere with a given distance ... then make it rather transparent > like soap bobbles ...) ... the idea of this is to highlight areas > within a given distance away from this atom > - then I would like to read out all other side chains that are > within such an area ( in a table or so) ... and eventually > highlight them with specific colors ... > > Elaine, is there an easy way to do this ? > Tx, > -Thomas > ---------------------------------------------------------------------- > --------- > > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) Hi Thomas, You can definitely (1) select the atoms or residues within a specified cutoff of some other atoms and write a list of what is selected to the Reply Log or to a file. Slightly trickier is (2) displaying a "bubble." (1) The following command selects all atoms within 4.5 angstroms of atom NZ in lysine 92, chain A (example structure 2gbp): select :92.a at nz za<4.5 to select the whole residues with any atom in the zone, use "z" or "zr" instead of "za", and to use all the atoms of that lysine, just omit "@nz" from the command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones This selection process can also be done by Ctrl-clicking to select the atom and then using Select... Zone. You can write out a list of the selection with Actions... Write List (click Log if you want to send it to the Reply Log instead). The default is a list of all the atoms individually, but you can set it to "residues" instead to just get one line of output per residue. The command to do that same thing is "writesel" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html (2) The "bubble." I imagine something like Volume Eraser would be nice (check it out: Tools... Volume Data... Volume Eraser). However, that does not let you specify particular coordinates for the center. You have to move it around by hand. Volume Eraser really just makes a big atom and gives it a transparent color. You could add an atom in Build Structure (under Tools... Structure Editing), color it a transparent color, and change its radius with "vdwdefine" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html#build http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html It doesn't let you enter specific coordinates for the atom. However, if you add the atom as a "new model" you can match it to different locations on the first. For example, if the new atom is model 1 and the structure of interest (say 2gbp) is model 0: rep sphere #1 colordef tpink 1 .6 .6 .6 color tpink #1 vdwdef 3.0 #1 vdwdef +1 #1 vdwdef +1 #1 match #1 #0:147.a at nz select #1 za<5 & #0 [... etc. ...] The radius would just be for display purposes. You'd still have to specify the zone distance when selecting. A couple of failed ideas: (a) You can make a spherical surface of specified radius with the command "shape" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html but you cannot directly specify coordinates for the center or easily modify radius after it has been created. (b) Create a spherical object in BILD format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Disadvantages are inability to make it transparent and having to delete/recreate the object just to change its radius. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > > From brignole at scripps.edu Tue Jun 24 14:11:19 2008 From: brignole at scripps.edu (Edward Brignole) Date: Tue, 24 Jun 2008 14:11:19 -0700 Subject: [Chimera-users] multiscale models and morph conformations References: <200806161851.m5GIp0OW1832725@guanine.cgl.ucsf.edu> <4856DE12.7030700@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0D8@EXCHV1.lj.ad.scripps.edu> <48575B36.1000402@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DB@EXCHV1.lj.ad.scripps.edu> <48583B57.9050904@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DF@EXCHV1.lj.ad.scripps.edu> <485AA067.5070202@cgl.ucsf.edu> Message-ID: <558F6B7F5360E046B597A008686EAFBF51A0E2@EXCHV1.lj.ad.scripps.edu> Tom, So now I've got pdb's fit into my maps (using the excellent volume segmentation by color, volume eraser, and fitting tools!) and I'm trying to model the conformational changes. The fit pdb's for each EM structure (all saved into one large pdb with submodels that can conveniently be repositioned relative to one another) have exactly the same chains just with rearranged positions of the original domains, but submodel 0.1 of each model had two chains so morph conformations gets confused cause the rest of the submodels 0.2-12 only had one chain. Morph-conformations works fine if I save my pdb as mol2, then there are no longer submodels. That's not such a pain, except that mol2 doesn't preserve residue number so displaying particular residues becomes difficult. So now I am trying to display EM-like structures in motion by using multiscale models of the intermediate conformations but the multiscale model doesn't follow its chain. So I suppose at this point the only way to visualize this is to write out each of the 60 intermediate pdb's, then through some scripting open each individually, make the multiscale model, display appropriately, save image. And then use ImageMagick to string these images into an animation to visualize the Morphing conformations. Also I can easily color the atoms of different chains but I'm having difficulty applying these colors to the multiscale models. Oops, wait I just discovered that MultiScale.color_surfaces_to_match_atoms() only works if I first select chains! Excellent. Still need some advice on multiscale movies though. Many thanks for all your help. Ed PS. The problem with findlevels wasn't that the map was inverted...I arrive at negative thresholds because I hadn't set the voxel size correctly. Doh! All goes well after that. Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4142 bytes Desc: not available URL: From meng at cgl.ucsf.edu Tue Jun 24 16:46:46 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Jun 2008 16:46:46 -0700 Subject: [Chimera-users] how to draw lines in Chimera In-Reply-To: References: Message-ID: <9F3EEE7D-925E-4385-8510-4ED5889E61A2@cgl.ucsf.edu> On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html -------------- next part -------------- A non-text attachment was scrubbed... Name: sticks.bild Type: application/octet-stream Size: 619 bytes Desc: not available URL: -------------- next part -------------- From gregc at cgl.ucsf.edu Thu Jun 26 15:34:50 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 26 Jun 2008 15:34:50 -0700 (PDT) Subject: [Chimera-users] upcoming production release Message-ID: Hello, We are currently getting ready to put out another chimera production release. At this point, we consider the daily builds to be release candidates, so please download one and try it out. Not all of the daily builds will be production releases, in particular, the Mac OS X Aqua version is not quite ready, and will be a snapshot release. And the Linux off-screen OpenGL version is experimental and will probably stay as a daily build. Greg Couch UCSF Computer Graphics Lab Daily builds: New features: From bala at igib.res.in Thu Jun 26 23:54:53 2008 From: bala at igib.res.in (bala) Date: Fri, 27 Jun 2008 12:24:53 +0530 Subject: [Chimera-users] hydrophobic pocket Message-ID: <7E7071C8392C6E41916C9A6AE2843C7F10AA61@n1ex> Dear Chimerian's, How do i detect hydrophobic pockets in a protein using chimera ?. Thanks in advance, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From ibdeno at gmail.com Fri Jun 27 01:10:08 2008 From: ibdeno at gmail.com (=?ISO-8859-1?Q?Miguel_Ortiz-Lombard=EDa?=) Date: Fri, 27 Jun 2008 10:10:08 +0200 Subject: [Chimera-users] hydrophobic pocket In-Reply-To: <7E7071C8392C6E41916C9A6AE2843C7F10AA61@n1ex> References: <7E7071C8392C6E41916C9A6AE2843C7F10AA61@n1ex> Message-ID: That's a good question... In a first approximation you could assume that all atoms not classified as acceptors/donors of protons would be hydrophobic. This is essentially carbons. If you represent the surface of the molecule colored by elements you should see these pockets. More sophisticated approaches include the program GRID ( http://www.moldiscovery.com/soft_grid.php) to compute the hydrophobic potential (Goodford, P.J., A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. *J. Med. Chem. **28*, 849-57.) Unfortunately, GRID is not free, not even for academics (though there is a special price for the license). Anyway, I think it would be nice if chimera could map the hydrophobic potential maps onto molecular surfaces. Best, Miguel 2008/6/27 bala : > Dear Chimerian's, > > How do i detect hydrophobic pockets in a protein using chimera ?. > > Thanks in advance, > Bala > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en libert? Dans les jardins mal fr?quent?s! Georges Brassens -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Jun 27 09:25:09 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 27 Jun 2008 09:25:09 -0700 Subject: [Chimera-users] Question about avi files in chimera In-Reply-To: <016201c8d7f3$630b0330$800a000a@homeip.net> References: <016201c8d7f3$630b0330$800a000a@homeip.net> Message-ID: <48651465.9030001@cgl.ucsf.edu> Hi Jaap, The AVI files produced by Chimera movie recorder use the MSMPEG-4v2 (Microsoft MPEG4 version 2) video codec and the encoding is done by the open source ffmpeg program. The file size depends on the movie recorder "bit rate" setting (default 2000 Kbits/sec = 250 Kbytes/sec = 15 Mbytes/min). Changing this setting allows you to trade off file size versus image quality. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.html Tom Jaap Brink wrote: > > Hi Tom, > > > > I was wondering given the size difference in avi files that chimera > generates versus other program (Video Edit Magic for instance), which > video codec is being used? I searched the list of embedded software > packages in chimera and found the library of libavcodecs. > > > > Thanks in advance, > > > > Jaap > From meng at cgl.ucsf.edu Fri Jun 27 10:04:24 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Jun 2008 10:04:24 -0700 Subject: [Chimera-users] hydrophobic pocket In-Reply-To: <7E7071C8392C6E41916C9A6AE2843C7F10AA61@n1ex> References: <7E7071C8392C6E41916C9A6AE2843C7F10AA61@n1ex> Message-ID: Hi Bala, There are several possibilities, but one easy thing is to use "Presets... Interactive 3 (hydrophobicity surface)" in the Chimera menu. This will display a molecular surface and color it by amino acid hydrophobicity (Kyte-Doolittle scale) from dodger blue at the most polar end, to white, to orange for the most hydrophobic. You can then visually inspect the surface for orange-ish pockets. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets A figure showing a hydrophobic pocket is included in the new "Structure Analysis and Comparison" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html#surfaces You can use Render by Attribute to map different coloring schemes to Kyte-Doolittle hydrophobicity, as described in that tutorial. You can also read in different hydrophobicity scales as described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html That covers the "what is hydrophobic?" part of the question. As for "what is a pocket?", you may wish to simply use visual inspection, as described above. Another approach is to use the CASTp database of pockets - very useful, but it does not include everything in the PDB. You can open a structure and its CASTp pocket data in Chimera using "File... Fetch by ID" or the command "open", for example: open castp:2gbp or open castp:4enl Just use the PDB ID of your structure. However, you may get a message saying your structure is not in that database. Here is the documentation on viewing CASTp data in Chimera: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From dtan at aecom.yu.edu Fri Jun 27 11:08:26 2008 From: dtan at aecom.yu.edu (Dong-Yan Tan) Date: Fri, 27 Jun 2008 14:08:26 -0400 (EDT) Subject: [Chimera-users] (no subject) Message-ID: <93735ab894c71ecce1caeff308dbf06f.squirrel@netmail.aecom.yu.edu> Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan at aecom.yu.edu From dtan at aecom.yu.edu Fri Jun 27 11:11:49 2008 From: dtan at aecom.yu.edu (Dong-Yan Tan) Date: Fri, 27 Jun 2008 14:11:49 -0400 (EDT) Subject: [Chimera-users] "Floating exception" error message Message-ID: <88d6514c0df6611e42a1e7ca996d17e9.squirrel@netmail.aecom.yu.edu> Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan at aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan at aecom.yu.edu From dtan at aecom.yu.edu Fri Jun 27 11:11:50 2008 From: dtan at aecom.yu.edu (Dong-Yan Tan) Date: Fri, 27 Jun 2008 14:11:50 -0400 (EDT) Subject: [Chimera-users] "Floating exception" error message Message-ID: <1ead8487e7121e92a6ef42d72262b797.squirrel@netmail.aecom.yu.edu> Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan at aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan at aecom.yu.edu From pett at cgl.ucsf.edu Fri Jun 27 11:38:13 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 27 Jun 2008 11:38:13 -0700 Subject: [Chimera-users] "Floating exception" error message In-Reply-To: <1ead8487e7121e92a6ef42d72262b797.squirrel@netmail.aecom.yu.edu> References: <1ead8487e7121e92a6ef42d72262b797.squirrel@netmail.aecom.yu.edu> Message-ID: We haven't had anyone else report this problem. What I recommend is that you download a daily build and try that (go to www.cgl.ucsf.edu/ chimera and follow the "Daily Builds" link). We are very close to making another production release and the daily builds are basically release candidates now. We would be very interested in fixing bugs in those builds, and it's a lot easier for us to work on a problem in the daily build since it corresponds to our current code. Let us know if it works or still fails for you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 27, 2008, at 11:11 AM, Dong-Yan Tan wrote: > > Dear all, > > We have just installed chimera-1.2470-linux.exe in our Linux computer > (SUSE LINUX 9.0 ). We keep getting error message "Floating > exeptions" when > we are just trying to open a PDB file and the program quits > automatically. > Has anyone encountered such a problem or have clues about where to > look > for solutions? Thanks a lot. > > Dong-Yan > > -- > Dong-Yan Tan > Laboratory of Dr. Hernando Sosa > Dept. of Physiology and Biophysics > Albert Einstein College of Medicine > Bronx, NY 10461 > Tel: 718-430-3451 > Email: dtan at aecom.yu.edu > > > > -- > Dong-Yan Tan > Laboratory of Dr. Hernando Sosa > Dept. of Physiology and Biophysics > Albert Einstein College of Medicine > Bronx, NY 10461 > Tel: 718-430-3451 > Email: dtan at aecom.yu.edu > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Fri Jun 27 11:41:01 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 27 Jun 2008 11:41:01 -0700 (PDT) Subject: [Chimera-users] "Floating exception" error message In-Reply-To: <88d6514c0df6611e42a1e7ca996d17e9.squirrel@netmail.aecom.yu.edu> References: <88d6514c0df6611e42a1e7ca996d17e9.squirrel@netmail.aecom.yu.edu> Message-ID: On Fri, 27 Jun 2008, Dong-Yan Tan wrote: > Dear all, > > We have just installed chimera-1.2470-linux.exe in our Linux computer > (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when > we are just trying to open a PDB file and the program quits automatically. > Has anyone encountered such a problem or have clues about where to look > for solutions? Thanks a lot. > > Dong-Yan This sounds like a Linux kernel bug or C library bug. Please make sure that you have applied all of the recommended patches to your SUSE system (use the yast program to update it). In particular, there is a security patch related to floating point exceptions, that should be applied (). It's not clear if that patch will fix the problem, so please apply the rest. I would also expect upgrading to the current SUSE Linux to fix the problem. Good luck, Greg Couch UCSF Computer Graphics Lab From hsosa at aecom.yu.edu Fri Jun 27 13:01:07 2008 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Fri, 27 Jun 2008 16:01:07 -0400 Subject: [Chimera-users] "Floating exception" error message In-Reply-To: References: <88d6514c0df6611e42a1e7ca996d17e9.squirrel@netmail.aecom.yu.edu> Message-ID: <48654703.4070409@aecom.yu.edu> >I would also expect upgrading to the current SUSE Linux to fix the >problem. One thing (not particularly related to Chimera) that is preventing us to upgrade the system, is the risk of breaking other programs. In a particular the newer versions of Linux come without G77 (Fortran 77 compiler) and come with the newer "better" G90 compiler. I suspect a big headache when trying to compile old Fortran coded programs that we still use. Greg Couch wrote: > On Fri, 27 Jun 2008, Dong-Yan Tan wrote: > > >> Dear all, >> >> We have just installed chimera-1.2470-linux.exe in our Linux computer >> (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when >> we are just trying to open a PDB file and the program quits automatically. >> Has anyone encountered such a problem or have clues about where to look >> for solutions? Thanks a lot. >> >> Dong-Yan >> > > This sounds like a Linux kernel bug or C library bug. Please make sure > that you have applied all of the recommended patches to your SUSE system > (use the yast program to update it). In particular, there is a security > patch related to floating point exceptions, that should be applied > (). > It's not clear if that patch will fix the problem, so please apply the > rest. > > I would also expect upgrading to the current SUSE Linux to fix the > problem. > > Good luck, > > Greg Couch > UCSF Computer Graphics Lab > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From gregc at cgl.ucsf.edu Fri Jun 27 13:58:05 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 27 Jun 2008 13:58:05 -0700 (PDT) Subject: [Chimera-users] "Floating exception" error message In-Reply-To: <48654703.4070409@aecom.yu.edu> References: <88d6514c0df6611e42a1e7ca996d17e9.squirrel@netmail.aecom.yu.edu> <48654703.4070409@aecom.yu.edu> Message-ID: We compile a little bit of fortran code for chimera, and so far, we have not had any problems substituting gfortran for g77. But I understand your reluctance. For chimera, we use a newer version of gcc than what comes with the system by compiling our own from source and giving the "--prefix=/home/chimera" configuration option. Then users, who wish to use that compiler, put ~chimera/bin into the PATH environment variable and ~chimera/lib into the LD_LIBRARY_PATH environment variable. You could do something similar to check if the new compiler is really a problem or not before upgrading. You could also upgrade Linux and install an older compiler in a similar fashion. - Greg On Fri, 27 Jun 2008, hsosa at aecom.yu.edu wrote: >> I would also expect upgrading to the current SUSE Linux to fix the problem. > > One thing (not particularly related to Chimera) that is preventing us to > upgrade the system, is the risk of breaking other programs. In a particular > the newer versions of Linux come without G77 (Fortran 77 compiler) and come > with the newer "better" G90 compiler. I suspect a big headache when trying to > compile old Fortran coded programs that we still use. > > Greg Couch wrote: >> On Fri, 27 Jun 2008, Dong-Yan Tan wrote: >> >> >>> Dear all, >>> >>> We have just installed chimera-1.2470-linux.exe in our Linux computer >>> (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when >>> we are just trying to open a PDB file and the program quits automatically. >>> Has anyone encountered such a problem or have clues about where to look >>> for solutions? Thanks a lot. >>> >>> Dong-Yan >>> >> >> This sounds like a Linux kernel bug or C library bug. Please make sure >> that you have applied all of the recommended patches to your SUSE system >> (use the yast program to update it). In particular, there is a security >> patch related to floating point exceptions, that should be applied >> (). >> It's not clear if that patch will fix the problem, so please apply the >> rest. >> >> I would also expect upgrading to the current SUSE Linux to fix the problem. >> >> Good luck, >> >> Greg Couch >> UCSF Computer Graphics Lab >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> > > -- > ----------------------------------- > Hernando Sosa > Dept. of Physiology and Biophysics > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > FAX (718) 430-8819 > email hsosa at aecom.yu.edu > ----------------------------------- > > > > From goddard at cgl.ucsf.edu Tue Jun 24 14:51:59 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 24 Jun 2008 14:51:59 -0700 Subject: [Chimera-users] multiscale models and morph conformations In-Reply-To: <558F6B7F5360E046B597A008686EAFBF51A0E2@EXCHV1.lj.ad.scripps.edu> References: <200806161851.m5GIp0OW1832725@guanine.cgl.ucsf.edu> <4856DE12.7030700@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0D8@EXCHV1.lj.ad.scripps.edu> <48575B36.1000402@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DB@EXCHV1.lj.ad.scripps.edu> <48583B57.9050904@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0DF@EXCHV1.lj.ad.scripps.edu> <485AA067.5070202@cgl.ucsf.edu> <558F6B7F5360E046B597A008686EAFBF51A0E2@EXCHV1.lj.ad.scripps.edu> Message-ID: <48616C7F.2080508@cgl.ucsf.edu> Hi Ed, So you have morphed several molecules and want to show the same morph with the molecules represented by low resolution surfaces. You are right that the multiscale tool does not handle changing atom coordinates. I don't think using multiscale is a good approach. I'd use the molmap Chimera command to make a low resolution surface and I'd do it each frame using the Per-Frame / Define Script... capabilities of the MD Movie dialog. The molmap command would look like "molmap #2:.B 8.5 gridSpacing 1" to put a surface on model #2 chain B at 8.5 A resolution with a grid spacing of 1A (for smooth appearance). The molmap command by default removes a previous map calculated for the same set of atoms, so each frame will replace the surface. You could have one molmap command for each model or chain you want to put a surface on. Tom Edward Brignole wrote: > Tom, > > So now I've got pdb's fit into my maps (using the excellent volume segmentation by color, volume eraser, and fitting tools!) and I'm trying to model the conformational changes. The fit pdb's for each EM structure (all saved into one large pdb with submodels that can conveniently be repositioned relative to one another) have exactly the same chains just with rearranged positions of the original domains, but submodel 0.1 of each model had two chains so morph conformations gets confused cause the rest of the submodels 0.2-12 only had one chain. Morph-conformations works fine if I save my pdb as mol2, then there are no longer submodels. That's not such a pain, except that mol2 doesn't preserve residue number so displaying particular residues becomes difficult. > > So now I am trying to display EM-like structures in motion by using multiscale models of the intermediate conformations but the multiscale model doesn't follow its chain. So I suppose at this point the only way to visualize this is to write out each of the 60 intermediate pdb's, then through some scripting open each individually, make the multiscale model, display appropriately, save image. And then use ImageMagick to string these images into an animation to visualize the Morphing conformations. Also I can easily color the atoms of different chains but I'm having difficulty applying these colors to the multiscale models. Oops, wait I just discovered that MultiScale.color_surfaces_to_match_atoms() only works if I first select chains! Excellent. Still need some advice on multiscale movies though. > > Many thanks for all your help. > > Ed > > PS. The problem with findlevels wasn't that the map was inverted...I arrive at negative thresholds because I hadn't set the voxel size correctly. Doh! All goes well after that. > > Hi Ed, > > The Morph Conformations tool works with submodels. It will not work > between two models or submodels that have different numbers of chains. > The error message you get means that you are giving it models with > different numbers of chains. > > Tom > > > Edward Brignole wrote: > >> Tom, >> >> ... I'd like to use morph conformations between two pdbs each >> composed of the same submodels/chains. I've tried to do this through the >> dialog but it displays an error telling me "cannot interpolate the >> models have different numbers of chains". The only way I can see to do >> this is to write the pdb as a mol2 so that all atoms are in a single >> model without submodels, open the mol2, and run morph conformations. >> Is there another method or is this the simplest? >> >> Thanks, >> Ed >> > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From JeanDidier.Marechal at uab.cat Mon Jun 30 06:28:53 2008 From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal) Date: Mon, 30 Jun 2008 15:28:53 +0200 Subject: [Chimera-users] Dummy atoms Message-ID: <1cbece67647b.4868fbb5@uab.es> Dear all, I think the question was already posted but I can't find it. I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera? All the best JD Dr. Jean-Didier Mar?chal Professor Lector Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es ----- Missatge original ----- De: chimera-users-request at cgl.ucsf.edu Data: Dimarts, Juny 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 21 > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: how could u know the order of atoms? (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Jun 2008 14:22:31 -0700 > From: Eric Pettersen > Subject: Re: [Chimera-users] how could u know the order of atoms? > To: Kamal Al Nasr > Cc: chimera-users at cgl.ucsf.edu > Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4 at cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > > > Dear Sir/Madam, > > > > I am using Chimera viewer..and it is a great viewer ever... > > Thanks! I'm glad you like it. > > > I kindly have a question... how could you know (from PDB file) > the > > coorect bonding between atoms? I mean that how could you know > that > > this atom is connected with CA not N nor C.....do u have all > these > > bonds stored already in a database? or you use atom positions to > > determine that? > > For standard amino and nucleic acids, Chimera has templates > containing the correct connectivity. For non-standard residues it > bases the connectivity on inter-atomic distances, with a few added > heuristics (e.g. hydrogens can only have one bond). > > The templates are accessible in the Python layer with the > chimera.restmplFindResidue() function. You can look in the > Rotamers > extension for examples of its use. The distance-based connectivity > > function is also available for an entire molecule as > chimera.connectMolecule(). It takes the molecule as its only > argument and adds bonds to it. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.cgl.ucsf.edu/pipermail/chimera- > users/attachments/20080623/1de25fda/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 21 > ********************************************* > From meng at cgl.ucsf.edu Mon Jun 30 09:05:22 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 Jun 2008 09:05:22 -0700 Subject: [Chimera-users] Dummy atoms In-Reply-To: <1cbece67647b.4868fbb5@uab.es> References: <1cbece67647b.4868fbb5@uab.es> Message-ID: <8BD43835-614F-41F2-B22D-955D846EE650@cgl.ucsf.edu> Hi JD, Currently there is no dummy atom type in Chimera. List of types: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 30, 2008, at 6:28 AM, Jean Didier Pie Marechal wrote: > Dear all, > > I think the question was already posted but I can't find it. > I would like to make an atom I placed as an helium to a Dummy: What > is the corresponding atom type in Chimera? > > All the best > JD > > > > Dr. Jean-Didier Mar?chal > Professor Lector > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal at uab.es From yasser_est at fbio.uh.cu Fri Jun 27 12:33:58 2008 From: yasser_est at fbio.uh.cu (Yasser Almeida =?iso-8859-1?Q?Hern=E1ndez?=) Date: Fri, 27 Jun 2008 15:33:58 -0400 (CDT) Subject: [Chimera-users] Mutate by D- res... Message-ID: <56971.200.55.139.216.1214595238.squirrel@webmail.fbio.uh.cu> Can Chimera mutate by D-residues? If this is possible, how i can do it? Thanks... -- Yasser Almeida Hern?ndez Estudiante, 4to A?o Bioqu?mica Facultad de Biolog?a Universidad de la Habana From meng at cgl.ucsf.edu Mon Jun 30 10:53:33 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 Jun 2008 10:53:33 -0700 Subject: [Chimera-users] Mutate by D- res... In-Reply-To: <56971.200.55.139.216.1214595238.squirrel@webmail.fbio.uh.cu> References: <56971.200.55.139.216.1214595238.squirrel@webmail.fbio.uh.cu> Message-ID: <764C8677-6BC4-423C-BBE8-81F8CB48429F@cgl.ucsf.edu> Hi Yasser, Sorry, mutation with the Rotamers tool (or swapaa command) is only to L-amino acids. Some less convenient alternatives: - use Build Structure (under Tools... Structure Editing) to build out the D- side chain manually. Note the resulting bond lengths and angles are approximate. - open another structure that contains the D- amino acid, match the backbone atoms of the residue you wish to substitute, write out coordinates "relative to" the first structure, then manually edit the PDB file to substitute that sidechain for the one originally in the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 27, 2008, at 12:33 PM, Yasser Almeida Hern?ndez wrote: > Can Chimera mutate by D-residues? If this is possible, how i can do > it? > > Thanks... > -- > Yasser Almeida Hern?ndez > Estudiante, 4to A?o Bioqu?mica > Facultad de Biolog?a > Universidad de la Habana From pett at cgl.ucsf.edu Mon Jun 30 11:05:47 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 30 Jun 2008 11:05:47 -0700 Subject: [Chimera-users] Mutate by D- res... In-Reply-To: <764C8677-6BC4-423C-BBE8-81F8CB48429F@cgl.ucsf.edu> References: <56971.200.55.139.216.1214595238.squirrel@webmail.fbio.uh.cu> <764C8677-6BC4-423C-BBE8-81F8CB48429F@cgl.ucsf.edu> Message-ID: <155AC33A-341E-4684-8280-44FAED2F2C7D@cgl.ucsf.edu> You can also make Chimera add D amino acids via a relatively simple change in its Python code. If you edit / share/Rotamers/__init__.py, you will find a line that looks like this: xform, rmsd = matchPositions(_coordArray([n, ca, c]), (approximately line #53). Change it to this: xform, rmsd = matchPositions(_coordArray([c, ca, n]), i.e. swap the 'c' and then 'n'. This will have the effect of making it place the CB atom at the D position instead of the L position. Of course, when you are done make sure to swap the c and the n back or Chimera will add D amino acids forever. The other thing to keep in mind is that the rotamer libraries are developed for L amino acids and therefore are basically of little assistance in choosing a side chain conformation for D amino acids. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 30, 2008, at 10:53 AM, Elaine Meng wrote: > Hi Yasser, > Sorry, mutation with the Rotamers tool (or swapaa command) is only to > L-amino acids. > > Some less convenient alternatives: > > - use Build Structure (under Tools... Structure Editing) to build out > the D- side chain manually. Note the resulting bond lengths and > angles are approximate. > > - open another structure that contains the D- amino acid, match the > backbone atoms of the residue you wish to substitute, write out > coordinates "relative to" the first structure, then manually edit the > PDB file to substitute that sidechain for the one originally in the > structure. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > On Jun 27, 2008, at 12:33 PM, Yasser Almeida Hern?ndez wrote: > >> Can Chimera mutate by D-residues? If this is possible, how i can do >> it? >> >> Thanks... >> -- >> Yasser Almeida Hern?ndez >> Estudiante, 4to A?o Bioqu?mica >> Facultad de Biolog?a >> Universidad de la Habana > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: