From goddard at cgl.ucsf.edu Tue Aug 1 10:56:34 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 1 Aug 2006 10:56:34 -0700 (PDT) Subject: [Chimera-users] X3D to VRML conversion In-Reply-To: <561eeeda0607312008u1267ea4g24b2a3ee3bba2014@mail.gmail.com> (ndebroy@gmail.com) References: <561eeeda0607312008u1267ea4g24b2a3ee3bba2014@mail.gmail.com> Message-ID: <200608011756.k71HuYIJ1630104@guanine.cgl.ucsf.edu> Hi Nihshanka, Many others have mentioned the difficulty converting X3D to VRML. Janet Iwasa at UCSF has had some success using the X3dToVrml97.xslt conversion program, but says it is very slow and runs out of memory for large systems. I'll send you her email address in a separate email if you would like to ask her questions. In Chimera version 1.2255 the "File/Export Scene"menu entry allows directly exporting surfaces as VRML, but does not export molecule models (ribbons, ball+stick). Greg Couch in our lab has improved that code to also export molecular models, but we have not yet distributed a version of Chimera with that capability. I just tested it and find that it correctly exports molecules in ball and stick style and sphere style, but ribbons were not exported correctly (the VRML only showed a little piece). Hopefully the working version will be available in the next Chimera snapshot (within a few weeks or months). Greg is at a conference, and could give a better estimate of when it will be available when he returns later this week. Tom From goddard at cgl.ucsf.edu Tue Aug 1 13:09:34 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 1 Aug 2006 13:09:34 -0700 (PDT) Subject: [Chimera-users] X3D to VRML conversion Message-ID: <200608012009.k71K9Yp81683904@guanine.cgl.ucsf.edu> > Date: Tue, 01 Aug 2006 12:27:52 -0700 > From: Ben Morris > > Hey Tom, > > Were you using the chimera VRML viewer when you tested the new x3d2vrml > output? I had the same exact problem in my testing of the code before > submitting it, and Conrad told me that the Chimera vrml viewer is less > than perfect when it comes to complex geometry (surfaces and ribbons). I > don't know if you were using Chimera, or even if it is the only problem, > but when I tested the code using a third party viewer, ribbons and > surfaces worked fine! > > ~Ben Hi Ben, Yeah, I tested Chimera VRML output by reading it back into Chimera. I agree that the fact that ribbons did not display properly could very well be a problem with the Chimera VRML renderer rather than the output. I just displayed a Chimera round ribbon (1a0m) using FreeWRL 1.15 on Linux and it displayed correctly. It gave about 30 warnings like the following which may or may not be important: WARNING -- node Normal may not be ok as a field of type normal (...called from VRML::Field::SFNode, 1363) It sounds like you are the one who have worked on the Chimera VRML output rather than Greg. Thanks for working on this. I think it will be useful to many people. Tom From vincent.zoete at gmail.com Fri Aug 4 01:58:15 2006 From: vincent.zoete at gmail.com (Vincent Zoete) Date: Fri, 4 Aug 2006 10:58:15 +0200 Subject: [Chimera-users] Coloring binding modes according to an energy term with ViewDock Message-ID: <200608041058.16405.zoete@unil.ch> Hi, Does it exist a way to color the different ligand positions obtained during a docking run, and displayed by the Viewdock module of chimera, as a function of a given energy term present in the columns of the viewdock table? If not, I think this could be an useful option to add to chimera. Also, it could be interesting to have the possibility to display the color scale as a function of the energy term together with the structures. If it cannot be done in the chimera display, it could be in the generated figures. Otherwise, congratulation for the great job the UCSF computer graphics lab is making with Chimera! Thank you for your time. Sincerely, Vincent From meng at cgl.ucsf.edu Fri Aug 4 07:56:17 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Aug 2006 07:56:17 -0700 Subject: [Chimera-users] Coloring binding modes according to an energy term with ViewDock In-Reply-To: <200608041058.16405.zoete@unil.ch> References: <200608041058.16405.zoete@unil.ch> Message-ID: <3aeb7d1bdb89397985f0b28a7e25eb2b@cgl.ucsf.edu> Hi Vincent, Thanks for the encouragement! (a) Coloring by ViewDock score: Currently you cannot color the docked compounds based on values in the ViewDock table (except manually/individually), but that is a very good idea. It sounds like the values in each numerical column should be assigned as model attributes to the docked compounds. Then you could just use the Render by Attribute tool to define a color mapping, as can be done now for other attributes. We will need to do similar things in the future for scores/energies/probabilities of modeled structures, modeled loops, and sidechain rotamers when related features are added to Chimera. I mainly deal with the user interface and do not know if there are any difficult implementation issues, but this is definitely a good feature to put on the "to do" list. (b) Coloring "key": We haven't thought much about providing a key for the color mapping, but there was another similar request recently. Another thing to consider. Thanks for your suggestions, Elaine On Aug 4, 2006, at 1:58 AM, Vincent Zoete wrote: > Hi, > > Does it exist a way to color the different ligand positions obtained > during a > docking run, and displayed by the Viewdock module of chimera, as a > function > of a given energy term present in the columns of the viewdock table? > If not, I think this could be an useful option to add to chimera. > Also, it > could be interesting to have the possibility to display the color > scale as a > function of the energy term together with the structures. If it cannot > be > done in the chimera display, it could be in the generated figures. > > Otherwise, congratulation for the great job the UCSF computer graphics > lab is > making with Chimera! > > Thank you for your time. > Sincerely, > Vincent > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > ----- 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 nsmaan at gmail.com Fri Aug 4 11:57:48 2006 From: nsmaan at gmail.com (Narender Singh Maan) Date: Fri, 4 Aug 2006 13:57:48 -0500 Subject: [Chimera-users] coloring carbon and deleting hydrogens Message-ID: <731d86770608041157p78778434ua07d2e167fafa487@mail.gmail.com> Dear all, I am trying to show two residues of a protein structure with 50% surface transparency along with a stick model (rest of the protein is 0% surface transparent). Now in this i am having trouble in showing those stick residues in a different color (for e.g. the default for C atom is gray, which i want to show in green). Is there anyway in which i can do it?. also for those two residues i want to delete the hydrogens (only in stick, and not in surface representation)? any suggestions would be of great help. Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 4 13:28:14 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Aug 2006 13:28:14 -0700 Subject: [Chimera-users] coloring carbon and deleting hydrogens In-Reply-To: <731d86770608041157p78778434ua07d2e167fafa487@mail.gmail.com> References: <731d86770608041157p78778434ua07d2e167fafa487@mail.gmail.com> Message-ID: <6e738c5ae6a6613d0093170f08d5ba85@cgl.ucsf.edu> Hi Narender, There are several ways to accomplish each of those things. (1) Coloring atoms differently from surface: The command way is the shortest. For example, color green,a C will color carbon atoms but not their surfaces green, and color hot pink,s C will color the surfaces of carbon atoms but not the atoms hot pink. A longer way is to select the atoms you want to color and then use the Actions...Color menu. In that menu, first set the target to "atoms/bonds", then use the menu again to do the coloring. If you choose the dotted line at the top of the menu, that "tears off" the menu so it stays open until closed. After the coloring, you might want to set the target in the menu back to "all of the above" so it won't be confusing later. Since the surface is in the way for selecting by clicking on the atoms, you might want to hide the surface, select the atoms, and then re-show the surface (or, use a command or the Select menu to select the atoms instead of picking from the screen). You can toggle the whole surface hidden/shown using the Model Panel. (2) Undisplaying hydrogens: if you want the hydrogens to be surfaced but not shown, they should be undisplayed rather than deleted. The following command would undisplay all hydrogens: ~display H Or, you could use Select...Chemistry...element...H and then Actions...atoms/bonds... hide. If you delete the hydrogens, however, there would not be "holes" in the surface; instead, the surface would be recomputed for the structure without them. So maybe you really do want to delete them, for example: delete H You might want to take a look at the Getting Started tutorials (Help...Tutorials); one uses mostly the menu, one uses mostly commands, so you could pick the approach you prefer. I hope this helps, Elaine On Aug 4, 2006, at 11:57 AM, Narender Singh Maan wrote: > Dear all, > I am trying to show two residues of a protein structure with 50% > surface transparency along with a stick model (rest of the protein is > 0% surface transparent). Now in this i am having trouble in showing > those stick residues in a different color (for e.g. the default for C > atom is gray, which i want to show in green). Is there anyway in which > i can do it?. also for those two residues i want to delete the > hydrogens (only in stick, and not in surface representation)? any > suggestions would be of great help. > Thank you > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > ----- 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 ndebroy at gmail.com Sun Aug 6 23:36:06 2006 From: ndebroy at gmail.com (Nihshanka Debroy) Date: Mon, 7 Aug 2006 02:36:06 -0400 Subject: [Chimera-users] Electrostatic Potentials Message-ID: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> Hi everyone, I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes. Also, is there a way to get the actual potential values at each surface coordinate? Thanks a lot for the help. Sincerely, Nihshanka -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 7 16:15:52 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 7 Aug 2006 16:15:52 -0700 Subject: [Chimera-users] Electrostatic Potentials In-Reply-To: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> References: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> Message-ID: <61DA7B9F-841B-43AB-8978-389F76FB7C7F@cgl.ucsf.edu> Hi Nihshanka, It is necessary to delete atoms you don't want included in the calculation before initiating the calculation. Undisplaying atoms or surface does not make a difference - the atoms are still there, just undisplayed. Later, you could open the electrostatic potential map with the original full structure, if you wanted to display parts that had been deleted for the potential calculation. The "Electrostatic Surface Coloring" tool does get a potential value at each surface point in order to do the coloring, but the values are not available from the user interface. The "Values at Atom Positions" tool could be used to get the potential at the positions of atoms, but not the surface. If you knew particular coordinates you wanted to look at, you could make a PDB file with fake atoms at those positions and use the latter tool. However, if you really did want all the surface point values, I must defer to others who know python and the under-the-hood details. Electrostatic Surface Coloring man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html Values at Atom Positions man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ density.html Best, Elaine On Aug 6, 2006, at 11:36 PM, Nihshanka Debroy wrote: > Hi everyone, > I have a couple of questions about the > electrostatic potentials generated in Chimera using the Delphi > Controller. If I have a protein with 5 chains A,B,C,D,E, and I > choose to show the surfaces of all chains except C (but keep the > wireframe of chain C's atoms) and then run Delphi using the > DelphiController, does that mean that the potential surface > generated is in the absence of chain C (which is what I want)? I'm > trying to generate the potential surface without taking into > account chain C, but would like to see C's wire frame for analysis > purposes. > Also, is there a way to get the actual potential > values at each surface coordinate? > > Thanks a lot for the help. > Sincerely, > Nihshanka > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 7 16:24:58 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 7 Aug 2006 16:24:58 -0700 Subject: [Chimera-users] Electrostatic Potentials In-Reply-To: <61DA7B9F-841B-43AB-8978-389F76FB7C7F@cgl.ucsf.edu> References: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> <61DA7B9F-841B-43AB-8978-389F76FB7C7F@cgl.ucsf.edu> Message-ID: <2A7608E6-E779-49B5-A67C-7584D8605169@cgl.ucsf.edu> You could also select chain C, use File...Save PDB to save just the selected atoms (there's a check button for that in the dialog) and then delete chain C, run Delphi, and then read in the file you saved. --Eric On Aug 7, 2006, at 4:15 PM, Elaine Meng wrote: > Hi Nihshanka, > It is necessary to delete atoms you don't want included in the > calculation before initiating the calculation. Undisplaying atoms > or surface does not make a difference - the atoms are still there, > just undisplayed. Later, you could open the electrostatic > potential map with the original full structure, if you wanted to > display parts that had been deleted for the potential calculation. > > The "Electrostatic Surface Coloring" tool does get a potential > value at each surface point in order to do the coloring, but the > values are not available from the user interface. The "Values at > Atom Positions" tool could be used to get the potential at the > positions of atoms, but not the surface. If you knew particular > coordinates you wanted to look at, you could make a PDB file with > fake atoms at those positions and use the latter tool. However, if > you really did want all the surface point values, I must defer to > others who know python and the under-the-hood details. > > Electrostatic Surface Coloring man page: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ > surfcolor.html > > Values at Atom Positions man page: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ > density.html > > Best, > Elaine > > On Aug 6, 2006, at 11:36 PM, Nihshanka Debroy wrote: > >> Hi everyone, >> I have a couple of questions about the >> electrostatic potentials generated in Chimera using the Delphi >> Controller. If I have a protein with 5 chains A,B,C,D,E, and I >> choose to show the surfaces of all chains except C (but keep the >> wireframe of chain C's atoms) and then run Delphi using the >> DelphiController, does that mean that the potential surface >> generated is in the absence of chain C (which is what I want)? I'm >> trying to generate the potential surface without taking into >> account chain C, but would like to see C's wire frame for analysis >> purposes. >> Also, is there a way to get the actual potential >> values at each surface coordinate? >> >> Thanks a lot for the help. >> Sincerely, >> Nihshanka >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > ----- > 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 > > > > > _______________________________________________ > 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 Aug 7 17:22:17 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 7 Aug 2006 17:22:17 -0700 (PDT) Subject: [Chimera-users] Electrostatic Potentials In-Reply-To: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> (ndebroy@gmail.com) References: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> Message-ID: <200608080022.k780MH9P1718483@guanine.cgl.ucsf.edu> Hi Nihshanka, If you want to just dump all the xyz coordinates of the surfaces points and the electrostatic potential you could modify the Chimera code in a small way. You would modify file chimera/share/Surface_Color/__init__.py using any text editor. After line 157 def point_colors(self, vertices, vertex_xform): values, outside = self.volume_values(vertices, vertex_xform) add the "for" and "print" statements shown below. def point_colors(self, vertices, vertex_xform): values, outside = self.volume_values(vertices, vertex_xform) for i in range(len(values)): print vertices[i], values[i] Indentation is important so indent as shown. This change will print each xyz coordinate and the potential value to the Chimera reply log (menu Favorites / Reply Log). Printing a huge list of surface points and potential values may not be that useful since it will be hard to determine what atoms the surface points are near. Here is a differnt approach to check the potential at specific points. The basic idea is to place a marker and move it to where you want to know the potential. Place the marker using volume path tracer, menu entry Tools / Volume Data / Volume Path Tracer. Turn on the switches "Drop markers on empty space" and also "Move markers with mouse" in the path tracer dialog. Then click with mouse button 3 with the Ctrl keyboard key held down to drop a marker. You can drag the marker using Ctrl-button-3 to whatever location you want. Now use the Values at Atom Positions tool, menu entry Tools / Volume Data / Values at Atom Positions. Select "marker set 1" from the Molecule menu. This is the fake molecule that contains the marker you just dropped which is a fake atom. Now press the Histogram button on the values at atom positions dialog. That will show another dialog giving the potential value at the marker position. To get the value at a new position, drag the marker and press the Histogram button again. Would be nicer to be able to just click on the surface to get the potential value at that surface point. That is not currently possible but I'll add to my list of requested features. Tom From halic at lmb.uni-muenchen.de Tue Aug 8 10:08:10 2006 From: halic at lmb.uni-muenchen.de (Mario Halic) Date: Tue, 08 Aug 2006 19:08:10 +0200 Subject: [Chimera-users] spaceball Message-ID: <1155056890.26621.531.camel@cryosun3.lmb.uni-muenchen.de> hi!, can I use spaceball 5000 as input device in chimera? thanks, Mario From goddard at cgl.ucsf.edu Tue Aug 8 18:31:30 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 8 Aug 2006 18:31:30 -0700 (PDT) Subject: [Chimera-users] Electrostatic Potentials In-Reply-To: <561eeeda0608081753t7c2048c5u54c9caed2deb6e3d@mail.gmail.com> (ndebroy@gmail.com) References: <561eeeda0608062336r50008b4dm4eab8f3298a86985@mail.gmail.com> <200608080022.k780MH9P1718483@guanine.cgl.ucsf.edu> <561eeeda0608081753t7c2048c5u54c9caed2deb6e3d@mail.gmail.com> Message-ID: <200608090131.k791VU9Y1914238@guanine.cgl.ucsf.edu> Hi Nihshanka, Oops! My previous descriptions of how to determine electrostatic potential values at specific surface points assumed you were using the Surface Color tool to display the potential (menu entry Tools / Structure&Binding Analysis / Electrostatic Surface Coloring, or menu entry Tools / Volume Data / Surface Color). But you are using DelphiController and it has its own code for displaying potential values for which my previously described techniques will not work. To print the potential values at every surface point when the potential display was done with Delphi Controller you could put a print statement in chimera/share/DelphiViewer/MSMSTexturer.py at line 155, after the following lines of code else: # Point is outside of phi map. phivalue = 0 add the line print v_rs, phivalue Make sure the "print" line is indented the same as the "else:". This is going to print many thousands of lines in the Reply Log so be prepared to wait a bit. You could also use my previously described methods for showing potential values by using the Electrostatic Surface Coloring tool. Show a surface for your PDB model using Actions / Suface / show. Then in the Electrostatic Surface Coloring dialog press the "Open map data..." button and select the *.phi file generated by DelPhi (the one computed when running Delphi Controller). Then press the Color button on the surface color dialog. My previous code modification or the marker probe method could them be used. Tom From gregc at cgl.ucsf.edu Wed Aug 9 11:23:30 2006 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 9 Aug 2006 11:23:30 -0700 (PDT) Subject: [Chimera-users] spaceball In-Reply-To: <1155056890.26621.531.camel@cryosun3.lmb.uni-muenchen.de> References: <1155056890.26621.531.camel@cryosun3.lmb.uni-muenchen.de> Message-ID: On Tue, 8 Aug 2006, Mario Halic wrote: > can I use spaceball 5000 as input device in chimera? It's on my list of things to do, but right now the answer is no. - Greg From raquel_hernandez at ncsu.edu Fri Aug 11 13:50:37 2006 From: raquel_hernandez at ncsu.edu (Raquel Hernandez) Date: Fri, 11 Aug 2006 16:50:37 -0400 Subject: [Chimera-users] structure slice Message-ID: <7.0.0.16.2.20060811164204.021216c8@ncsu.edu> Hello chimera e-mail, I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks. Raquel Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047 From meng at cgl.ucsf.edu Sat Aug 12 12:14:08 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 12 Aug 2006 12:14:08 -0700 Subject: [Chimera-users] structure slice In-Reply-To: <7.0.0.16.2.20060811164204.021216c8@ncsu.edu> References: <7.0.0.16.2.20060811164204.021216c8@ncsu.edu> Message-ID: <58b473b66f7442a45343631c838f4614@cgl.ucsf.edu> Hi Raquel, Assuming you are viewing electron density (such as from EM) rather than atomic coordinates, you might want to look at the page of helpful hints for volume viewing in Chimera, especially the sections "slicing and capping" and "slab clipping": http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/ volumetour.html#capping http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/ volumetour.html#slab Also, the Chimera User's Guide (Help... User's Guide in the Chimera menu) includes manual pages for the tools mentioned in the volume viewing tips (Volume Viewer, Side View, Surface Capping, Per-Model Clipping, etc.). I hope this helps, Elaine On Aug 11, 2006, at 1:50 PM, Raquel Hernandez wrote: > Hello chimera e-mail, > > I have received from a colleague data set from a virus > reconstruction. I am a novice in the use of your program but have > managed to make an image of my virus. I would like to add an image > of a slice of the virus through the center perpendicular to the three > fold axis. Can you please advise me on what I need to do to make a > slice? I can get the tech people here to help if you tell me the > tools, etc that I need to use. Thanks. > > Raquel > > Raquel Hernandez > Research Associate Professor > Department of Molecular and Structural Biochemistry > 128 Polk Hall > North Carolina State University > Raleigh, NC 27695 > office:919-515-5765 > lab: 919-515-5786 > Fax: 919-515-2047 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > ----- 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 Annalisa.Mercuri at uea.ac.uk Mon Aug 14 04:31:23 2006 From: Annalisa.Mercuri at uea.ac.uk (Annalisa Mercuri) Date: Mon, 14 Aug 2006 12:31:23 +0100 (BST) Subject: [Chimera-users] Surfactant Message-ID: <1381.139.222.112.20.1155555083.squirrel@ueawebmail.uea.ac.uk> Hallo everybody, I'm working with surfactants and emulsions. I'd like to use Chimera to reconstruct a micelle with my components, but I have no clue how to do that. Further my emulsion is made by a mixture of two surfactants. I would like to have a emulsion droplet image like the virus one. What do you suggest? Thank you for your help and advices Annalisa Mercuri MSc PhD Student School of Chemical Sciences and Pharmacy University of East Anglia Norwich Norfolk NR4 7TJ UK From meng at cgl.ucsf.edu Mon Aug 14 09:59:18 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 14 Aug 2006 09:59:18 -0700 Subject: [Chimera-users] Surfactant In-Reply-To: <1381.139.222.112.20.1155555083.squirrel@ueawebmail.uea.ac.uk> References: <1381.139.222.112.20.1155555083.squirrel@ueawebmail.uea.ac.uk> Message-ID: <60AF6C29-5FD9-4BF5-B627-DDF5313CD5BD@cgl.ucsf.edu> Hi Annalisa, Chimera (at least currently) does not have much building ability or features for solvating structures or constructing assemblies such as micelles. To show a micelle with Multiscale Models in Chimera, you would need: (a) coordinates for a minimal repeating unit in the "micelle" (each molecule a separate chain) (b) matrices describing the symmetry operations to apply to those coordinates to construct the whole "micelle" Look at the contents of your virus PDB input as an example. You would need to know the size of the desired micelle in order to create the symmetry operators. Actually, this "micelle" would be an approximation only, because as I understand it, micelles are disordered as opposed to the symmetrical construct you would obtain with the information above. Another approach is to use some other program to build the micelle and read it into Chimera. Multiscale Models would show a separate "blob" for each chain in the input (i.e. give a different chain ID to each thing you want to be a separate blob). My best guess is that molecular mechanics/molecular dynamics programs may have micelle-building capabilities. I recommend looking at papers that involve atomistic models of micelles and looking at their "materials and methods" sections to see how others have constructed such models. Best, Elaine On Aug 14, 2006, at 4:31 AM, Annalisa Mercuri wrote: > Hallo everybody, > > I'm working with surfactants and emulsions. I'd like to use Chimera to > reconstruct a micelle with my components, but I have no clue how to do > that. Further my emulsion is made by a mixture of two surfactants. > I would > like to have a emulsion droplet image like the virus one. What do you > suggest? > > Thank you for your help and advices > > > Annalisa Mercuri MSc > PhD Student > School of Chemical Sciences and Pharmacy > University of East Anglia > Norwich > Norfolk > NR4 7TJ > UK ----- 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 meng at cgl.ucsf.edu Mon Aug 14 10:20:33 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 14 Aug 2006 10:20:33 -0700 Subject: [Chimera-users] Fwd: Chimera and Macs References: Message-ID: <1C25C9FF-5A1E-448F-9316-2F800CAEDF56@cgl.ucsf.edu> Hello Mac users! When the Chimera window gets obscured by other windows on a Mac, clicking the X11 icon will bring it to the front (assuming you are using the recommended Mac/X11 version of Chimera). Begin forwarded message: > From: Kevin Dalby > Date: August 13, 2006 11:54:43 PM PDT > To: Elaine Meng > Subject: Re: Chimera and Macs > > Hi Elaine > > I think we spoke briefly at the enzymes GRC. > > I am not a sophisticated chimera user. I use it on my mac while > working with another 10 programs . Usually i cant see the chimera > screen when i need it. Normally, when I want to get back to a > program that is hidden i go to the doc and just click on the > program icon and it comes to the front. This does not happen for > chimera. I know other spoilt mac users would enjoy a remedy. > > > best wishes > > Kevin > > > Kevin Dalby > Associate Professor of Medicinal Chemistry > University of Texas at Austin > tel 512-4719267 > fax 512-2322606 > > > > ----- 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 goddard at cgl.ucsf.edu Mon Aug 14 15:56:02 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 14 Aug 2006 15:56:02 -0700 (PDT) Subject: [Chimera-users] structure slice In-Reply-To: <7.0.0.16.2.20060811164204.021216c8@ncsu.edu> (message from Raquel Hernandez on Fri, 11 Aug 2006 16:50:37 -0400) References: <7.0.0.16.2.20060811164204.021216c8@ncsu.edu> Message-ID: <200608142256.k7EMu2k91872991@guanine.cgl.ucsf.edu> Hi Raquel, The documentation Elaine suggests will help show a slab of your virus EM map. Here are a few specific details. Open your map using Chimera menu entry File / Open.... I used em_1015 from the VIPERdb web site. Figure out where the 3 fold and fold axes are. I used menu entry Tools / Higher-Order Structure / Icosahedron Surface and displayed the different orientation to find one that matches the map. Orient the 3-fold axis perpendicular to the screen. The map I tried had 2-fold axes along x, y, and z axes (orientation xyz 2-fold axes in icosahedron tool). So I displayed the Chimera command line with menu entry Favorites / Command Line and typed command "turn y 20.905157448" This rotates the models about the screen y axis by 20.9 degrees which is the angular separation between a 2-fold axis and nearest 3-fold axis. If you have rotated your model with the mouse, first put it back to the standard orientation by typing the command "reset". Next I used menu Favorites / Side View and dragged the left vertical yellow line in the side view window into the particle. That is the front clip plane. And I dragged the back clip plane (right vertical yellow line) into the particle. Then I used menu entry Tools / Depiction / Surface Capping and turned on the switch to "Cap surfaces at clip planes". This covers the holes left when clipping the surface. You can adjust the contour threshold level by moving the vertical bar on the histogram in the volume dialog which appeared when you first opened the EM map. You can precisely control the thickness of the slab using the Camera tab of the Side View window, setting the numeric values of the near and far clip plane. You can color the sliced part of the map according to density value using menu entry Tools / Volume Data / Surface Color described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorcap The side view clip planes I used are always parallel to the screen. You can use "per-model clip planes" that rotate with the model using menu entry Tools / Depiction / Per-Model Clipping. Alot to figure out. Tom From goddard at cgl.ucsf.edu Mon Aug 14 16:13:17 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 14 Aug 2006 16:13:17 -0700 (PDT) Subject: [Chimera-users] Surfactant In-Reply-To: <1381.139.222.112.20.1155555083.squirrel@ueawebmail.uea.ac.uk> (Annalisa.Mercuri@uea.ac.uk) References: <1381.139.222.112.20.1155555083.squirrel@ueawebmail.uea.ac.uk> Message-ID: <200608142313.k7ENDHG31857075@guanine.cgl.ucsf.edu> Hi Annalisa, The Chimera Multiscale tool makes a low resolution surface for each chain of a PDB model. You could put all of type A surfactant molecules in one chain, and all type B surfactant molecules in another chain. Open the model in Chimera (menu File / Open) then use menu entry Tools / Higher-Order Structure / Multiscale Models, select Multimer type "None" at the bottom of the dialog and press the "Make models" button near the bottom. You'll probably want a higher surface resolution than the default 8 angstroms. Press the Select "All" button at the top of the multiscale dialog, then change the resolution value (middle of dialog) from 8 to 3 and press the Resurface button. By using two PDB chains you will have two surfaces -- one for each type of surfactant. Each can be colored by selecting it (hold ctrl and click on it with mouse button 1), then press the Color button in the multiscale dialog and choose a new color. The multiscale dialog is also able to use matrices to position copies of molecules as Elaine noted. But since your surfactant molecules are all in different conformations I don't think that will help you. Tom From ndebroy at gmail.com Mon Aug 14 20:38:59 2006 From: ndebroy at gmail.com (Nihshanka Debroy) Date: Mon, 14 Aug 2006 23:38:59 -0400 Subject: [Chimera-users] addH utility and PDB files Message-ID: <561eeeda0608142038p7b56b3c8q4032647c192030cb@mail.gmail.com> Hi, I have a couple of questions about the addH utility built into Chimera, and about PDB files in general. I used addH to protonate (add hydrogens) to PDB files. Does it use a force field of some kind in the process, like Amber or Charmm? It seems that depending on the force field used to protonate a PDB, the values for the partial charges and the van der waals radii are different. Specifically, I am using these charges and radii in the DelphiController. Another thing I've noticed is that when adding hydrogens, for the same amino acid, the hydrogens are sometimes different in name or number. For example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added for the gamma sulphur, balancing out charges completely. In other cases, the HG is not added, and so the amino acid ends up with a net negative charge. I was just wondering if this is supposed to happen. Here's another example. For Alanine, I was getting 1H, 2H and 3H attached to the nitrogen in some cases. In other cases, I just got "H" attached to the nitrogen. Does this mean those particular instances of ALA in the PDB had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a net negative charge on the ALA? Thanks for all the help and for this mailing list. It is a wonderful resource. Sincerely, Nihshanka Debroy -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 15 10:00:19 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 15 Aug 2006 10:00:19 -0700 Subject: [Chimera-users] addH utility and PDB files In-Reply-To: <561eeeda0608142038p7b56b3c8q4032647c192030cb@mail.gmail.com> References: <561eeeda0608142038p7b56b3c8q4032647c192030cb@mail.gmail.com> Message-ID: <899CFEF0-1095-4DEB-A44A-7F3941FB430A@cgl.ucsf.edu> Hi Nihshanka, I'll try to answer your questions in a brief manner, but see the AddH man page for a full description: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html AddH does not use a force field. It uses the atom types and rules to place hydrogens. For example, if there is an sp3-hybridized carbon, it knows there should be four bonds from that carbon in tetrahedral arrangement. If two things are already bonded to that carbon, two hydrogens will be added to complete the known valence. For some atoms, this completely determines the position of the hydrogens. For other atoms, such as a hydroxyl group, there is a degree of freedom, and additional information is used to place the hydrogen. The choices are "steric only" and "also consider H-bonds" - the first places the H to avoid clashes and the second places the H to both avoid clashes and form H-bonds where possible. AddH does not put charges on the structure. You could do that with Add Charge (or Dock Prep, which calls Add Charge). HOWEVER, DelPhi completely ignores the radii and charges that Chimera knows about. DelPhi uses only the radii and charges in the parameter files that you specify in DelPhiController. Depending on which parameter files you use in DelPhi, it might not even be necessary to add hydrogens. If an amino acid is forming different bonds, it will be protonated differently. If a residue is on the N-terminus of a chain, the most likely protonation state (and the one chosen by AddH) is -NH3(+). If a residue is on the C-terminus, the backbone ends in a carboxylate with the most likely protonation state -CO2(-). Force fields, or at least Amber, have different sets of charges for the same residue depending whether it is on the N-terminus, C-terminus, or in the middle of the chain. If the PDB file says that a cysteine is disulfide-bonded to another cysteine (sidechains forming an S-S bond), then no hydrogens are put on those sulfurs because they are already forming all the bonds they can. Histidine is a little different - the sidechain can be positively charged or neutral depending on its environment. You can have the program decide, or control it yourself by changing the residue name as described in the man page. In all these cases the force field will have different sets of charges for the different bonding patterns, usually indicated by different residue names, that add up to the appropriate formal charges. What these residue names should be depends on the specific force field or DelPhi parameter file. I hope this helps, Elaine On Aug 14, 2006, at 8:38 PM, Nihshanka Debroy wrote: > Hi, > I have a couple of questions about the addH utility built into > Chimera, and about PDB files in general. I used addH to protonate > (add hydrogens) to PDB files. Does it use a force field of some > kind in the process, like Amber or Charmm? It seems that depending > on the force field used to protonate a PDB, the values for the > partial charges and the van der waals radii are different. > Specifically, I am using these charges and radii in the > DelphiController. > Another thing I've noticed is that when adding hydrogens, for > the same amino acid, the hydrogens are sometimes different in name > or number. For example if I have a Cysteine, in some cases, an HG > (gamma hydrogen) is added for the gamma sulphur, balancing out > charges completely. In other cases, the HG is not added, and so the > amino acid ends up with a net negative charge. I was just wondering > if this is supposed to happen. > Here's another example. For Alanine, I was getting 1H, 2H and 3H > attached to the nitrogen in some cases. In other cases, I just got > "H" attached to the nitrogen. Does this mean those particular > instances of ALA in the PDB had one only hydrogen attached to the > nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a > net negative charge on the ALA? > Thanks for all the help and for this mailing list. It is a > wonderful resource. > > Sincerely, > Nihshanka Debroy > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 -------------- An HTML attachment was scrubbed... URL: From sabuj.pattanayek at vanderbilt.edu Fri Aug 18 18:25:24 2006 From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek) Date: Fri, 18 Aug 2006 20:25:24 -0500 Subject: [Chimera-users] RealD (Stereographics) E2SGI emitter on Quadro 3450? Message-ID: <44E66884.407@vanderbilt.edu> Hi all, Anyone know if it's possible to use a RealD (Stereographics) E2SGI emitter on Quadro hardware? Thanks, Sabuj Pattanayek From hsosa at aecom.yu.edu Sat Aug 19 11:41:44 2006 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Sat, 19 Aug 2006 14:41:44 -0400 Subject: [Chimera-users] Volume color zones Message-ID: <44E75B68.5060508@aecom.yu.edu> Is is possible to use different colors for different Volume zones ?. I have a volume (MRC format) and have defined two marker sets using the Volume-Path-Tracer. Then I select one of the path and colored the surface volume around using the Volume Color Zone utility. This work fine but then if I selected the other markers and do the same the volume close to the new markers get colored but anything else get uncolored, including the areas previously colored. Am I doing something wrong ?. Can I color several Volume zones independently ? Thanks Hernando -- From meng at cgl.ucsf.edu Sat Aug 19 12:04:02 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 19 Aug 2006 12:04:02 -0700 Subject: [Chimera-users] Volume color zones In-Reply-To: <44E75B68.5060508@aecom.yu.edu> References: <44E75B68.5060508@aecom.yu.edu> Message-ID: <2e00783b62ab8c3928f348cb58c3dd47@cgl.ucsf.edu> Hi Hernando, The way to get multiple color zones is to get all of the markers (that you want to make zones around) selected at the same time, and then use Color Zone in one step. The markers can have multiple different colors, resulting in differently colored volume zones. However, this means you can't use different radii for different markers. 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 Aug 19, 2006, at 11:41 AM, hsosa at aecom.yu.edu wrote: > Is is possible to use different colors for different Volume zones ?. > > I have a volume (MRC format) and have defined two marker sets using the > Volume-Path-Tracer. Then I select one of the path and colored the > surface volume around using the Volume Color Zone utility. > This work fine but then if I selected the other markers and do the same > the volume close to the new markers get colored but anything else get > uncolored, including the areas previously colored. > Am I doing something wrong ?. > Can I color several Volume zones independently ? > > Thanks > > Hernando > From goddard at cgl.ucsf.edu Mon Aug 21 10:04:20 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 21 Aug 2006 10:04:20 -0700 (PDT) Subject: [Chimera-users] Volume color zones In-Reply-To: <44E75B68.5060508@aecom.yu.edu> (hsosa@aecom.yu.edu) References: <44E75B68.5060508@aecom.yu.edu> Message-ID: <200608211704.k7LH4Kgc1874499@guanine.cgl.ucsf.edu> Hi Hernando, Elaine's suggestions about how to color multiple volume zones is the way to go. It is currently not possible to color separate regions of the map in separate steps -- they all have to be colored in one use of the Color Zone tool. The technical reason for that is that Chimera automatically updates the coloring if you change the volume surface, for example, by changing the contour level. If coloring in several steps were allowed Chimera would need to remember the sequence of colorings you applied. This makes the code more complex. Remembering the sequence of coloring steps would also be needed for saving Chimera sessions. I'll think about whether the extra complexity of the code is worth the added flexibility. Tom From johns at ks.uiuc.edu Fri Aug 18 20:33:36 2006 From: johns at ks.uiuc.edu (John Stone) Date: Fri, 18 Aug 2006 22:33:36 -0500 Subject: [Chimera-users] vmd-l: RealD (Stereographics) E2SGI emitter on Quadro 3450? In-Reply-To: <44E66884.407@vanderbilt.edu> References: <44E66884.407@vanderbilt.edu> Message-ID: <20060819033327.GA21345@moline.ks.uiuc.edu> Hi, Not with the normal cable. I haven't checked the voltage or polarity of the sync signal output on the Quadro VESA stereo sync connector, but I do know that at the very least it's not pin-compatible with the old emitters. The old emitters could be made to work with various machines with adapter cables, but all of the old SGI/Sun/HP workstations I used had compatible sync signals from the point of view of peak-to-peak voltage, and so on. We have various old E2SGI emitters, some EPROs, an ENT (VESA) and while I've used the EPROs on almost all of the commercial Unix workstations, I've only ever used the ENT on the PC/Mac graphics boards like the Quadro. The ReadlD (stereographics) site may have pinouts and specs for the VESA stereo outputs, but you may have to do a bit of digging to figure out if that can be made to work with the E2SGI emitters. John On Fri, Aug 18, 2006 at 08:25:24PM -0500, Sabuj Pattanayek wrote: > Hi all, > > Anyone know if it's possible to use a RealD (Stereographics) E2SGI > emitter on Quadro hardware? > > Thanks, > Sabuj Pattanayek -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns at ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From roex0050 at umn.edu Wed Aug 23 18:22:26 2006 From: roex0050 at umn.edu (Dave Roe) Date: Wed, 23 Aug 2006 20:22:26 -0500 Subject: [Chimera-users] addH/removeH for charged a.a. Message-ID: <20060824012226.GB9737@droe-rt-dsl.real-time.com> Is there functionality that will - add a hydrogen (if needed) to all Lysines and Arginines to give the protonated form - remove a hydrogen (if needed) from Aspartic and Glutamic acids to give the deprotonated form? -- Dave Roe roex0050 at umn.edu From meng at cgl.ucsf.edu Thu Aug 24 09:45:22 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 24 Aug 2006 09:45:22 -0700 Subject: [Chimera-users] addH/removeH for charged a.a. In-Reply-To: <20060824012226.GB9737@droe-rt-dsl.real-time.com> References: <20060824012226.GB9737@droe-rt-dsl.real-time.com> Message-ID: Hi Dave, Just use the AddH tool or the command "addh" to add hydrogens to your structure: The residues are defined to give the most likely protonation states at physiological pH: lysine and arginine sidechains will be "protonated" (formal charge +1) and aspartic and glutamic acid sidechains will be "deprotonated" (formal charge -). Protonation states are mentioned in the AddH man page: http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/addh/ addh.html If you actually wanted the less common neutral states, it is easy for lysine and arginine: just select (Ctrl-click) the hydrogen(s) you want to delete and use Actions... Atoms/Bonds... delete (or the command "delete sel"). For aspartic and glutamic acids, you would need to force the program to add a hydrogen that it normally wouldn't, which can be done but involves a longer explanation. If you want that explanation, let me know. 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 Aug 23, 2006, at 6:22 PM, Dave Roe wrote: > Is there functionality that will > - add a hydrogen (if needed) to all Lysines and Arginines to give the > protonated form > - remove a hydrogen (if needed) from Aspartic and Glutamic acids to > give the > deprotonated form? > > -- > Dave Roe roex0050 at umn.edu > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From roex0050 at umn.edu Sat Aug 26 12:53:13 2006 From: roex0050 at umn.edu (Dave Roe) Date: Sat, 26 Aug 2006 14:53:13 -0500 Subject: [Chimera-users] addH/removeH for charged a.a. In-Reply-To: References: <20060824012226.GB9737@droe-rt-dsl.real-time.com> Message-ID: <20060826195313.GA10857@droe-rt-dsl.real-time.com> Thanks Elaine, The key for me was that I needed to delete all hydrogens first and then use the AddH tool. It wouldn't remove the hydrogen from the acids if they were already there. * Elaine Meng [2006-08-24 09:45 -0700]: > Hi Dave, > Just use the AddH tool or the command "addh" to add hydrogens to your > structure: > > The residues are defined to give the most likely protonation states > at physiological pH: lysine and arginine sidechains will be > "protonated" (formal charge +1) and aspartic and glutamic acid > sidechains will be "deprotonated" (formal charge -). Protonation > states are mentioned in the AddH man page: > http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/addh/ > addh.html > > If you actually wanted the less common neutral states, it is easy for > lysine and arginine: just select (Ctrl-click) the hydrogen(s) you > want to delete and use Actions... Atoms/Bonds... delete (or the > command "delete sel"). For aspartic and glutamic acids, you would > need to force the program to add a hydrogen that it normally > wouldn't, which can be done but involves a longer explanation. If > you want that explanation, let me know. > > 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 Aug 23, 2006, at 6:22 PM, Dave Roe wrote: > > >Is there functionality that will > >- add a hydrogen (if needed) to all Lysines and Arginines to give the > > protonated form > >- remove a hydrogen (if needed) from Aspartic and Glutamic acids to > >give the > > deprotonated form? > > > >-- > >Dave Roe roex0050 at umn.edu > > > >_______________________________________________ > >Chimera-users mailing list > >Chimera-users at cgl.ucsf.edu > >http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- Dave Roe roex0050 at umn.edu From yunierkis at uclv.edu.cu Mon Aug 28 12:48:01 2006 From: yunierkis at uclv.edu.cu (Yunierkis Perez Castillo) Date: Mon, 28 Aug 2006 15:48:01 -0400 Subject: [Chimera-users] change chain id Message-ID: <1156794481.5425.8.camel@amphitrite.cbq.uclv.edu.cu> Hi all, I need to change the chain ID for a protein, that is, change the chain A to chain B. Can I do that with chimera? Thanks in advance Yunierkis -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 28 13:36:31 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Aug 2006 13:36:31 -0700 Subject: [Chimera-users] change chain id In-Reply-To: <1156794481.5425.8.camel@amphitrite.cbq.uclv.edu.cu> References: <1156794481.5425.8.camel@amphitrite.cbq.uclv.edu.cu> Message-ID: <164E5447-10E3-4FCC-B1BA-7E7C345E494A@cgl.ucsf.edu> Hi Yunierkis, Sorry, there is no way to change the chain ID in Chimera. You would need to text-edit A to B in the PDB file before opening it. (Or, if you're fetching the structure from the PDB, write it out in PDB format, edit the file, and read it back in.) Depending on what you are trying to do, there may be some way of doing it without changing chain ID. Best, Elaine On Aug 28, 2006, at 12:48 PM, Yunierkis Perez Castillo wrote: > Hi all, > > I need to change the chain ID for a protein, that is, change the > chain A to chain B. > Can I do that with chimera? > > Thanks in advance > Yunierkis > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 28 13:51:06 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 28 Aug 2006 13:51:06 -0700 Subject: [Chimera-users] change chain id In-Reply-To: <164E5447-10E3-4FCC-B1BA-7E7C345E494A@cgl.ucsf.edu> References: <1156794481.5425.8.camel@amphitrite.cbq.uclv.edu.cu> <164E5447-10E3-4FCC-B1BA-7E7C345E494A@cgl.ucsf.edu> Message-ID: There is kind of a "cheaty" way to do it if you are using the 1.2255 snapshot by saving a session file and editing it. You need to use an editor that can handle long lines, like TextEdit.app on a Mac or WordPad on Windows. Search for the string 'chain' (including the quotes). You'll see some text that looks something like: 'chain': (29, 'A', {}) change the A to B so it looks like: 'chain': (29, 'B', {}) save the edited session and open it in Chimera and the chain ID will have changed. --Eric On Aug 28, 2006, at 1:36 PM, Elaine Meng wrote: > Hi Yunierkis, > Sorry, there is no way to change the chain ID in Chimera. You > would need to text-edit A to B in the PDB file before opening it. > (Or, if you're fetching the structure from the PDB, write it out in > PDB format, edit the file, and read it back in.) > > Depending on what you are trying to do, there may be some way of > doing it without changing chain ID. > Best, > Elaine > > On Aug 28, 2006, at 12:48 PM, Yunierkis Perez Castillo wrote: > >> Hi all, >> >> I need to change the chain ID for a protein, that is, change the >> chain A to chain B. >> Can I do that with chimera? >> >> Thanks in advance >> Yunierkis >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > ----- > 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 > > > > > _______________________________________________ > 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 yunierkis at uclv.edu.cu Mon Aug 28 15:02:38 2006 From: yunierkis at uclv.edu.cu (Yunierkis Perez Castillo) Date: Mon, 28 Aug 2006 18:02:38 -0400 Subject: [Chimera-users] change chain id In-Reply-To: References: <1156794481.5425.8.camel@amphitrite.cbq.uclv.edu.cu> <164E5447-10E3-4FCC-B1BA-7E7C345E494A@cgl.ucsf.edu> Message-ID: <1156802558.5425.11.camel@amphitrite.cbq.uclv.edu.cu> Thanks Erick, it work fine and it's easy to do. On Mon, 2006-08-28 at 13:51 -0700, Eric Pettersen wrote: > There is kind of a "cheaty" way to do it if you are using the 1.2255 > snapshot by saving a session file and editing it. You need to use an > editor that can handle long lines, like TextEdit.app on a Mac or > WordPad on Windows. Search for the string 'chain' (including the > quotes). You'll see some text that looks something like: > > > > 'chain': (29, 'A', {}) > > > change the A to B so it looks like: > > > 'chain': (29, 'B', {}) > > > save the edited session and open it in Chimera and the chain ID will > have changed. > > > --Eric > > > On Aug 28, 2006, at 1:36 PM, Elaine Meng wrote: > > > > > Hi Yunierkis, > > > > Sorry, there is no way to change the chain ID in Chimera. You would > > need to text-edit A to B in the PDB file before opening it. (Or, if > > you're fetching the structure from the PDB, write it out in PDB > > format, edit the file, and read it back in.) > > > > > > Depending on what you are trying to do, there may be some way of > > doing it without changing chain ID. > > Best, > > Elaine > > > > > > On Aug 28, 2006, at 12:48 PM, Yunierkis Perez Castillo wrote: > > > > > > > > > Hi all, > > > > > > I need to change the chain ID for a protein, that is, change the > > > chain A to chain B. > > > Can I do that with chimera? > > > > > > Thanks in advance > > > Yunierkis > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users at cgl.ucsf.edu > > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > ----- > > 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 > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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 Sanket.S.Shah at uth.tmc.edu Thu Aug 31 13:21:09 2006 From: Sanket.S.Shah at uth.tmc.edu (Shah, Sanket S) Date: Thu, 31 Aug 2006 15:21:09 -0500 Subject: [Chimera-users] question about annealing residues in pdb file Message-ID: <1F423A0A78EC5442A3DE45AF10059EAE1BDBE2@UTHEVS3.mail.uthouston.edu> Hello, I have been using chimera extensively for pdb rendering and manipulation. I needed some information that i couldn't find in the archives. I am aware that chimera displays the pdb file according to the co-ordinates mentioned in the pdb file. However in my situation I have changed co-ordinates of some of the secondary structure elements like helices to do a better fit. and I have saved the new coordinates in the same pdb file. So now when i render this pdb file it shows me the structure with the modified orientation, however chimera displays a continuous model. In the sense, the breaks that I had introduced by changing the angles of some of the helices and thus making the linkage discontinuous are somehow annealed by chimera. So my question is what sort of algorithm chimera employs to seal breaks in the pdb structure. The same pdb strucutre when viewed in swiss model deepview software contains gaps/breaks at the junctions where the coordinates of the helices have been modified from the original ones. however no such breaks are seen when displayed through chimera. First I thought chimera does energy minimization to find out the best way to arrange the loops between the helices so as to create the best continuous structure. However it seems that chimera doesn't do energy minimization, yet it's able to display a complete structure. Could you please inform me about how this is accomplished. Thanks Sanket From meng at cgl.ucsf.edu Thu Aug 31 15:14:05 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 31 Aug 2006 15:14:05 -0700 Subject: [Chimera-users] question about annealing residues in pdb file In-Reply-To: <1F423A0A78EC5442A3DE45AF10059EAE1BDBE2@UTHEVS3.mail.uthouston.edu> References: <1F423A0A78EC5442A3DE45AF10059EAE1BDBE2@UTHEVS3.mail.uthouston.edu> Message-ID: Hi Sanket, If I am understanding the problem correctly, it's easy to fix; just use the command "longbond". http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html Chimera shows the connections because the PDB file (I am guessing) still implies they are there: the residues are in the same chain and don't have TER between them. DeepView probably applies some distance test similar to "longbond" automatically when a structure is opened. I hope this helps, Elaine On Aug 31, 2006, at 1:21 PM, Shah, Sanket S wrote: > Hello, > I have been using chimera extensively for pdb rendering and > manipulation. I needed some information that i couldn't find in the > archives. I am aware that chimera displays the pdb file according > to the co-ordinates mentioned in the pdb file. However in my > situation I have changed co-ordinates of some of the secondary > structure elements like helices to do a better fit. and I have > saved the new coordinates in the same pdb file. So now when i > render this pdb file it shows me the structure with the modified > orientation, however chimera displays a continuous model. In the > sense, the breaks that I had introduced by changing the angles of > some of the helices and thus making the linkage discontinuous are > somehow annealed by chimera. So my question is what sort of > algorithm chimera employs to seal breaks in the pdb structure. The > same pdb strucutre when viewed in swiss model deepview software > contains gaps/breaks at the junctions where the coordinates of the > helices have been modified! > from the original ones. however no such breaks are seen when > displayed through chimera. First I thought chimera does energy > minimization to find out the best way to arrange the loops between > the helices so as to create the best continuous structure. However > it seems that chimera doesn't do energy minimization, yet it's able > to display a complete structure. Could you please inform me about > how this is accomplished. > Thanks > Sanket > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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