From Zongli_Li at hms.harvard.edu Fri Jan 2 13:49:42 2015 From: Zongli_Li at hms.harvard.edu (Li, Zongli) Date: Fri, 2 Jan 2015 16:49:42 -0500 Subject: [Chimera-users] mmaker usage with md-movie perframe In-Reply-To: <63812110-AE54-4CF9-BF08-B6F4EABC09D8@cgl.ucsf.edu> References: , <63812110-AE54-4CF9-BF08-B6F4EABC09D8@cgl.ucsf.edu> Message-ID: Hi Elain, Happy new year! I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, how can I do it in Chimera? Thanks! Zongli From meng at cgl.ucsf.edu Fri Jan 2 14:05:31 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Jan 2015 14:05:31 -0800 Subject: [Chimera-users] saving a map after rotation In-Reply-To: References: , <63812110-AE54-4CF9-BF08-B6F4EABC09D8@cgl.ucsf.edu> Message-ID: <9CFED846-C44D-4063-B7CF-216A3D8FD884@cgl.ucsf.edu> Hi Zongli, Happy new year! The main issue is that the map file format doesn?t include rotation information. If you rotated your map to go with some atomic structure (PDB file), it is better to save a new PDB relative to the map instead. If you rotated your map (?map1?) to go with some other map (?map2?), you could create a new map (?map3?) by resampling map1 on the grid of map2 with the ?vop resample? command. Please see ?Saving Maps After Fitting? here for the details and links: I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 2, 2015, at 1:49 PM, Li, Zongli wrote: > Hi Elain, > Happy new year! > > I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, > how can I do it in Chimera? > > Thanks! > Zongli From Zongli_Li at hms.harvard.edu Fri Jan 2 16:16:25 2015 From: Zongli_Li at hms.harvard.edu (Li, Zongli) Date: Fri, 2 Jan 2015 19:16:25 -0500 Subject: [Chimera-users] saving a map after rotation In-Reply-To: <9CFED846-C44D-4063-B7CF-216A3D8FD884@cgl.ucsf.edu> References: , <63812110-AE54-4CF9-BF08-B6F4EABC09D8@cgl.ucsf.edu> , <9CFED846-C44D-4063-B7CF-216A3D8FD884@cgl.ucsf.edu> Message-ID: Thank you, Elaine! Best, Zongli ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Friday, January 02, 2015 5:05 PM To: Li, Zongli Cc: Mailing List Subject: saving a map after rotation Hi Zongli, Happy new year! The main issue is that the map file format doesn?t include rotation information. If you rotated your map to go with some atomic structure (PDB file), it is better to save a new PDB relative to the map instead. If you rotated your map (?map1?) to go with some other map (?map2?), you could create a new map (?map3?) by resampling map1 on the grid of map2 with the ?vop resample? command. Please see ?Saving Maps After Fitting? here for the details and links: I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 2, 2015, at 1:49 PM, Li, Zongli wrote: > Hi Elain, > Happy new year! > > I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, > how can I do it in Chimera? > > Thanks! > Zongli From rodrigogalindo at gmail.com Mon Jan 5 13:33:01 2015 From: rodrigogalindo at gmail.com (ros) Date: Mon, 5 Jan 2015 14:33:01 -0700 Subject: [Chimera-users] Parsing a new 3D file format Message-ID: Hello! I would like to ask for advice and starting directions to be able to parse a new file format in Chimera so I can use Chimera's tools and generate images. The file format that I want to be able to open is generated from the Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) The AIMAll program of course can also do visualization and is very good at it. I am attaching an example of how a molecule looks. The problem is that if you want to work with big biomolecules (like DNA), the program is not very good to cloak/hide/select atoms so you have to click atom by atom to hide it and make some sense of the visualization. So, I will try to make a parser (or something that you would recommend) to open the file in Chimera and use Chimera's masking rules to select/deselect, hide/show atoms, which is very powerful. The text output generated by AIMAll has an XYZ list for each atom like this: Nuclear Charges and Cartesian Coordinates: ------------------------------------------------------------------------------- Atom Charge X Y Z ------------------------------------------------------------------------------- C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 That is easy, I think. But as you can see from the attached image, I want to be able to visualize the green spheres (which are called critical points and represents special properties of the electron density, extracted from quantum mechanical calculations). Those points are represented in the output file as: CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 -9.60854463947958E-01 Type = (3,-1) BCP C1 C3 Rho = 2.4067790431E-01 GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 3.5682199801E-01 HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 7.8991714842E-01 HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 6.1321358320E-01 DelSqRho = -5.2432458207E-01 Bond Ellipticity = 1.0071370222E-02 V = -2.5219393995E-01 G = 6.0556397216E-02 CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 1.96757752864282E-18 Type = (3,-1) BCP H4 C1 Rho = 2.9524693796E-01 GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 4.1039750300E-01 HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 0.0000000000E+00 DelSqRho = -1.1711322730E+00 Bond Ellipticity = 9.3591342377E-03 V = -3.7782718105E-01 G = 4.2522056404E-02 etc etc etc First line indicates the critical point number followed by the XYZ coordinate of the point, and the second line shows which atoms are involved between that critical point. The rest is the electronic properties of the critical point (nothing to visualize there) So, I am guessing that the critical points can be represented as dummy atoms in Chimera following the XYZ coordinates? The idea is that first the molecule coordinates are parsed and the molecule is displayed and then display the critical points of each atom. If possible, show lines joining atoms that have a critical point between them... I know it is a difficult task, but maybe you can provide some starting directions? Anything will help because right now is double clicking 1000+ atoms! Thank you so much and have a good day, Rodrigo. ------------------------- Rodrigo Galindo-Murillo, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) -------------- next part -------------- A non-text attachment was scrubbed... Name: aimall-example.jpg Type: image/jpeg Size: 73620 bytes Desc: not available URL: From goddard at sonic.net Mon Jan 5 14:08:10 2015 From: goddard at sonic.net (Tom Goddard) Date: Mon, 5 Jan 2015 14:08:10 -0800 Subject: [Chimera-users] WebGL viewer In-Reply-To: <8D250BF2-3D4E-40C0-B841-80C73C47CECC@sanfordburnham.org> References: <8D250BF2-3D4E-40C0-B841-80C73C47CECC@sanfordburnham.org> Message-ID: <77FB2CA7-8C53-4E3F-BA67-C51FBC19197F@sonic.net> Hi Thomas, That?s cool. When you change the density threshold slider it switches to showing a new surface model for that threshold. For that new surface to have the same orientation as the previously shown surface you have to add a little code that sets the positioning matrix of the new surface to be the same as the matrix for the previous surface. Here?s how I did it. Here?s the original code that handles the slider motion $("#slider").change(function(){ var i = $('#slider')[0].value; myscene.models = new Array(); myscene.add(mymodels[i]); myscene.defineBuffers(mymodels[i]); myscene.render(); setThreshold(requiredJsonFiles[i]); }); and here is the revised code that preserves the orientation var last_model = null; $("#slider").change(function(){ var i = $('#slider')[0].value; myscene.models = new Array(); if (last_model != null) mymodels[i].matrix = mymodels[last_model].matrix last_model = i; myscene.add(mymodels[i]); myscene.defineBuffers(mymodels[i]); myscene.render(); setThreshold(requiredJsonFiles[i]); }); I added a new variable ?last_model? that keeps track of the index for the previously shown surface and a copy the position matrix from that surface to the new one. I tried it and it works. I?m impressed you were able to modify the Chimera exported webgl html file to do this. I have been working on an html and webgl map viewer for density map time series (for 5d optical microscopy) . It shows the maps, has a slider to display different times, and lets you place colored markers on features and save those to the server. Here?s a screenshot of it. I?d be happy to let you try it but the data I?m using is unpublished cell motion data from another researcher. If you want I could make a fake time series where time corresponds to different density thresholds and let you try that. I can provide you the webgl code if you want to tinker with it. Sorry for the delay replying to your email. I just returned from vacation. Tom > On Dec 27, 2014, at 11:29 AM, Thomas Hrabe wrote: > > Hi everyone, > > I am trying to implement a EM density viewer in a HTML page based on the chimera webgl & html export feature. > The original page chimera exports when you save a webgl / html scene has been modified to load multiple JSON objects with densities as they come from chimera. > The bar at the bottom of the page essentially performs a coarse density sliding similar to chimera. > Almost all works great but what I am missing is how to connect the rotation that was applied to one model and to propagate it to all other models. > What is happening now is that when one rotates one model and slides the bar, the next model will not be rotated but will be in it?s original position. > > Here?s my page I am currently working on > http://localize.pytom.org/php/displayWebGL.php?jobID=tutorial > > I tried catching the mouse event with a loop, but it seems it fails to propagate the rotation to the other models. > Check the block at line 916 in the code > > try { > var rotMat = vsphere(mouse_position, new_position); > var camera = this.camera; > var matrix = new Mat4; > matrix.$translate(camera.target[0], camera.target[1], > camera.target[2]); > matrix.$mulMat4(rotMat); > matrix.$translate(-camera.target[0], -camera.target[1], > -camera.target[2]); > for (var i = 0, models = this.scene.models, l = models.length; i < l; ++i) { > var elem = models[i]; > elem.matrix = matrix.mulMat4(elem.matrix); > } > } > > Thank you in advance for your help, > Thomas > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: webmap.png Type: image/png Size: 517149 bytes Desc: not available URL: From pett at cgl.ucsf.edu Mon Jan 5 19:43:01 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 5 Jan 2015 19:43:01 -0800 Subject: [Chimera-users] Parsing a new 3D file format In-Reply-To: References: Message-ID: Hi Rodrigo, There is code in Chimera to read XYZ files, which are somewhat similar, so you could base you code off of that. The XYZ-reading code is in /share/ReadXYZ/__init__.py, the readXYZ() function. On a Mac, "" is actually Chimera.app/Contents/Resources. Anyway, there is a lot of error-checking in that code so it may be hard to see the most relevant parts for your purposes. Here's a digest version: import objects/functions we will be using from chimera import Molecule, Element, Coord, connectMolecule create a new empty molecule m = Molecule() create a residue named UNK in that molecule, with sequence position 1, no chain ID, and no insertion code r = m.newResidue("UNK", " ", 1, " ") assign a name to the molecule for display in the model panel and so forth m.name = "molecule_name" create the appropriate chemical element element = Element(text or integer) make a new atom with the appropriate name and element a = m.newAtom("atom_name", element) add the atom to the residue r.addAtom(a) assign the atom's xyz coordinate a.setCoord(Coord(x, y, z)) assign a serial number to the atom a.serialNumber = serial make appropriate bonds between the atoms connectMolecule(m) return a list of models (Molecules) to open return [m] Geez, that already was a lot. Anyway, let's ignore the file's "critical points" for a second so that we can finish with getting this open in Chimera. Basically, you will package this as an extension to Chimera that doesn't put anything in the Tools menu (or model panel) but just adds to the file types that Chimera knows how to open with the File->Open dialog and with the "open" command (ala "open coords.xyz"). To do so, in the same folder as your file-reading code you will need a file named ChimeraExtension.py that has this in it: ---- def aimallOpen(fileName): from ReadAimall import readAimall return readAimall(fileName) import chimera chimera.fileInfo.register("AIMAll mgpviz", aimallOpen, [".mgpviz"], ["mpgviz"], category=chimera.FileInfo.STRUCTURE) ---- The above code assumes that the folder containing your code is named "ReadAimall", that the file-reading function is named "readAimall", that it is in a file named "__init__.py" in the folder, and that the files are ".mgpviz" files. The second list in the register call (["mpgviz"]) allows the file type to be specified with a "mpgviz:" prefix in an "open" command should the file not actually have a .mgpviz suffix. You can then get Chimera to find this extension by adding the folder above the ReadAimall folder to the list in the Locations section of Chimera's Tools preferences (remember to click Save afterward), i.e. you add the folder containing new tools (in this case, the folder above ReadAimall) rather than each tool folder itself. Okay, back to the critical points. Depending somewhat on what you want to learn from them, I see four possible options: 1) fake atoms; 2) markers; 3) sphere shapes; 4) bond colors. In the below, I tend to put the critical points in their own model, since having fake atoms mixed into a real molecule will mess up things like hydrogen bond finding, aromatic ring determination, etc. Fake Atoms In this scenario, you would create a second Molecule as you read the file and add the critical points as atoms to that. You include the additional Molecule in the list of models you return ("return [m, m2]"). You would not call connectMolecule() on the second Molecule, but might add pseudobonds from the critical points to the appropriate atoms (you can't add regular bonds between models). The second molecule will have the same ID and sub-ID # as the first one, and will move in tandem with it. It will show up in the model panel. Markers Markers are what the Volume Tracer tool uses to mark volume data. They're really fake atoms, but have their own little support infrastructure. A simple example of using them is in the markeruse.py script on our Scripts page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts . They would have the same limitation in that they could only connect to the "real" atoms via pseudobonds. Also, they would only move in tandem with the real molecule as long as both models are "active" (which is usually the case unless you specifically do something to make their active states different). Sphere Shapes These are shapes (surfaces, really) created by the "shape" command. Probably the easiest way to create them is something like: from chimera import runCommand runCommand("shape sphere radius rad center x,y,z modelName 'critical points' modelId 100") which would put them all in model #100. If you wanted them in the same model number as the molecule, that would require fancier code. You could look at Aniso/__init__.py or at sphere_shape() in Shape/shapecmd.py for examples of that. Bond Colors If the critical points are really associated with bonds and are trying to convey properties of the bonds, you could vary the thickness or color of the bonds instead. To find the Bond object b between Atoms a1 and a2, you would do this: b = a1.atomsMap(a2) To change the bond radius, you would show it as stick and change the radius: b.drawMode = chimera.Bond.Stick b.radius = radius To change the color, you would make sure it wasn't in "halfbond" mode (each half colored the same as its endpoint atom) and then set the color: b.halfbond = False b.color = chimera.MaterialColor(red, green, blue, opacity) red / green / blue / opacity all in the range 0-1. So finally, this is really a developer-oriented subject, so I have directed follow ups to chimera-dev instead of chimera-users. Feel free to ask additional questions there? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 5, 2015, at 1:33 PM, ros wrote: > Hello! > > I would like to ask for advice and starting directions to be able to > parse a new file format in Chimera so I can use Chimera's tools and > generate images. > > The file format that I want to be able to open is generated from the > Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) > > The AIMAll program of course can also do visualization and is very > good at it. I am attaching an example of how a molecule looks. The > problem is that if you want to work with big biomolecules (like DNA), > the program is not very good to cloak/hide/select atoms so you have to > click atom by atom to hide it and make some sense of the > visualization. So, I will try to make a parser (or something that you > would recommend) to open the file in Chimera and use Chimera's masking > rules to select/deselect, hide/show atoms, which is very powerful. > > The text output generated by AIMAll has an XYZ list for each atom like this: > > Nuclear Charges and Cartesian Coordinates: > ------------------------------------------------------------------------------- > Atom Charge X Y Z > ------------------------------------------------------------------------------- > C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 > C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 > C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 > H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 > H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 > C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 > H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 > H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 > C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 > H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 > H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 > H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 > H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 > > > That is easy, I think. But as you can see from the attached image, I > want to be able to visualize the green spheres (which are called > critical points and represents special properties of the electron > density, extracted from quantum mechanical calculations). Those > points are represented in the output file as: > > CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 > -9.60854463947958E-01 > Type = (3,-1) BCP C1 C3 > Rho = 2.4067790431E-01 > GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 > HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 > 3.5682199801E-01 > HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 > 0.0000000000E+00 > HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 > 7.8991714842E-01 > HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 > 6.1321358320E-01 > DelSqRho = -5.2432458207E-01 > Bond Ellipticity = 1.0071370222E-02 > V = -2.5219393995E-01 > G = 6.0556397216E-02 > CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 > 1.96757752864282E-18 > Type = (3,-1) BCP H4 C1 > Rho = 2.9524693796E-01 > GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 > HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 > 4.1039750300E-01 > HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 > 0.0000000000E+00 > HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 > 1.0000000000E+00 > HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 > 0.0000000000E+00 > DelSqRho = -1.1711322730E+00 > Bond Ellipticity = 9.3591342377E-03 > V = -3.7782718105E-01 > G = 4.2522056404E-02 > > etc etc etc > > First line indicates the critical point number followed by the XYZ > coordinate of the point, and the second line shows which atoms are > involved between that critical point. The rest is the electronic > properties of the critical point (nothing to visualize there) > > So, I am guessing that the critical points can be represented as dummy > atoms in Chimera following the XYZ coordinates? > > The idea is that first the molecule coordinates are parsed and the > molecule is displayed and then display the critical points of each > atom. If possible, show lines joining atoms that have a critical > point between them... > > I know it is a difficult task, but maybe you can provide some starting > directions? Anything will help because right now is double clicking > 1000+ atoms! > > Thank you so much and have a good day, > > Rodrigo. -------------- next part -------------- An HTML attachment was scrubbed... URL: From darrellh at niaid.nih.gov Mon Jan 5 20:49:07 2015 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Tue, 6 Jan 2015 04:49:07 +0000 Subject: [Chimera-users] Distance Grid SES calculation available? Message-ID: Hi Chimera friends, This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). Is there some way to call the routine, especially in a script? Python maybe? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit , @NIH3Dprint Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From goddard at sonic.net Tue Jan 6 12:01:40 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 6 Jan 2015 12:01:40 -0800 Subject: [Chimera-users] Distance Grid SES calculation available? In-Reply-To: References: Message-ID: <0653319B-7668-495B-B081-4BA071C431C7@sonic.net> Hi Darrell, Ok, there is a secret Chimera 1 option to the surface command to let you use the distance grid SES calculation: surface #0 grid 0.5 The value of the grid option is the grid spacing and 0.5 Angstroms is reasonable, smaller values will produce a more finely triangulated surface. This surface cannot be colored to match the atom colors in the same way as a normal molecular surface because it lacks an association between surface points and atoms (although the color zone tool can get the same effect if you need it). This is an undocumented feature because if we add all our cool new features to Chimera 1 then we will never have time to get Chimera 2 produced. But since you need it here it is. Tom > On Jan 5, 2015, at 8:49 PM, Hurt, Darrell (NIH/NIAID) [E] wrote: > > Hi Chimera friends, > > This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: > http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html > > The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). > > Is there some way to call the routine, especially in a script? Python maybe? > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 5601 Fishers Lane, 4A31 > North Bethesda, MD 20852 > Office: 240-669-2741 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit , @NIH3Dprint > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From darrellh at niaid.nih.gov Tue Jan 6 13:50:06 2015 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Tue, 6 Jan 2015 21:50:06 +0000 Subject: [Chimera-users] Distance Grid SES calculation available? In-Reply-To: <0653319B-7668-495B-B081-4BA071C431C7@sonic.net> References: <0653319B-7668-495B-B081-4BA071C431C7@sonic.net> Message-ID: Hi Tom, Thank you for sharing so publicly. It works wonderfully and oh so fast! I do not want to get in the way at all of the progress of Chimera 2, so I hope this doesn't put you too off course. Long live UCSF Chimera! Thanks and Happy New Year! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20892-2135 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit , @NIH3Dprint Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard > Date: Tuesday, January 6, 2015 3:01 PM To: Darrell Hurt > Cc: "chimera-users at cgl.ucsf.edu" > Subject: Re: [Chimera-users] Distance Grid SES calculation available? Hi Darrell, Ok, there is a secret Chimera 1 option to the surface command to let you use the distance grid SES calculation: surface #0 grid 0.5 The value of the grid option is the grid spacing and 0.5 Angstroms is reasonable, smaller values will produce a more finely triangulated surface. This surface cannot be colored to match the atom colors in the same way as a normal molecular surface because it lacks an association between surface points and atoms (although the color zone tool can get the same effect if you need it). This is an undocumented feature because if we add all our cool new features to Chimera 1 then we will never have time to get Chimera 2 produced. But since you need it here it is. Tom On Jan 5, 2015, at 8:49 PM, Hurt, Darrell (NIH/NIAID) [E] > wrote: Hi Chimera friends, This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). Is there some way to call the routine, especially in a script? Python maybe? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit , @NIH3Dprint Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From agmalyut at umail.iu.edu Wed Jan 7 08:40:21 2015 From: agmalyut at umail.iu.edu (Andrey Malyutin) Date: Wed, 7 Jan 2015 11:40:21 -0500 Subject: [Chimera-users] VR in Chimera? Message-ID: Good morning, With recent resurgence in virtual reality technology, such as Oculus Rift and Samsung Gear VR, is it possible that we'll see support for VR headsets in future releases of Chimera? Thank you, Andrey -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Jan 7 12:40:38 2015 From: goddard at sonic.net (Tom Goddard) Date: Wed, 7 Jan 2015 12:40:38 -0800 Subject: [Chimera-users] VR in Chimera? In-Reply-To: References: Message-ID: <698B5B05-2113-41D1-8F77-2F014D340B63@sonic.net> Hi Andrey, We have been playing with Oculus Rift in our next generation Chimera for about a year now. http://www.cgl.ucsf.edu/chimera/data/oculus-jan2014/oculus.html http://www.cgl.ucsf.edu/Outreach/technotes/oculusnote.html That next generation Chimera is not released (optimistically 6 months to a year away). Immersive visualization with the Oculus Rift is amazing, but is it useful? We have a demo flying around collagen matrix and a dendritic cell. Unfortunately it would require a whole new user interface to actually do anything beyond flying around since menus, typed commands, mouse interaction, is all gone once you put on the Oculus. We have not tried any user interface other than flying. Maybe the best use of Oculus in molecular visualization for years to come will be flying around molecules and cells to get some inspiration. The value of that wears off after about 10 minutes of use, but it has been good for outreach to high school and college students the past year. Tom > On Jan 7, 2015, at 8:40 AM, Andrey Malyutin wrote: > > Good morning, > > With recent resurgence in virtual reality technology, such as Oculus Rift and Samsung Gear VR, is it possible that we'll see support for VR headsets in future releases of Chimera? > > Thank you, > > Andrey > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariasaqib.87 at gmail.com Thu Jan 8 00:52:34 2015 From: mariasaqib.87 at gmail.com (Maria Saqib) Date: Thu, 8 Jan 2015 13:52:34 +0500 Subject: [Chimera-users] need guidence Message-ID: Dear user i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? Waiting for your reply Maria -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jan 8 15:29:35 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Jan 2015 15:29:35 -0800 Subject: [Chimera-users] coloring labels-only In-Reply-To: References: Message-ID: <2442F855-2539-4822-9A4C-A960176F87A6@cgl.ucsf.edu> Hi Maria, The label colors will follow the atom colors unless you specify coloring the labels only. (A) if commands: use the "color" command, with ",l" after the color name, where the last character is a lowercase letter L to indicate labels only. For example: color red,l ?for all labels, or to color only the labels of specific atoms, you can specify those atoms at the end, for example: color red,l ligand If menu, use Actions? Color? all options to show the color-actions dialog. Then in that dialog change "Coloring applies to" to one of the label choices. Then select the atoms or residues that have the labels with colors you want to change, then click a color in the color-actions dialog or the Actions? Color menu. (then you would probably change "Coloring applies to" back to "all of the above" to avoid later confusion) I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 8, 2015, at 12:52 AM, Maria Saqib wrote: > Dear user > i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? > Waiting for your reply > Maria From meng at cgl.ucsf.edu Thu Jan 8 15:48:14 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Jan 2015 15:48:14 -0800 Subject: [Chimera-users] coloring labels-only In-Reply-To: <2442F855-2539-4822-9A4C-A960176F87A6@cgl.ucsf.edu> References: <2442F855-2539-4822-9A4C-A960176F87A6@cgl.ucsf.edu> Message-ID: <325A8FBD-D17C-4AFB-A689-68F5F26B8DC8@cgl.ucsf.edu> Hi Maria, Another possibility instead of using the regular labels that are attached to the structure is to use 2D Labels. 2D labels do not move when you move the structure; they just stay where you put them. In that case you would first generate the view of the protein for the image without any labels, then use 2D Labels (in menu under Tools? Utilities). You can create several different 2D labels in different colors and sizes, including Greek letters, symbols, and arrows. Click the Help button on the 2D Labels dialog to see more information, or view here: There are also examples of 2D labels in the image tutorials: Elaine On Jan 8, 2015, at 3:29 PM, Elaine Meng wrote: > Hi Maria, > The label colors will follow the atom colors unless you specify coloring the labels only. > > (A) if commands: use the "color" command, with ",l" after the color name, where the last character is a lowercase letter L to indicate labels only. For example: > > color red,l > > ?for all labels, or to color only the labels of specific atoms, you can specify those atoms at the end, for example: > > color red,l ligand > > If menu, use Actions? Color? all options to show the color-actions dialog. Then in that dialog change "Coloring applies to" to one of the label choices. Then select the atoms or residues that have the labels with colors you want to change, then click a color in the color-actions dialog or the Actions? Color menu. (then you would probably change "Coloring applies to" back to "all of the above" to avoid later confusion) > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 8, 2015, at 12:52 AM, Maria Saqib wrote: > >> Dear user >> i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? >> Waiting for your reply >> Maria From mikej at nc.rr.com Sat Jan 10 14:01:32 2015 From: mikej at nc.rr.com (Mike) Date: Sat, 10 Jan 2015 17:01:32 -0500 Subject: [Chimera-users] New to Chimera Message-ID: <000001d02d20$fe951190$fbbf34b0$@nc.rr.com> This is my first day with Chimera. I'm trying to find how to draw a small molecule, minimize the structure of the small molecule and then have it interact with my protein of interest. However, I don't see any way for me to draw a small molecule (potential drug). Can you provide any direction ? Thanks, Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jan 12 14:11:00 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2015 14:11:00 -0800 Subject: [Chimera-users] building a molecule in Chimera In-Reply-To: <000001d02d20$fe951190$fbbf34b0$@nc.rr.com> References: <000001d02d20$fe951190$fbbf34b0$@nc.rr.com> Message-ID: <4C618F55-91D2-475F-B5FA-C53F58700EAF@cgl.ucsf.edu> Hi Mike, There is no quick 2D sketching to create a small molecule, only building it up atom-by-atom. You can also enter a SMILES string or specify a PubChem CID to generate a small molecule in Chimera, which could be used as a starting point for further atom-by-atom building if necessary. It's easier than building the whole thing atom by atom. If you don't want to deal with SMILES, you can search PubChem Compound to find the CID number of your molecule or a similar molecule to use as a starting point. These options are all with the Build Structure tool (in menu under Tools? Structure Editing). See the Start Structure and Modify Structure sections in that tool. For example, after starting Build Structure in Chimera, in its Start Structure section you could enter SMILES string: c1ccccc1OC or PubChem CID: 31231 ? and click Apply to get the specified molecule. Then you could Ctrl-click one of the hydrogens to select it and change it to bromine using the Modify Structure section of Build Stucture (Element: Br, Bonds: 1, click Apply). Or you could change it to a methyl group (Element: C, Bonds:4, Geometry: tetrahedral, Apply) and then select one of the hydrogens on the new methyl group to continue building out further. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 10, 2015, at 2:01 PM, "Mike" wrote: > This is my first day with Chimera. I?m trying to find how to draw a small molecule, minimize the structure of the small molecule and then > have it interact with my protein of interest. However, I don?t see any way for me to draw a small molecule (potential drug). > Can you provide any direction ? > > Thanks, > Mike From meng at cgl.ucsf.edu Mon Jan 12 14:57:26 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2015 14:57:26 -0800 Subject: [Chimera-users] building a molecule in Chimera In-Reply-To: <4C618F55-91D2-475F-B5FA-C53F58700EAF@cgl.ucsf.edu> References: <000001d02d20$fe951190$fbbf34b0$@nc.rr.com> <4C618F55-91D2-475F-B5FA-C53F58700EAF@cgl.ucsf.edu> Message-ID: Hi Mike, I got caught up in the building and forgot to address the subsequent steps you'd mentioned. So, to continue: (A) energy-minimization can be done with Minimize Structure (in menu under Tools? Structure Editing) or equivalently, the "minimize" command. (B) people use "docking" to predict possible binding orientations of a small molecule relative to a protein structure. For high-level sampling of orientations, including flexibility, or searching a whole database of small molecules, you would have to use some other program outside of Chimera (DOCK, AutoDock, GOLD, etc.) although there is a handy ViewDock tool for looking at the results. However, for just docking one small molecule to a protein and only getting a small number of output orientations, you can use the AutoDock Vina tool in the menu under Tools? Surface/Binding Analysis: It runs AutoDock Vina using a web service and then shows the results in the ViewDock tool. You can also try to dock the structures by hand, e.g. freezing the protein in place and moving only the small molecule, and even rotating bonds, but this can be difficult. I wouldn't recommend it unless you have some guiding evidence such as residues known to contact the small molecule. I hope this helps, Elaine On Jan 12, 2015, at 2:11 PM, Elaine Meng wrote: > Hi Mike, > There is no quick 2D sketching to create a small molecule, only building it up atom-by-atom. You can also enter a SMILES string or specify a PubChem CID to generate a small molecule in Chimera, which could be used as a starting point for further atom-by-atom building if necessary. It's easier than building the whole thing atom by atom. If you don't want to deal with SMILES, you can search PubChem Compound to find the CID number of your molecule or a similar molecule to use as a starting point. > > These options are all with the Build Structure tool (in menu under Tools? Structure Editing). See the Start Structure and Modify Structure sections in that tool. > > > For example, after starting Build Structure in Chimera, in its Start Structure section you could enter > > SMILES string: c1ccccc1OC > or > PubChem CID: 31231 > > ? and click Apply to get the specified molecule. Then you could Ctrl-click one of the hydrogens to select it and change it to bromine using the Modify Structure section of Build Stucture (Element: Br, Bonds: 1, click Apply). Or you could change it to a methyl group (Element: C, Bonds:4, Geometry: tetrahedral, Apply) and then select one of the hydrogens on the new methyl group to continue building out further. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 10, 2015, at 2:01 PM, "Mike" wrote: > >> This is my first day with Chimera. I?m trying to find how to draw a small molecule, minimize the structure of the small molecule and then >> have it interact with my protein of interest. However, I don?t see any way for me to draw a small molecule (potential drug). >> Can you provide any direction ? >> >> Thanks, >> Mike From mikej at nc.rr.com Mon Jan 12 17:34:26 2015 From: mikej at nc.rr.com (Mike) Date: Mon, 12 Jan 2015 20:34:26 -0500 Subject: [Chimera-users] building a molecule in Chimera In-Reply-To: References: <000001d02d20$fe951190$fbbf34b0$@nc.rr.com> <4C618F55-91D2-475F-B5FA-C53F58700EAF@cgl.ucsf.edu> Message-ID: <000001d02ed1$11a12380$34e36a80$@nc.rr.com> Hi Elaine, Thank you so much for your reply! You have described things perfectly. I'll give it a try in the next few days and hopefully things will go well. Thank you! Mike -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Monday, January 12, 2015 5:57 PM To: Mike Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] building a molecule in Chimera Hi Mike, I got caught up in the building and forgot to address the subsequent steps you'd mentioned. So, to continue: (A) energy-minimization can be done with Minimize Structure (in menu under Tools. Structure Editing) or equivalently, the "minimize" command. (B) people use "docking" to predict possible binding orientations of a small molecule relative to a protein structure. For high-level sampling of orientations, including flexibility, or searching a whole database of small molecules, you would have to use some other program outside of Chimera (DOCK, AutoDock, GOLD, etc.) although there is a handy ViewDock tool for looking at the results. However, for just docking one small molecule to a protein and only getting a small number of output orientations, you can use the AutoDock Vina tool in the menu under Tools. Surface/Binding Analysis: It runs AutoDock Vina using a web service and then shows the results in the ViewDock tool. You can also try to dock the structures by hand, e.g. freezing the protein in place and moving only the small molecule, and even rotating bonds, but this can be difficult. I wouldn't recommend it unless you have some guiding evidence such as residues known to contact the small molecule. I hope this helps, Elaine On Jan 12, 2015, at 2:11 PM, Elaine Meng wrote: > Hi Mike, > There is no quick 2D sketching to create a small molecule, only > building it up atom-by-atom. You can also enter a SMILES string or > specify a PubChem CID to generate a small molecule in Chimera, which > could be used as a starting point for further atom-by-atom building if > necessary. It's easier than building the whole thing atom by atom. If > you don't want to deal with SMILES, you can search PubChem Compound to > find the CID number of your molecule or a similar molecule to use as a > starting point. > > These options are all with the Build Structure tool (in menu under Tools. Structure Editing). See the Start Structure and Modify Structure sections in that tool. > ting.html> > > For example, after starting Build Structure in Chimera, in its Start > Structure section you could enter > > SMILES string: c1ccccc1OC > or > PubChem CID: 31231 > > . and click Apply to get the specified molecule. Then you could Ctrl-click one of the hydrogens to select it and change it to bromine using the Modify Structure section of Build Stucture (Element: Br, Bonds: 1, click Apply). Or you could change it to a methyl group (Element: C, Bonds:4, Geometry: tetrahedral, Apply) and then select one of the hydrogens on the new methyl group to continue building out further. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department > of Pharmaceutical Chemistry University of California, San Francisco > > On Jan 10, 2015, at 2:01 PM, "Mike" wrote: > >> This is my first day with Chimera. I'm trying to find how to draw a >> small molecule, minimize the structure of the small molecule and then have it interact with my protein of interest. However, I don't see any way for me to draw a small molecule (potential drug). >> Can you provide any direction ? >> >> Thanks, >> Mike From olibclarke at gmail.com Tue Jan 13 20:02:33 2015 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 13 Jan 2015 23:02:33 -0500 Subject: [Chimera-users] shown/hidden state of axes/planes not saved with scene Message-ID: <7CE309ED-51FB-4DEE-B176-02E09E22EADD@gmail.com> Hi all, Planes seem to be shown by default when I load a scene, regardless of whether they were displayed when I saved the scene. This is not normally an issue, but it is a little problematic when preparing animations using many different scenes - I will often have a plane defined at the start so I can use it to align the x/y/z axes to the normal of that plane (e.g. aligning the fourfold axis of an ion channel), but I do not want the plane displayed during the animation, and I don?t want to have to delete it from each scene and re-arrange the animation timeline if I can avoid doing so. Would it be possible to alter this behavior such that chimera knows the displayed/undisplayed states of axes/planes/centroids when saving a scene or session? Best, Oliver Clarke. From m.schledorn at gmail.com Wed Jan 14 02:55:48 2015 From: m.schledorn at gmail.com (Maarten Schledorn) Date: Wed, 14 Jan 2015 11:55:48 +0100 Subject: [Chimera-users] Distance measurement in density map Message-ID: Dear reader, I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at? With my sincere thanks in advance, Maarten -------------- next part -------------- An HTML attachment was scrubbed... URL: From fjchichon at cnb.csic.es Wed Jan 14 06:49:55 2015 From: fjchichon at cnb.csic.es (=?UTF-8?B?RmNvIEphdmllciBDaGljaMOzbg==?=) Date: Wed, 14 Jan 2015 15:49:55 +0100 Subject: [Chimera-users] vop add Message-ID: <54B68213.8080900@cnb.csic.es> Dear all I would like to merge several volumes. Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. Anyone know how to do that? Thanks -- ======================================================= Francisco Javier Chich?n Garc?a Centro.: Centro Nacional de Biotecnolog?a Dept.: Macromolecular Structure Lab.: S1-S0.1 Tel.: (+34) 91585-5497:4690 ======================================================= From meng at cgl.ucsf.edu Wed Jan 14 10:58:08 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 14 Jan 2015 10:58:08 -0800 Subject: [Chimera-users] Distance measurement in density map In-Reply-To: References: Message-ID: <8A42E290-C4E3-4C0F-82F4-98C79122A4C6@cgl.ucsf.edu> Dear Maarten, You can place ?markers? (dummy atoms) on the surfaces with the Volume Tracer tool, then measure the distances between markers as if they were atoms. Volume Tracer is in the volume viewer Tools menu and the main menu under Tools?Volume Data. The Mouse menu in Volume Tracer controls how markers are created and with which mouse button. You can choose ?Place markers on surfaces? to add a marker at the nearest surface point under the cursor when the assigned button is clicked. One way to measure atom-atom (or marker-marker) distances is to Ctrl-click one to select it, then Shift-Ctrl-doubleclick to select the second and then choose ?Show Distance" from the resulting context menu. There is also a ?measure distance? command, but it finds the closest distance between two different surfaces and/or atoms, not between surface points of your choosing? so I believe the marker approach is what you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2015, at 2:55 AM, Maarten Schledorn wrote: > Dear reader, > I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at? > With my sincere thanks in advance, > Maarten From pett at cgl.ucsf.edu Wed Jan 14 13:00:57 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 14 Jan 2015 13:00:57 -0800 Subject: [Chimera-users] shown/hidden state of axes/planes not saved with scene In-Reply-To: <7CE309ED-51FB-4DEE-B176-02E09E22EADD@gmail.com> References: <7CE309ED-51FB-4DEE-B176-02E09E22EADD@gmail.com> Message-ID: <5D7E7041-AE13-453D-B8BE-607B74127091@cgl.ucsf.edu> Hi Oliver, Thanks for pointing out this problem. Axes/planes/centroids weren't saving their display on/off state in scenes or sessions. I have fixed the code and the fix will be in tonight's daily build. Look for a build dated Jan. 14th or later. Using such a build you will be able to restore your session but will have to re-save the scenes where you have one or more axes/planes/centroids undisplayed in order to have the correct display state preserved in the scene. Then things should work as you expect. --Eric On Jan 13, 2015, at 8:02 PM, Oliver Clarke wrote: > Hi all, > > Planes seem to be shown by default when I load a scene, regardless of whether they were displayed when I saved the scene. > > This is not normally an issue, but it is a little problematic when preparing animations using many different scenes - I will often have a plane defined at the start so I can use it to align the x/y/z axes to the normal of that plane (e.g. aligning the fourfold axis of an ion channel), but I do not want the plane displayed during the animation, and I don?t want to have to delete it from each scene and re-arrange the animation timeline if I can avoid doing so. > > Would it be possible to alter this behavior such that chimera knows the displayed/undisplayed states of axes/planes/centroids when saving a scene or session? > > Best, > Oliver Clarke. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Wed Jan 14 14:50:51 2015 From: goddard at sonic.net (Tom Goddard) Date: Wed, 14 Jan 2015 14:50:51 -0800 Subject: [Chimera-users] vop add In-Reply-To: <54B68213.8080900@cnb.csic.es> References: <54B68213.8080900@cnb.csic.es> Message-ID: <2BBA101A-4E36-4031-BCC8-A77B224985DC@sonic.net> Hi Francisco, If you average two maps with ?vop add #0,1 scale 0.5,0.5? then where the maps do not overlap the density value will be reduced by averaging when one map has a point inside the structure and one map has the point outside. Another approach to ?merging? would be to take the maximum of the two maps with "vop maximum?. If you really want to average the maps where both are greater than some threshold density, but where only one is greater than the threshold you simply use that map?s value then you will get discontinuities in the merged map at the boundary where both maps are above the threshold. So I wouldn?t recommend that but it could be done with ?vop threshold? to make a 0/1 mask for each map where it is above threshold, add those two masks to get the number of map values (0, 1 or 2 for each grid point) then divide the sum of the maps by that map. Oops, there is no "vop divide?, only a ?vop multiply?. I don?t think you want to do that, but if you do let me know and I will add a vop divide to divide one map by another point-wise. Tom > On Jan 14, 2015, at 6:49 AM, Fco Javier Chich?n wrote: > > Dear all > > I would like to merge several volumes. > Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. > > Anyone know how to do that? > > Thanks > > -- > ======================================================= > Francisco Javier Chich?n Garc?a > > Centro.: Centro Nacional de Biotecnolog?a > Dept.: Macromolecular Structure > Lab.: S1-S0.1 > Tel.: (+34) 91585-5497:4690 > ======================================================= > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From m.schledorn at gmail.com Wed Jan 14 15:15:47 2015 From: m.schledorn at gmail.com (Maarten Schledorn) Date: Thu, 15 Jan 2015 00:15:47 +0100 Subject: [Chimera-users] Distance measurement in density map In-Reply-To: <8A42E290-C4E3-4C0F-82F4-98C79122A4C6@cgl.ucsf.edu> References: <8A42E290-C4E3-4C0F-82F4-98C79122A4C6@cgl.ucsf.edu> Message-ID: This is exactly the kind of solution I was looking for. Thank you so much for your time and help! Best, Maarten On Wednesday, 14 January 2015, Elaine Meng wrote: > Dear Maarten, > You can place "markers" (dummy atoms) on the surfaces with the Volume > Tracer tool, then measure the distances between markers as if they were > atoms. > > Volume Tracer is in the volume viewer Tools menu and the main menu under > Tools...Volume Data. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html > > > > The Mouse menu in Volume Tracer controls how markers are created and with > which mouse button. You can choose "Place markers on surfaces" to add a > marker at the nearest surface point under the cursor when the assigned > button is clicked. > > One way to measure atom-atom (or marker-marker) distances is to Ctrl-click > one to select it, then Shift-Ctrl-doubleclick to select the second and then > choose "Show Distance" from the resulting context menu. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances > > > > There is also a "measure distance" command, but it finds the closest > distance between two different surfaces and/or atoms, not between surface > points of your choosing... so I believe the marker approach is what you want. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 14, 2015, at 2:55 AM, Maarten Schledorn > wrote: > > > Dear reader, > > I'm looking at EM tomography data summarised in *.mrc density files. > Since there are no atoms defined in these files, the usual distance > measurement tool is inappropriate (I suppose). Is there another way to > assess the dimensions of the oligomerised protein I'm looking at? > > With my sincere thanks in advance, > > Maarten > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tevang3 at gmail.com Thu Jan 15 15:06:18 2015 From: tevang3 at gmail.com (Thomas Evangelidis) Date: Fri, 16 Jan 2015 01:06:18 +0200 Subject: [Chimera-users] dotted lines Message-ID: Greetings, I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed? thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang at pharm.uoa.gr tevang3 at gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ =============================================================== *Physics is the only real science. The rest are just stamp collecting.* *- Ernest Rutherford* -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jan 15 15:36:30 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 15 Jan 2015 15:36:30 -0800 Subject: [Chimera-users] dotted lines In-Reply-To: References: Message-ID: <8C7A7E34-40EB-42DD-B5B7-F91EF67E2B1C@cgl.ucsf.edu> Hi Thomas, Sure! The line style and line width are attributes of a pseudobond group (for example, all distance measurements), so you can only change them for the whole group at once. (1) One way is to use the Selection Inspector: select any distance line with Ctrl-click, then click the green magnifying glass icon near the bottom corner of the Chimera window to open the Selection Inspector. In the Inspector, inspect "Pseudobond Group" (not Pseudobond!) to change line style and/or line width. If you put the cursor over an entry in the dialog, it will show balloon help with the attribute name, which you would need if you wanted to use commands instead of the dialog. For example, this tells me that "line style" is the attribute "lineType" with values 1=solid, 2=dashed, 3=dotted, 4=dash-dot, 5=dash-dot-dot. (2) So, a second way is to use the "setattr" command. For example: setattr g lineType 2 setattr g lineWidth 3 ? would change ALL pseudobonds (distances but also any others like metal complex bonds) to dashed with line width 3. To change only specific pseudobond groups, you'd need to end with an atom-spec that includes both ends of least one pseudobond in that group, e.g. something like: setattr g lineType 4 :44,47 ? to make all distance pseudobonds dash-dot (assuming at least one distance measurement is between residues 44 and 47). (3) For distance measurements specifically, you can set how you want them to look when first created. To do that, show the Distances tool (in menu under Tools? Structure Analysis), then set the "Depiction options" on the right side of the dialog before adding the distance measurement. You can click Save to make these depiction settings apply to later uses of Chimera as well. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 15, 2015, at 3:06 PM, Thomas Evangelidis wrote: > Greetings, > I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed? > thanks, > Thomas > From meng at cgl.ucsf.edu Fri Jan 16 10:01:39 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 16 Jan 2015 10:01:39 -0800 Subject: [Chimera-users] dotted lines In-Reply-To: References: <8C7A7E34-40EB-42DD-B5B7-F91EF67E2B1C@cgl.ucsf.edu> Message-ID: <2312CF7C-EB48-4DB6-B3FF-595683A3A450@cgl.ucsf.edu> On Jan 16, 2015, at 8:46 AM, Thomas Evangelidis wrote: > Hi Elaine, > I don't know why, but none of the 3 approached works, even with the latest Chimera version. > [?] Hi Thomas, Your pseudobonds are in stick style. You would have to change the stick to wire before doing those other things; in Chimera there are no ?dotted or dashed? sticks, only wires (lines). E.g. in Selection Inspector, inspect: Pseudobond, change bond style to wire. That only changes the specific pseudobond(s) you have selected; if you first select one distance pseudobond, you can press keyboard up arrow to expand the selection to all the distance pseudobonds. Can also be done with setattr command, e.g.: setattr p drawMode 0 Hard to see on white background. Can change color with setattr too: setattr p color black When you first create distances they are normally already in wire style, which is why I didn?t mention the stick/wire issue before. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From fjchichon at cnb.csic.es Fri Jan 16 03:43:05 2015 From: fjchichon at cnb.csic.es (=?UTF-8?B?RmNvIEphdmllciBDaGljaMOzbg==?=) Date: Fri, 16 Jan 2015 12:43:05 +0100 Subject: [Chimera-users] vop add In-Reply-To: <2BBA101A-4E36-4031-BCC8-A77B224985DC@sonic.net> References: <54B68213.8080900@cnb.csic.es> <2BBA101A-4E36-4031-BCC8-A77B224985DC@sonic.net> Message-ID: <54B8F949.5020802@cnb.csic.es> Dear Tom Thank you very much for your response. We were trying to create the averaged volumes but most of the times we get an error message when using the scaleFactors options. we used the combination of vop threshold, scale, multiply etc trying to create mask... it was unsuccessful, mainly due the errors. At the end the less bad option was to use vop maximum. It will be better to average, but at least, it did not sum the intensities of the tomograms. It will be great to have a vop merge option if feasible. We will use this procedure very often, and chimera allow us to manually setup the volume fiting area and then, the fine positioning was generated perfectly with the volume-fit- tool. On 14/1/15 23:50, Tom Goddard wrote: > Hi Francisco, > > If you average two maps with ?vop add #0,1 scale 0.5,0.5? then where the maps do not overlap the density value will be reduced by averaging when one map has a point inside the structure and one map has the point outside. Another approach to ?merging? would be to take the maximum of the two maps with "vop maximum?. If you really want to average the maps where both are greater than some threshold density, but where only one is greater than the threshold you simply use that map?s value then you will get discontinuities in the merged map at the boundary where both maps are above the threshold. So I wouldn?t recommend that but it could be done with ?vop threshold? to make a 0/1 mask for each map where it is above threshold, add those two masks to get the number of map values (0, 1 or 2 for each grid point) then divide the sum of the maps by that map. Oops, there is no "vop divide?, only a ?vop multiply?. I don?t think you want to do that, but if you do let me know and I will add a vop divide to divide one map by another point-wise. > > Tom > > >> On Jan 14, 2015, at 6:49 AM, Fco Javier Chich?n wrote: >> >> Dear all >> >> I would like to merge several volumes. >> Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. >> >> Anyone know how to do that? >> >> Thanks >> >> -- >> ======================================================= >> Francisco Javier Chich?n Garc?a >> >> Centro.: Centro Nacional de Biotecnolog?a >> Dept.: Macromolecular Structure >> Lab.: S1-S0.1 >> Tel.: (+34) 91585-5497:4690 >> ======================================================= >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> -- ======================================================= Francisco Javier Chich?n Garc?a Centro.: Centro Nacional de Biotecnolog?a Dept.: Macromolecular Structure Lab.: S1-S0.1 Tel.: (+34) 91585-5497:4690 ======================================================= From alejandro.virrueta at yale.edu Fri Jan 16 12:20:51 2015 From: alejandro.virrueta at yale.edu (Alejandro Virrueta) Date: Fri, 16 Jan 2015 15:20:51 -0500 Subject: [Chimera-users] Ringer/Chimera/IDLE Message-ID: Hello, I am modifying some Ringer files for my own needs, but I am running into a weird issue. If I run Ringer via typical means: $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o ringer_out_${pdb_ID}.txt it works fine. However, when I step through it in what I think is my version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus --script `which idle2.7` /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), I run into this error: Traceback (most recent call last): File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in main() File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main move_set, pdb = structureFile(parameters, path) File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in structureFile pdb = chimera.openModels.open(parameters.pdbfileName) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1817, in open checkForChanges=False, noprefs=noprefs) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1644, in add makePseudoBondsToMetals(realMolecules) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1961, in makePseudoBondsToMetals cmPBG = mol.metalComplexGroup(issueHint=True) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 119, in _getMetalPbg am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 608, in get forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 179, in get return self._options[name].get(forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 80, in get return self.prefToVal(self.value) File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", line 1229, in _prefToColor return getColorByName(pref) File "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material Any suggestions? Cheers, Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Jan 16 12:34:39 2015 From: goddard at sonic.net (Tom Goddard) Date: Fri, 16 Jan 2015 12:34:39 -0800 Subject: [Chimera-users] vop add In-Reply-To: <54B8F949.5020802@cnb.csic.es> References: <54B68213.8080900@cnb.csic.es> <2BBA101A-4E36-4031-BCC8-A77B224985DC@sonic.net> <54B8F949.5020802@cnb.csic.es> Message-ID: <3D236880-8CA8-4C94-A907-2A0552B7A4B4@sonic.net> Hi Francisco, If you get an error, Chimera offers a Report a Bug button and you should use it. I don?t know what your suggested new ?vop merge? would do. The idea I suggested of using thresholds to determine the boundary of maps and averaging only where they overlap is very poor as I described in my previous email. Tom > On Jan 16, 2015, at 3:43 AM, Fco Javier Chich?n wrote: > > Dear Tom > > Thank you very much for your response. > > We were trying to create the averaged volumes but most of the times we get an error message when using the scaleFactors options. > > we used the combination of vop threshold, scale, multiply etc trying to create mask... it was unsuccessful, mainly due the errors. > > At the end the less bad option was to use vop maximum. It will be better to average, but at least, it did not sum the intensities of the tomograms. > > > It will be great to have a vop merge option if feasible. We will use this procedure very often, and chimera allow us to manually setup the volume fiting area and then, the fine positioning was generated perfectly with the volume-fit- tool. > > > > > On 14/1/15 23:50, Tom Goddard wrote: >> Hi Francisco, >> >> If you average two maps with ?vop add #0,1 scale 0.5,0.5? then where the maps do not overlap the density value will be reduced by averaging when one map has a point inside the structure and one map has the point outside. Another approach to ?merging? would be to take the maximum of the two maps with "vop maximum?. If you really want to average the maps where both are greater than some threshold density, but where only one is greater than the threshold you simply use that map?s value then you will get discontinuities in the merged map at the boundary where both maps are above the threshold. So I wouldn?t recommend that but it could be done with ?vop threshold? to make a 0/1 mask for each map where it is above threshold, add those two masks to get the number of map values (0, 1 or 2 for each grid point) then divide the sum of the maps by that map. Oops, there is no "vop divide?, only a ?vop multiply?. I don?t think you want to do that, but if you do let me know and I will add a vop divide to divide one map by another point-wise. >> >> Tom >> >> >>> On Jan 14, 2015, at 6:49 AM, Fco Javier Chich?n wrote: >>> >>> Dear all >>> >>> I would like to merge several volumes. >>> Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. >>> >>> Anyone know how to do that? >>> >>> Thanks >>> >>> -- >>> ======================================================= >>> Francisco Javier Chich?n Garc?a >>> >>> Centro.: Centro Nacional de Biotecnolog?a >>> Dept.: Macromolecular Structure >>> Lab.: S1-S0.1 >>> Tel.: (+34) 91585-5497:4690 >>> ======================================================= >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > -- > ======================================================= > Francisco Javier Chich?n Garc?a > > Centro.: Centro Nacional de Biotecnolog?a > Dept.: Macromolecular Structure > Lab.: S1-S0.1 > Tel.: (+34) 91585-5497:4690 > ======================================================= > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From tevang3 at gmail.com Fri Jan 16 13:23:45 2015 From: tevang3 at gmail.com (Thomas Evangelidis) Date: Fri, 16 Jan 2015 23:23:45 +0200 Subject: [Chimera-users] dotted lines In-Reply-To: <2312CF7C-EB48-4DB6-B3FF-595683A3A450@cgl.ucsf.edu> References: <8C7A7E34-40EB-42DD-B5B7-F91EF67E2B1C@cgl.ucsf.edu> <2312CF7C-EB48-4DB6-B3FF-595683A3A450@cgl.ucsf.edu> Message-ID: Thank you Elaine. One last thing, when I save an image using Chimera rendering it says that the effective maximum line width is 3.3333. Is there any way to increase it? Thomas On 16 January 2015 at 20:01, Elaine Meng wrote: > On Jan 16, 2015, at 8:46 AM, Thomas Evangelidis wrote: > > > Hi Elaine, > > I don't know why, but none of the 3 approached works, even with the > latest Chimera version. > > [?] > > Hi Thomas, > Your pseudobonds are in stick style. You would have to change the stick > to wire before doing those other things; in Chimera there are no ?dotted or > dashed? sticks, only wires (lines). E.g. in Selection Inspector, inspect: > Pseudobond, change bond style to wire. That only changes the specific > pseudobond(s) you have selected; if you first select one distance > pseudobond, you can press keyboard up arrow to expand the selection to all > the distance pseudobonds. > > Can also be done with setattr command, e.g.: > setattr p drawMode 0 > > Hard to see on white background. Can change color with setattr too: > setattr p color black > > When you first create distances they are normally already in wire style, > which is why I didn?t mention the stick/wire issue before. I hope this > helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang at pharm.uoa.gr tevang3 at gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ =============================================================== *Physics is the only real science. The rest are just stamp collecting.* *- Ernest Rutherford* -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jan 16 13:35:08 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 16 Jan 2015 13:35:08 -0800 Subject: [Chimera-users] dotted lines In-Reply-To: References: <8C7A7E34-40EB-42DD-B5B7-F91EF67E2B1C@cgl.ucsf.edu> <2312CF7C-EB48-4DB6-B3FF-595683A3A450@cgl.ucsf.edu> Message-ID: <86B0A71E-01A9-4004-96BB-596E93BE5B8A@cgl.ucsf.edu> Hi Thomas, You?re welcome! For getting a fatter line in a saved image, I usually recommend decreasing supersampling (see image save dialog) to 2x2. If you are saving a large number of pixels, even 1x1 may be good enough. For a little more explanation of this issue, see Best, Elaine On Jan 16, 2015, at 1:23 PM, Thomas Evangelidis wrote: > Thank you Elaine. One last thing, when I save an image using Chimera rendering it says that the effective maximum line width is 3.3333. Is there any way to increase it? > > Thomas > From mike.sivley354 at gmail.com Fri Jan 16 12:53:30 2015 From: mike.sivley354 at gmail.com (Mike Sivley) Date: Fri, 16 Jan 2015 14:53:30 -0600 Subject: [Chimera-users] Scripting image writing in Mac OSX Message-ID: <3CE83782-7E8F-4DFD-9F1B-4B76962D3A2A@gmail.com> I have a Chimera script that takes a set of attribute files and generates a collection of scenes images. This script is usually run on Scientific Linux using the Headless Linux 64-bit distribution of Chimera. I'm now trying to run this script on Mac OSX Mavericks and hitting issues with the GUI. If I pass the --nogui flag to Chimera, then the script fails, stating that the GUI is necessary to save images. If I remove the flag, the GUI starts up correctly, but scripted control stops once the new attributes are defined. The user is prompted by the Render by Attribute window, and the script will not progress until the user confirms the changes and closes the GUI. How can I get the script to run start-to-finish without stalling for user-interaction, the way it does in linux? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University From pett at cgl.ucsf.edu Fri Jan 16 16:39:37 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 16 Jan 2015 16:39:37 -0800 Subject: [Chimera-users] Scripting image writing in Mac OSX In-Reply-To: <3CE83782-7E8F-4DFD-9F1B-4B76962D3A2A@gmail.com> References: <3CE83782-7E8F-4DFD-9F1B-4B76962D3A2A@gmail.com> Message-ID: <626E3215-2D4D-4E46-AD56-93B5A724109B@cgl.ucsf.edu> Hi Mike, You don't specify whether this is a Chimera command script or a Python script, but I'm going to guess it's a command script and that you're using the defattr command. If so, you need to add raiseTool false to your command to suppress the Render by Attribute interface. I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 16, 2015, at 12:53 PM, Mike Sivley wrote: > I have a Chimera script that takes a set of attribute files and generates a collection of scenes images. This script is usually run on Scientific Linux using the Headless Linux 64-bit distribution of Chimera. I'm now trying to run this script on Mac OSX Mavericks and hitting issues with the GUI. If I pass the --nogui flag to Chimera, then the script fails, stating that the GUI is necessary to save images. If I remove the flag, the GUI starts up correctly, but scripted control stops once the new attributes are defined. The user is prompted by the Render by Attribute window, and the script will not progress until the user confirms the changes and closes the GUI. > > How can I get the script to run start-to-finish without stalling for user-interaction, the way it does in linux? > > Thanks! > > Mike Sivley > PhD Student in Biomedical Informatics > Center for Human Genetics Research > Vanderbilt University > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jlvl500 at york.ac.uk Sun Jan 18 07:55:03 2015 From: jlvl500 at york.ac.uk (Juan Luis Loredo Varela) Date: Sun, 18 Jan 2015 15:55:03 +0000 Subject: [Chimera-users] Creating a cubic box for a density map Message-ID: Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan -- Juan Luis Loredo Varela PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sun Jan 18 09:47:36 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 18 Jan 2015 09:47:36 -0800 Subject: [Chimera-users] Creating a cubic box for a density map In-Reply-To: References: Message-ID: <002B513E-934D-43FA-B0E3-F90499DEA693@cgl.ucsf.edu> Dear Juan, Take a look at the command ?vop cover? with box, ibox, or fbox option. I think that will do what you want: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 18, 2015, at 7:55 AM, Juan Luis Loredo Varela wrote: > Dear Chimera users > When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? > Thanks > Juan From goddard at sonic.net Sun Jan 18 10:29:36 2015 From: goddard at sonic.net (Tom Goddard) Date: Sun, 18 Jan 2015 10:29:36 -0800 Subject: [Chimera-users] Creating a cubic box for a density map In-Reply-To: References: Message-ID: Hi Juan, The Chimera Segger dialog menu entry Regions / Extract Densities let?s you make cube shaped maps for selected segmented regions. I guess you were using Segger menu File / Save Selected Regions which does not give that option. Tom > On Jan 18, 2015, at 7:55 AM, Juan Luis Loredo Varela wrote: > > Dear Chimera users > > When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? > > Thanks > > Juan > > > > -- > Juan Luis Loredo Varela > > PhD Student > Antson Group > York Structural Biology Laboratory L0 > Department of Chemistry > University of York > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From walker at chemistry.msu.edu Tue Jan 20 13:36:43 2015 From: walker at chemistry.msu.edu (Kevin D. Walker) Date: Tue, 20 Jan 2015 21:36:43 +0000 Subject: [Chimera-users] Simply, keep up the good work Message-ID: I really enjoy using the Chimera program, and I am trying to convince my lab members to make the switch. I hope you get these types of emails all of the time. Your program is duly acknowledged during my seminars. ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-research/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.feldman-salit at h-its.org Tue Jan 20 02:11:01 2015 From: anna.feldman-salit at h-its.org (Feldman-Salit, Anna) Date: Tue, 20 Jan 2015 10:11:01 +0000 Subject: [Chimera-users] UHBD map, generated with APBS Message-ID: <124d8959d41b45d3919ebfe1407557f8@VBMBX01.villa-bosch.de> My current "strange" problem: I use APBS stand-alone to generate electrostatic potential for a protein in PQR format. What I do is to ask for output in UHBD (GRD not DX) format. Unfortunately, the generated GRD file is not read by CHIMERA, which upsets me... Strange, but VMD seems to be less sensitive to the GRD generated with APBS to visualize the map. Another point: I am very glad that CHIMERA computes potential. Do you think one could save it not only in DX format? Maybe you could suggest me a way to convert DX to UHBD format? Thank you! Have a lovely working day! Greetings, Anna --- Dr. Anna Feldman-Salit Molecular and Cellular Modeling (MCM) Group HITS gGmbH, Schlo?-Wolfsbrunnenweg 35 69118 Heidelberg, Germany phone: +49-6221-533-260 fax: +49 6221 533298 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jan 20 14:28:43 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 20 Jan 2015 14:28:43 -0800 Subject: [Chimera-users] Simply, keep up the good work In-Reply-To: References: Message-ID: <5E11EDA3-91D8-4EC3-842C-071E2DEFEC5F@cgl.ucsf.edu> Thank you, that is so nice! We really appreciate your kind words and efforts toward user recruitment! Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 20, 2015, at 1:36 PM, "Kevin D. Walker" wrote: > I really enjoy using the Chimera program, and I am trying to convince my lab members to make the switch. > > I hope you get these types of emails all of the time. Your program is duly acknowledged during my seminars. From meng at cgl.ucsf.edu Tue Jan 20 15:05:54 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 20 Jan 2015 15:05:54 -0800 Subject: [Chimera-users] UHBD map, generated with APBS In-Reply-To: <124d8959d41b45d3919ebfe1407557f8@VBMBX01.villa-bosch.de> References: <124d8959d41b45d3919ebfe1407557f8@VBMBX01.villa-bosch.de> Message-ID: Hi Anna, Issue 1: reading UHBD grd format. Chimera does read the binary format from UHBD, for which we use the .grd filename extension: I don't know how the UHBD grid format from your ABPS standalone is different. The APBS documentation only says "legacy UHBD format" without a full description. You could try using Chimera menu: Help? Report a Bug, making sure to attach the file and include your email address for feedback if you believe it is the binary UHBD format that Chimera should read. Problem 2: if you are using Chimera to make a dx file, I guess you are using the APBS tool. This calculation is not run within Chimera but using an APBS web service provided by the NBCR. This web service may not have all the options of standalone APBS. I haven't used it myself, but I found a program online that is supposed to convert the formats: Apparently it is a tool included with the APBS distribution. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 20, 2015, at 2:11 AM, "Feldman-Salit, Anna" wrote: > My current "strange" problem: > > I use APBS stand-alone to generate electrostatic potential for a protein in PQR format. What I do is to ask for output in UHBD (GRD not DX) format. Unfortunately, the generated GRD file is not read by CHIMERA, which upsets me... Strange, but VMD seems to be less sensitive to the GRD generated with APBS to visualize the map. > > Another point: > I am very glad that CHIMERA computes potential. Do you think one could save it not only in DX format? Maybe you could suggest me a way to convert DX to UHBD format? > > Thank you! > Have a lovely working day! > > Greetings, > Anna > From alejandro.virrueta at yale.edu Tue Jan 20 15:34:20 2015 From: alejandro.virrueta at yale.edu (Alejandro Virrueta) Date: Tue, 20 Jan 2015 18:34:20 -0500 Subject: [Chimera-users] Alternate conformations in residues Message-ID: Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Tue Jan 20 16:16:49 2015 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 20 Jan 2015 19:16:49 -0500 Subject: [Chimera-users] Morph conformations - estimated time to completion in status bar? Message-ID: <76C6F1F3-3581-463C-B5A1-569A2E6BA595@gmail.com> Hi all - silly little feature suggestion, but I was wondering if it would be possible to add an live-updating ?x % complete? or ?estimated time to completion? entry in the status bar when running Morph Conformations? When morphing two structures with very large numbers of atoms, morph conformations can take a long time (hours) to complete, and it would be handy to know whether it is nearly done or not (currently it just shows ?computing interpolation 1? until it is finished). On a related note, is there any way to speed up morph conformations for large structures? E.g calculating transformations using C-alpha atoms only? Best, Oliver. From kay_jay at earthlink.net Tue Jan 20 23:32:27 2015 From: kay_jay at earthlink.net (Kenward Vaughan) Date: Tue, 20 Jan 2015 23:32:27 -0800 Subject: [Chimera-users] How can one create a sculpted view of a cellular assembly? Message-ID: <54BF560B.7030302@earthlink.net> As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? Sorry for the long question... ;-/ Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca From meng at cgl.ucsf.edu Wed Jan 21 08:51:23 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Jan 2015 08:51:23 -0800 Subject: [Chimera-users] How can one create a sculpted view of a cellular assembly? In-Reply-To: <54BF560B.7030302@earthlink.net> References: <54BF560B.7030302@earthlink.net> Message-ID: Hi Kenward, Those suggestions all make sense for exploring and displaying a multicomponent structure. In fact, the cellpack.org ?use? page shows an HIV model depicted in other software that shows some of your suggested features: This page also lists the available Cellpack models that you can open with Fetch by ID in Chimera 1.10.1 or daily build. Currently just HIV-1_0.1.6_6 but we expect additional ones soon. Chimera does have some capabilities along the lines of your suggestions, but not fully. Here?s what it has now (others, please chime in if I forgot anything): (1) The Per-Model Clipping tool (in menu under Tools? Depiction) allows single-plane or slab clipping that only applies to a single model and also rotates with that model. If you fetch the Cellpack model mentioned above, then in Model Panel choose to ?ungroup,? you will see that all the different components of that HIV overall model are different models in Chimera that could be shown/hidden or per-model clipped separately. The Cellpack component models are surface models in Chimera. (2) Although clipping will show parts of individual components, you can avoid that by instead selecting and hiding some subset of the surfaces, since each surface piece is selected as a whole. You can drag out selection areas with Ctrl-drag, then hide all the surfaces that were in that area with menu: Actions? Surface? hide. The trick is to select only the surfaces that you really wanted to hide, as the drag will select all the stuff in the area. I could first drag out a selection area, then subtract specific models from that selection, e.g. command: ~select #0.17 (3) There is a Volume Eraser tool (under Tools? Volume Data) that lets you erase volume data (grid data, density maps mainly) within a spherical bubble that you can move around manually. However, as the name suggests, it is for volume data, not surface models. Similarly there are ?vop? commands for chopping out octants of volume data. (4) Multiscale Models does allow selecting all like components (copies of the same molecule) so that they can all be shown/hidden at the same time. What you might need instead to implement your suggestions is a selection tool that selects surface pieces within a sphere, wedge, or other more complicated shape, or fancier set of controls specifically meant for working with Cellpack models. I hope this helps somewhat! Good ideas, thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 20, 2015, at 11:32 PM, Kenward Vaughan wrote: > As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. > > In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: > > 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). > > Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? > > Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. > > Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. > > > One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. > > > Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? > > Sorry for the long question... ;-/ > > > Kenward > -- > In a completely rational society, the best of us would aspire to be > _teachers_ and the rest of us would have to settle for something less, > because passing civilization along from one generation to the next > ought to be the highest honor and the highest responsibility anyone > could have. - Lee Iacocca > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From reachsampaul at gmail.com Wed Jan 21 02:09:49 2015 From: reachsampaul at gmail.com (Sam Paul D.) Date: Wed, 21 Jan 2015 15:39:49 +0530 Subject: [Chimera-users] how to find non-bonded interactions between a protein and a ligand? Message-ID: Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: From hoang at ipk-gatersleben.de Wed Jan 21 02:16:45 2015 From: hoang at ipk-gatersleben.de (Phan Trong Hoang) Date: Wed, 21 Jan 2015 10:16:45 +0000 Subject: [Chimera-users] How to predict/model the structure of two known structure proteins Message-ID: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BC9B@XCH-MBX2.ipk-gatersleben.de> Dear UCSF developers, I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). Is this function available in your software? If yes can you show me how to manipulate with it. I would like appreciate it very much Thank you for your attention and I am looking forward to hearing from you. Best regards Hoang Phan -------------- next part -------------- An HTML attachment was scrubbed... URL: From hernando.sosa at einstein.yu.edu Wed Jan 21 09:20:00 2015 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Wed, 21 Jan 2015 17:20:00 +0000 Subject: [Chimera-users] SDF file Message-ID: I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From aldosegura at gmail.com Wed Jan 21 11:34:37 2015 From: aldosegura at gmail.com (Aldo Segura) Date: Wed, 21 Jan 2015 14:34:37 -0500 Subject: [Chimera-users] SDF file In-Reply-To: References: Message-ID: Hi Hernando, I think Chimera does not deal with sdf files (either 2D or 3D). Chimera team please correct me if I'm wrong :) You should try to open your 2D sdf file with Avogadro program and run some geometry optimizations. Then, save your file in mol2, pdb, etc. and open it with chimera if that's what you want. Best, Aldo 2015-01-21 12:20 GMT-05:00 Hernando J Sosa : > I have an sdf file with a small ligand molecule in 2D (it looks flat > when opened in chimera). What would be the best way to make it 3D (i.e. > assign/minimize the proper bond angles & distances). Is it possible to do > it in chimera? > > Thanks > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- ========================================= Aldo Segura-Cabrera Research Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera at cchmc.org ; aldosegura at gmail.com ========================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Jan 21 12:15:56 2015 From: goddard at sonic.net (Tom Goddard) Date: Wed, 21 Jan 2015 12:15:56 -0800 Subject: [Chimera-users] How can one create a sculpted view of a cellular assembly? In-Reply-To: References: <54BF560B.7030302@earthlink.net> Message-ID: <1C4CD29C-5C2E-495C-8614-C4E5B0EB3143@sonic.net> Hi Kenward, As Elaine points out you can do some fancy cut open views in Chimera now, although the user interface is difficult ? requires that you know a lot about Chimera. I?ve attached 3 images of the cellPACK HIV model cut open and here are the commands I used to do it. First I used menu File / Fetch by Id and entered cellPACK identifier HIV-1_0.1.6_6 to load an HIV virus model. Then I held the ctrl key and drag selected a box having one corner at the center of the virus to select one octant. This takes a long time ? with my 2 year old Mac graphics it took 10 seconds for that selection to happen, older graphics will be slower still. Then I hid all the selected molecules with command sop hidePieces sel That command is "surface operation? hide the selected pieces. That gave the first image I?ve attached. In the second image I add back all molecules within 40 nm of the virus center. First I place a marker at the virus center with command ac mz This runs keyboard accelerator ?mz? which puts a marker at 0,0,0 which happens to be the center of the virus. Then I select everything within 400 Angstroms: zonesel #1 400 # Here the marker is model #1 (you can see this in Model Panel) ? it says select everything in # (that is notation for all models) within 400 Angstroms of #1. Then show those molecule surfaces: sop showPieces sel This gives the second image. Now I wanted to show the full HIV capsid core in the third image so I used: sop showPieces #0.23 because model #0.23 is the core capsid according to Model Panel. I have long thought we need simpler user interface to do these kinds of things. I even think I added a feature request to our Chimera database for the fancy clipping mode you suggested where all surfaces that intercept the clip plane are shown in their entirety to give a bumpy clip surface. We have been working on Chimera 2 a year and these kinds of features are more likely to bei put into Chimera 2 than in Chimera 1. Tom > On Jan 21, 2015, at 8:51 AM, Elaine Meng wrote: > > Hi Kenward, > Those suggestions all make sense for exploring and displaying a multicomponent structure. In fact, the cellpack.org ?use? page shows an HIV model depicted in other software that shows some of your suggested features: > > > This page also lists the available Cellpack models that you can open with Fetch by ID in Chimera 1.10.1 or daily build. Currently just HIV-1_0.1.6_6 but we expect additional ones soon. > > Chimera does have some capabilities along the lines of your suggestions, but not fully. Here?s what it has now (others, please chime in if I forgot anything): > > (1) The Per-Model Clipping tool (in menu under Tools? Depiction) allows single-plane or slab clipping that only applies to a single model and also rotates with that model. If you fetch the Cellpack model mentioned above, then in Model Panel choose to ?ungroup,? you will see that all the different components of that HIV overall model are different models in Chimera that could be shown/hidden or per-model clipped separately. The Cellpack component models are surface models in Chimera. > > > (2) Although clipping will show parts of individual components, you can avoid that by instead selecting and hiding some subset of the surfaces, since each surface piece is selected as a whole. You can drag out selection areas with Ctrl-drag, then hide all the surfaces that were in that area with menu: Actions? Surface? hide. The trick is to select only the surfaces that you really wanted to hide, as the drag will select all the stuff in the area. I could first drag out a selection area, then subtract specific models from that selection, e.g. command: ~select #0.17 > > > > (3) There is a Volume Eraser tool (under Tools? Volume Data) that lets you erase volume data (grid data, density maps mainly) within a spherical bubble that you can move around manually. However, as the name suggests, it is for volume data, not surface models. Similarly there are ?vop? commands for chopping out octants of volume data. > > > > (4) Multiscale Models does allow selecting all like components (copies of the same molecule) so that they can all be shown/hidden at the same time. > > > What you might need instead to implement your suggestions is a selection tool that selects surface pieces within a sphere, wedge, or other more complicated shape, or fancier set of controls specifically meant for working with Cellpack models. > > I hope this helps somewhat! Good ideas, thanks! > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jan 20, 2015, at 11:32 PM, Kenward Vaughan wrote: > >> As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. >> >> In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: >> >> 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). >> >> Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? >> >> Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. >> >> Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. >> >> >> One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. >> >> >> Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? >> >> Sorry for the long question... ;-/ >> >> >> Kenward >> -- >> In a completely rational society, the best of us would aspire to be >> _teachers_ and the rest of us would have to settle for something less, >> because passing civilization along from one generation to the next >> ought to be the highest honor and the highest responsibility anyone >> could have. - Lee Iacocca >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hiv-pacman.jpeg Type: image/jpeg Size: 29575 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hiv-innerball.jpeg Type: image/jpeg Size: 29609 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hiv-capsid.jpeg Type: image/jpeg Size: 29791 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Jan 21 12:42:37 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Jan 2015 12:42:37 -0800 Subject: [Chimera-users] how to find non-bonded interactions between a protein and a ligand? In-Reply-To: References: Message-ID: <894A6232-1515-4288-9403-3DA6F4404693@cgl.ucsf.edu> Hi Sam, There is a ?findclash? command for finding favorable contacts and close contacts. It has the same features as in the ?Find Clashes/Contacts? graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use: I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools? Structure Analysis? Find Clashes/Contacts) to decide what settings you want to use. However, here is one example command using some standard settings for finding contacts, assuming that ?protein? and ?ligand? specify the desired parts of your structure: findclash protein test ligand overlap -0.4 hbond 0.0 reveal true ? or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms: findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true There are many ways to specify atoms (e.g. protein and ligand) in the command line: There is another example of using the ?findclash? command in the Opened Interface image tutorial: ? and the ?Find Clashes/Contacts? too is used in the Structure Analysis & Comparison tutorial: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 2:09 AM, Sam Paul D. wrote: > Hi, > I need to find non-bonded interactions between a protein and a ligand through command line. > Could anyone please suggest which chimera command to use with the syntax? > With regards, > Sam From mike.sivley at vanderbilt.edu Wed Jan 21 10:45:05 2015 From: mike.sivley at vanderbilt.edu (R. Michael Sivley) Date: Wed, 21 Jan 2015 12:45:05 -0600 Subject: [Chimera-users] Mesh defined by distance to selection Message-ID: <906CEB82-613B-4D34-A790-FA22D48D2B6E@vanderbilt.edu> I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for. I found this in the Chimera help pages, and it seems to be exactly what I need: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#zone I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful. Could you help me identify the missing step in this process? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2015-01-21 at 12.43.53 PM.png Type: image/png Size: 238743 bytes Desc: Screen Shot 2015-01-21 at 12.43.53 PM.png URL: From meng at cgl.ucsf.edu Wed Jan 21 12:49:32 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Jan 2015 12:49:32 -0800 Subject: [Chimera-users] SDF file In-Reply-To: References: Message-ID: Hi Hernando, Chimera does read SDF files, but only 3D SDF files will be useful. 2D SDF files are used for when people just want to display the chemical diagrams. In my opinion, you can?t really convert these into 3D by minimization in Chimera because the atom types won?t be recognized correctly in the first place, just from the flat diagram. You would need to obtain a 3D SDF of the molecule instead. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 9:20 AM, Hernando J Sosa wrote: > I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? > Thanks > From meng at cgl.ucsf.edu Wed Jan 21 13:04:24 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Jan 2015 13:04:24 -0800 Subject: [Chimera-users] Mesh defined by distance to selection In-Reply-To: <906CEB82-613B-4D34-A790-FA22D48D2B6E@vanderbilt.edu> References: <906CEB82-613B-4D34-A790-FA22D48D2B6E@vanderbilt.edu> Message-ID: Hi Mike, Volume Viewer zoning does not create the mesh. Instead it acts on a pre-existing density map shown with mesh isosurface; it hides the isosurface parts beyond the zone. You can ?fake? a density map for a set of atoms using the ?molmap? command. Basically this uses the positions of the specified atoms and smears them out. Then in Volume Viewer, you could show the density map with a mesh isosurface, then select some of the original atoms and show only the mesh in the zone of those atoms. However, you may need to experiment with the resolution and which atoms should be specified in the molmap command, the isosurface contour level, etc. and I don?t know how well the result would match what you have in mind. Some example molmap commands: molmap protein 6 molmap :1-100.A at CA 5 ? see the man page for an explanation of how it works and additional command-line options: Volume Viewer docs: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 10:45 AM, R. Michael Sivley wrote: > I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for. > > I found this in the Chimera help pages, and it seems to be exactly what I need: > http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#zone > > I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful. > > Could you help me identify the missing step in this process? Thanks! > > Mike Sivley > PhD Student in Biomedical Informatics > Center for Human Genetics Research > Vanderbilt University From alejandro.virrueta at yale.edu Wed Jan 21 13:20:02 2015 From: alejandro.virrueta at yale.edu (Alejandro Virrueta) Date: Wed, 21 Jan 2015 16:20:02 -0500 Subject: [Chimera-users] Alternate conformations in residues Message-ID: Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Jan 21 13:31:33 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 21 Jan 2015 13:31:33 -0800 Subject: [Chimera-users] Alternate conformations in residues In-Reply-To: References: Message-ID: On Jan 20, 2015, at 3:34 PM, Alejandro Virrueta wrote: > Hello all, > > Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Hi Alex, It's a little ugly but very possible. The treatment of alt locs in Chimera 2 will be less arcane, but Chimera 1 is all there is right now. Anyway, You can get the atoms involved in a particular chi angle by using the "chiAtoms" function: from chimera.phipsi import chiAtoms chiExemplar = chiAtoms(res, 2) # for chi2 Now, these are just the first atoms in the residue, usually alt loc A (or blank, for residues with no alt locs). To find the corresponding B alt loc atoms, you will have to rummage through the residue: bAtoms = [] for ce in chiExemplar: for a in res.atomsMap[ce.name]: if a.altLoc == 'B': bAtoms.append(a) break else: raise AssertionError("No B alt loc for atom %s" % ce.name) Then finally you can compute the chi angle: from chimera import dihedral chi = dihedral(*[a.coord() for a in bAtoms]) Like I said, a little ugly, but doable. --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 Wed Jan 21 14:01:37 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Jan 2015 14:01:37 -0800 Subject: [Chimera-users] How to predict/model the structure of two known structure proteins In-Reply-To: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BC9B@XCH-MBX2.ipk-gatersleben.de> References: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BC9B@XCH-MBX2.ipk-gatersleben.de> Message-ID: <2FB778A4-D62E-4BCD-AD98-E575FBB1424C@cgl.ucsf.edu> Dear Hoang, Yes, but there are a few steps. You would need to: (1) use a text-editor to make a plain text fasta-format file of the fusion protein sequence, if you don?t already have such a file. Fasta format description: Make the name of your file end with ?.fasta" (2) open the fasta file in Chimera. Then from sequence window menu: Info? Blast Protein to search the PDB for matching structures. In the Blast Protein results, find the two structure proteins and choose both lines (click, ctrl-click in the results dialog), then click the ?Show in MAV? and ?Load Structure? buttons at the bottom of the dialog. (3) now you will have a new sequence alignment window with 3 sequences in it: the fusion protein and the two protein structures, and in the main Chimera window, the two structures. (4) In Chimera, delete any extra protein chains. In other words, if there are extra copies of those structures, just delete them so that you have only one copy to use as the template. Make sure that the remaining copy of each is associated with its sequence in the alignment (sequence alignment window menu: Structures? Associations?) (5) position the two structures so that the termini are in a somewhat reasonable place relative to each other to template the fusion protein. You can ?freeze? one in place by deactivating it and move just the other with the mouse as described here: 6) from the sequence alignment window menu choose: Structure? Modeller (homology) to show the Modeller dialog. Choose the query as the target and both structures as the template, etc. as in the modeling tutorials. You may also want to turn on ?Use thorough optimization? in the Advanced Options section. I don?t know which homology-modeling tutorial you have been using, but here is one: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 2:16 AM, Phan Trong Hoang wrote: > Dear UCSF developers, > I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). > Is this function available in your software? If yes can you show me how to manipulate with it. > I would like appreciate it very much > Thank you for your attention and I am looking forward to hearing from you. > Best regards > Hoang Phan From mborgnia at nih.gov Wed Jan 21 14:14:02 2015 From: mborgnia at nih.gov (Mario J. Borgnia) Date: Wed, 21 Jan 2015 17:14:02 -0500 Subject: [Chimera-users] Coot capabilities in Chimera Message-ID: <54C024AA.2010302@nih.gov> Dear all, WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves refining structures. The blunt question is, should I move to Coot and leave behind Chimera for that or are there overlapping functions and what will I be missing if I choose to stay with Chimera. I have some ideas about the answers but would like to read what the developers and power users have to say on the issue. Thanks!!! From gregc at cgl.ucsf.edu Wed Jan 21 14:15:58 2015 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 21 Jan 2015 14:15:58 -0800 Subject: [Chimera-users] Ringer/Chimera/IDLE In-Reply-To: References: Message-ID: <54C0251E.3090601@cgl.ucsf.edu> (This question is a developer question and not a user question, but since it was asked on chimera-users, the response is there as well. Followups should go to chimera-dev at cgl.ucsf.edu.) The "ValueError: missing default material" means that the script was not run by chimera, which we don't support. We also don't support using an IDLE other than the one you get by running chimera and using Tools / General Tools / IDLE. We only support using chimera's Python code in scripts that are invoked by chimera. That is why the ringer shell script is: "$CHIMERA_HOME"/bin/chimera --nogui --silent --script "$RINGER"/ringer/main.py -- "$@" In the same vein, if you replaced "$RINGER"/ringer/main.py with the following 2 line script: import chimera print chimera.MaterialColor(1, 1, 1) Everything works. Long ago, we considered what it would take to get chimera's Python code working in a different application. In that scenario, you would need to: 1. Set the CHIMERA environment variable to the root of the Chimera installation 2. Set other environment variables that are set in CHIMERA/bin/chimera for your platform 3. Add $CHIMERA/share to your Python's sys.path 4. import chimeraInit; chimeraInit.init([], nogui=True, eventloop=False, exitonquit=False) But since chimera uses a modified Python, that is insufficient. For example, chimera changes Python's default string to unicode conversion to use utf-8 instead of ASCII. We've also backported some of Python 3's unicode support that chimera depends on. If you are lucky, your use of chimera's Python code will not be affected by those changes. HTH, Greg P.S. Your immediate problem might be fixed by calling chimera.initializeColors(), but that is a hack that is not guaranteed to keep working. On 01/16/2015 12:20 PM, Alejandro Virrueta wrote: > Hello, > > I am modifying some Ringer files for my own needs, but I am running > into a weird issue. If I run Ringer via typical means: > > $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o > ringer_out_${pdb_ID}.txt > > it works fine. However, when I step through it in what I think is my > version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus > --script `which idle2.7` > /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), > I run into this error: > > Traceback (most recent call last): > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in > > main() > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main > move_set, pdb = structureFile(parameters, path) > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in > structureFile > pdb = chimera.openModels.open(parameters.pdbfileName) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1817, in open > checkForChanges=False, noprefs=noprefs) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1644, in add > makePseudoBondsToMetals(realMolecules) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1961, in makePseudoBondsToMetals > cmPBG = mol.metalComplexGroup(issueHint=True) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 119, in _getMetalPbg > am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 608, in get > forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 179, in get > return self._options[name].get(forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 80, in get > return self.prefToVal(self.value) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", > line 1229, in _prefToColor > return getColorByName(pref) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", > line 87, in getColorByName > color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) > ValueError: missing default material > > Any suggestions? > > Cheers, > Alex > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From kay_jay at earthlink.net Wed Jan 21 23:08:46 2015 From: kay_jay at earthlink.net (Kenward Vaughan) Date: Wed, 21 Jan 2015 23:08:46 -0800 Subject: [Chimera-users] How can one create a sculpted view of a cellular assembly? In-Reply-To: <1C4CD29C-5C2E-495C-8614-C4E5B0EB3143@sonic.net> References: <54BF560B.7030302@earthlink.net> <1C4CD29C-5C2E-495C-8614-C4E5B0EB3143@sonic.net> Message-ID: <54C0A1FE.10104@earthlink.net> On 01/21/2015 12:15 PM, Tom Goddard wrote: > Hi Kenward, > > As Elaine points out you can do some fancy cut open views in Chimera > now, although the user interface is difficult ? requires that you know a > lot about Chimera. I?ve attached 3 images of the cellPACK HIV model cut > open and here are the commands I used to do it. ... Thank you both for the pointers and examples of approaches for doing this. I had not paid attention to the information about the objects being surfaces for Chimera. After assimilating Tom's suggested commands and playing a bit, what was created fits what I am looking for, and I'm ready to play further to expand on it. Some of the selection methods Elaine suggested will help with that. Thank you so much with this! I expect I may have a few more questions down the line, and appreciate knowing the tremendous resource you folks represent to me and others using this wonderful software. Kenward >> On Jan 21, 2015, at 8:51 AM, Elaine Meng wrote: >> >> Hi Kenward, >> Those suggestions all make sense for exploring and displaying a >> multicomponent structure. In fact, the cellpack.org >> ?use? page shows an HIV model depicted in other >> software that shows some of your suggested features: >> >> >> This page also lists the available Cellpack models that you can open >> with Fetch by ID in Chimera 1.10.1 or daily build. Currently just >> HIV-1_0.1.6_6 but we expect additional ones soon. >> >> Chimera does have some capabilities along the lines of your >> suggestions, but not fully. Here?s what it has now (others, please >> chime in if I forgot anything): ... >> On Jan 20, 2015, at 11:32 PM, Kenward Vaughan wrote: >> >>> As I slowly approach the operational realization of my >>> computational/visualization lab, I received your lovely holiday card. >>> This seriously elevated my dreams of larger scale possibilities for >>> chemistry and biology students through the cellPack resources. >>> >>> In playing with it, I found myself wanting a more robust version of a >>> clipping plane which would have several characteristics: >>> >>> 3 dimensional - take a cell and hack out 1 or 2 adjoining octants ... -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca From hernando.sosa at einstein.yu.edu Thu Jan 22 06:21:30 2015 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Thu, 22 Jan 2015 14:21:30 +0000 Subject: [Chimera-users] SDF file In-Reply-To: References: Message-ID: Thanks Aldo, I tried Avogrado and it does do the trick. Best Hernando From: Aldo Segura [mailto:aldosegura at gmail.com] Sent: Wednesday, January 21, 2015 2:35 PM To: Hernando J Sosa Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] SDF file Hi Hernando, I think Chimera does not deal with sdf files (either 2D or 3D). Chimera team please correct me if I'm wrong :) You should try to open your 2D sdf file with Avogadro program and run some geometry optimizations. Then, save your file in mol2, pdb, etc. and open it with chimera if that's what you want. Best, Aldo 2015-01-21 12:20 GMT-05:00 Hernando J Sosa >: I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? Thanks _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -- ========================================= Aldo Segura-Cabrera Research Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera at cchmc.org; aldosegura at gmail.com ========================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jan 22 09:28:30 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 22 Jan 2015 09:28:30 -0800 Subject: [Chimera-users] How to predict/model the structure of two known structure proteins In-Reply-To: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BD65@XCH-MBX2.ipk-gatersleben.de> References: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BC9B@XCH-MBX2.ipk-gatersleben.de> <2FB778A4-D62E-4BCD-AD98-E575FBB1424C@cgl.ucsf.edu> <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BD65@XCH-MBX2.ipk-gatersleben.de> Message-ID: <437C9480-1A04-4BE4-93D3-EB8B18676BD6@cgl.ucsf.edu> Dear Hoang, Blast should find the matching PDB structures with those default settings. Just now I tried using a fasta file with only the last line of sequence shown in your image, and it correctly found PDB 2LW9. The results dialog first appears empty, but later when the search is done the results appear. So maybe you just needed to wait a few minutes for the results. However, if you wait a long time and still don't get results, you could skip the Blast part and instead: (A) create (outside of Chimera) a 3-sequence alignment containing your target fusion protein and the sequences of each of the template PDB structures, in any of the formats Chimera can read: (B) open that sequence alignment and the two template PDB structures in Chimera, then proceed starting with step #4 in my previous message. Another possibility that I forgot to mention before is to use the new "mda" multidomain assembler command (in Chimera 1.10.1 or newer daily build) with your fusion-protein fasta file as input. This automates several of the steps in my previous message, including running Blast, up to the point of opening the Modeller dialog. Of course, Blast will have to be working correctly, but my tests suggest that it is. The "mda" command has several options, and I don't know whether you would need to use any of those options for it to find the desired template structures. However, it might still be worth a try because then you don't have to do steps #2-5 yourself. See the syntax and option information here: I hope this helps, Elaine On Jan 22, 2015, at 6:05 AM, Phan Trong Hoang wrote: > Dear Meng, > Thank you very much for your reply. > I have tried as you wrote (please see figure 1), but I face the problem. There is a Blast:query appearance but there is no information about PDB....please have a look at the attached picture (figure 2). I tried with the sequence of one protein in PDB. The same table appeared with no more information. Could you show me how to fix it or there are other steps to avoid this step. > Thank you > Best regards > Hoang From reachsampaul at gmail.com Wed Jan 21 17:50:58 2015 From: reachsampaul at gmail.com (Sam Paul D) Date: Thu, 22 Jan 2015 07:20:58 +0530 Subject: [Chimera-users] how to find non-bonded interactions between a protein and a ligand? In-Reply-To: <894A6232-1515-4288-9403-3DA6F4404693@cgl.ucsf.edu> References: <894A6232-1515-4288-9403-3DA6F4404693@cgl.ucsf.edu> Message-ID: Hi Elaine, First of all thanks for all the suggestions. I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. Thanks! Sam Sent from my iPhone > On 22-Jan-2015, at 02:12, Elaine Meng wrote: > > Hi Sam, > There is a ?findclash? command for finding favorable contacts and close contacts. It has the same features as in the ?F > ind Clashes/Contacts? graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use: > > > I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools? Structure Analysis? Find Clashes/Contacts) to decide what settings you want to use. > > > However, here is one example command using some standard settings for finding contacts, assuming that ?protein? and ?ligand? specify the desired parts of your structure: > > findclash protein test ligand overlap -0.4 hbond 0.0 reveal true > > ? or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms: > > findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true > > There are many ways to specify atoms (e.g. protein and ligand) in the command line: > > > There is another example of using the ?findclash? command in the Opened Interface image tutorial: > orials/squalene.html> > > ? and the ?Find Clashes/Contacts? too is used in the Structure Analysis & Comparison tutorial: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jan 21, 2015, at 2:09 AM, Sam Paul D. wrote: >> >> Hi, >> I need to find non-bonded interactions between a protein and a ligand through command line. >> Could anyone please suggest which chimera command to use with the syntax? >> With regards, >> Sam > From hoang at ipk-gatersleben.de Thu Jan 22 06:05:10 2015 From: hoang at ipk-gatersleben.de (Phan Trong Hoang) Date: Thu, 22 Jan 2015 14:05:10 +0000 Subject: [Chimera-users] How to predict/model the structure of two known structure proteins In-Reply-To: <2FB778A4-D62E-4BCD-AD98-E575FBB1424C@cgl.ucsf.edu> References: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BC9B@XCH-MBX2.ipk-gatersleben.de> <2FB778A4-D62E-4BCD-AD98-E575FBB1424C@cgl.ucsf.edu> Message-ID: <8BFE1C5144D4FF4D8386B5FFA1FC8F2F76A1BD65@XCH-MBX2.ipk-gatersleben.de> Dear Meng, Thank you very much for your reply. I have tried as you wrote (please see figure 1), but I face the problem. There is a Blast:query appearance but there is no information about PDB....please have a look at the attached picture (figure 2). I tried with the sequence of one protein in PDB. The same table appeared with no more information. Could you show me how to fix it or there are other steps to avoid this step. Thank you Best regards Hoang -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Mittwoch, 21. Januar 2015 23:02 To: Phan Trong Hoang Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] How to predict/model the structure of two known structure proteins Dear Hoang, Yes, but there are a few steps. You would need to: (1) use a text-editor to make a plain text fasta-format file of the fusion protein sequence, if you don't already have such a file. Fasta format description: Make the name of your file end with ".fasta" (2) open the fasta file in Chimera. Then from sequence window menu: Info... Blast Protein to search the PDB for matching structures. In the Blast Protein results, find the two structure proteins and choose both lines (click, ctrl-click in the results dialog), then click the "Show in MAV" and "Load Structure" buttons at the bottom of the dialog. (3) now you will have a new sequence alignment window with 3 sequences in it: the fusion protein and the two protein structures, and in the main Chimera window, the two structures. (4) In Chimera, delete any extra protein chains. In other words, if there are extra copies of those structures, just delete them so that you have only one copy to use as the template. Make sure that the remaining copy of each is associated with its sequence in the alignment (sequence alignment window menu: Structures... Associations...) (5) position the two structures so that the termini are in a somewhat reasonable place relative to each other to template the fusion protein. You can "freeze" one in place by deactivating it and move just the other with the mouse as described here: 6) from the sequence alignment window menu choose: Structure... Modeller (homology) to show the Modeller dialog. Choose the query as the target and both structures as the template, etc. as in the modeling tutorials. You may also want to turn on "Use thorough optimization" in the Advanced Options section. I don't know which homology-modeling tutorial you have been using, but here is one: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 2:16 AM, Phan Trong Hoang wrote: > Dear UCSF developers, > I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). > Is this function available in your software? If yes can you show me how to manipulate with it. > I would like appreciate it very much > Thank you for your attention and I am looking forward to hearing from you. > Best regards > Hoang Phan -------------- next part -------------- A non-text attachment was scrubbed... Name: Blast Protein procedure1.JPG Type: image/jpeg Size: 162223 bytes Desc: Blast Protein procedure1.JPG URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Blast Protein result2.JPG Type: image/jpeg Size: 148951 bytes Desc: Blast Protein result2.JPG URL: From meng at cgl.ucsf.edu Thu Jan 22 10:16:21 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 22 Jan 2015 10:16:21 -0800 Subject: [Chimera-users] how to find non-bonded interactions between a protein and a ligand? In-Reply-To: References: <894A6232-1515-4288-9403-3DA6F4404693@cgl.ucsf.edu> Message-ID: Hi Sam, Well, those are the default settings for contacts, so we believe them to be reasonable. However, "optimal" would be too strong a word, and it surely depends on the resolution of the structure, local B-factors, whether you used docking to generate the complex, etc. As stated in the docs, "For detecting contacts, negative cutoff values of 0.0-(?1.0) ? are recommended along with a hydrogen bond allowance of 0.0 ?. The default contact criteria in the Find Clashes/Contacts graphical interface are ?0.4 and 0.0 ?, respectively." It is a typical example of setting parameters in computational chemistry. Software developers try to suggest something reasonable, but it is often the responsibility of the scientist to always pay attention to and critically evaluate the results, and perhaps explore a range of values to see what happens (especially for quick calculations like this). Often there is NOT one true correct value, and that's one reason they are user-adjustable in the interface. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 5:50 PM, Sam Paul D wrote: > Hi Elaine, > First of all thanks for all the suggestions. > I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. > Thanks! > Sam From thrabe at sanfordburnham.org Thu Jan 22 16:21:57 2015 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Fri, 23 Jan 2015 00:21:57 +0000 Subject: [Chimera-users] Find subsequence programatically Message-ID: <405D7224-4A5F-44C4-A09C-27BA3F5A910F@sanfordburnham.org> Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? Thank you, Thomas From pett at cgl.ucsf.edu Thu Jan 22 16:37:25 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 22 Jan 2015 16:37:25 -0800 Subject: [Chimera-users] Find subsequence programatically In-Reply-To: <405D7224-4A5F-44C4-A09C-27BA3F5A910F@sanfordburnham.org> References: <405D7224-4A5F-44C4-A09C-27BA3F5A910F@sanfordburnham.org> Message-ID: On Jan 22, 2015, at 4:21 PM, Thomas Hrabe wrote: > Hi Chimera Team, > > How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? I don't know what your context is here exactly, but if you have a Sequence object you can use its regexMatch or prositeMatch methods to find subsequences. They return lists of (start, end) tuples. If you need more info, provide some more detail about your usage context and I can help better. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Jan 22 16:55:56 2015 From: goddard at sonic.net (Tom Goddard) Date: Thu, 22 Jan 2015 16:55:56 -0800 Subject: [Chimera-users] Coot capabilities in Chimera In-Reply-To: <54C024AA.2010302@nih.gov> References: <54C024AA.2010302@nih.gov> Message-ID: <194FBFF9-E0B6-429F-8171-C213F6D6F90B@sonic.net> Hi Mario, This is a good question and many researchers pursuing 3-4A cryoEM structures are asking me the same question. I developed the Chimera map capabilities, much of it done 5 or more years ago when a 10A map was a good resolution. As the maps started coming out with resolutions seen for large molecules using x-ray crystallography I thought it would be natural to use x-ray refinement tools on those. I still think that is sensible advise. But it is apparent that refining an x-ray map at 3-4 Angstroms resolution was never easy and is not easy now. Chimera does not have tools to let you refine structures at the residue level. My observation is that most people working on such maps use multiple visualization, analysis and refinement programs including Chimera because no one program can do everything. Since I don?t know Coot well I can?t comment on what aspects of the work Chimera would do better. I have long discussed with Matt Baker in Wah Chiu?s lab integrating his Gorgon high resolution structure refinement for cryoEM into Chimera. It is something we are interested in for our next generation Chimera 2 that we have been working on for a year. We are still working on more basic capabilities of Chimera 2 so I can?t say that high resolution map capabilities will be available in Chimera soon. I think others who are refining 3-4 A cryoEM maps will have the best advice on which of the many software options has worked for them. Tom > On Jan 21, 2015, at 2:14 PM, Mario J. Borgnia wrote: > > Dear all, > > WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves > refining structures. The blunt question is, should I move to Coot and > leave behind Chimera for that or are there overlapping functions and > what will I be missing if I choose to stay with Chimera. > I have some ideas about the answers but would like to read what the > developers and power users have to say on the issue. > > Thanks!!! > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From thrabe at sanfordburnham.org Thu Jan 22 16:56:45 2015 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Fri, 23 Jan 2015 00:56:45 +0000 Subject: [Chimera-users] Find subsequence programatically In-Reply-To: References: <405D7224-4A5F-44C4-A09C-27BA3F5A910F@sanfordburnham.org>, Message-ID: Hi Eric , I have an algorithm that returns some subsequences of a structure and i want to color the corresponding structure segment automatically. Thanks Thomas from the road Am 22.01.2015 um 16:37 schrieb Eric Pettersen >: On Jan 22, 2015, at 4:21 PM, Thomas Hrabe > wrote: Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? I don't know what your context is here exactly, but if you have a Sequence object you can use its regexMatch or prositeMatch methods to find subsequences. They return lists of (start, end) tuples. If you need more info, provide some more detail about your usage context and I can help better. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From reachsampaul at gmail.com Thu Jan 22 19:46:33 2015 From: reachsampaul at gmail.com (Sam Paul D) Date: Fri, 23 Jan 2015 09:16:33 +0530 Subject: [Chimera-users] how to find non-bonded interactions between a protein and a ligand? In-Reply-To: References: <894A6232-1515-4288-9403-3DA6F4404693@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you so much for all the helpful suggestions. Regards, Sam Sent from my iPhone > On 22-Jan-2015, at 23:46, Elaine Meng wrote: > > Hi Sam, > Well, those are the default settings for contacts, so we believe them to be reasonable. However, "optimal" would be too strong a word, and it surely depends on the resolution of the structure, local B-factors, whether you used docking to generate the complex, etc. As stated in the docs, > > > "For detecting contacts, negative cutoff values of 0.0-(?1.0) ? are recommended along with a hydrogen bond allowance of 0.0 ?. The default contact criteria in the Find Clashes/Contacts graphical interface are ?0.4 and 0.0 ?, respectively." > > It is a typical example of setting parameters in computational chemistry. Software developers try to suggest something reasonable, but it is often the responsibility of the scientist to always pay attention to and critically evaluate the results, and perhaps explore a range of values to see what happens (especially for quick calculations like this). Often there is NOT one true correct value, and that's one reason they are user-adjustable in the interface. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jan 21, 2015, at 5:50 PM, Sam Paul D wrote: >> >> Hi Elaine, >> First of all thanks for all the suggestions. >> I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. >> Thanks! >> Sam > From d.g.norman at dundee.ac.uk Fri Jan 23 14:00:00 2015 From: d.g.norman at dundee.ac.uk (David Norman (Staff)) Date: Fri, 23 Jan 2015 22:00:00 +0000 Subject: [Chimera-users] modelling a dimer Message-ID: <459B6432-B2A0-4F9C-8421-4F5F820129A5@dundee.ac.uk> I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. Thanks David David Norman Ph.D Nucleic Acids Research Group School of Life Sciences MSI/WTB Complex Dow St. Dundee, DD1 5EH, Scotland, UK. phone +44(0)1382 384798 mobile +44(0)7808572788 E.mail d.g.norman at dundee.ac.uk Web site: http://www.lifesci.dundee.ac.uk/people/david-norman The University of Dundee is a Scottish Registered Charity, No. SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096 From meng at cgl.ucsf.edu Fri Jan 23 15:47:57 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 23 Jan 2015 15:47:57 -0800 Subject: [Chimera-users] modelling a dimer In-Reply-To: <459B6432-B2A0-4F9C-8421-4F5F820129A5@dundee.ac.uk> References: <459B6432-B2A0-4F9C-8421-4F5F820129A5@dundee.ac.uk> Message-ID: Hi David, Sorry, multi-chain comparative modelling cannot be done via the Chimera-Modeller interface: You would have to use Modeller directly to access functions such as multi-chain modeling that are not available via the Chimera graphical interface.. One could model a monomer and then open two copies of the model and superimpose them onto the monomers of a template dimer (or apply a known symmetry), but that would not necessarily exclude bad interactions between the copies. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 23, 2015, at 2:00 PM, David Norman (Staff) wrote: > I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. > Thanks David From conrad at cgl.ucsf.edu Mon Jan 26 14:35:12 2015 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Mon, 26 Jan 2015 14:35:12 -0800 Subject: [Chimera-users] Morph conformations - estimated time to completion in status bar? In-Reply-To: <76C6F1F3-3581-463C-B5A1-569A2E6BA595@gmail.com> References: <76C6F1F3-3581-463C-B5A1-569A2E6BA595@gmail.com> Message-ID: <54C6C120.1040801@cgl.ucsf.edu> The status messages for Morph are actually "frame counts". Unfortunately, the computation of frame 1 includes most of the hard work of finding corresponding residues, partitioning the model into pieces to interpolate separately, computing the overall transformation and for each step, creating the trajectory object, etc. The remainder of the frames can be calculated fairly quickly. I suspect that finding corresponding residues is taking all the time, which is why you only see "Computing interpolation 1". How many chains and residues do your models have (and are they identical, ie have the exact same number of atoms named in exactly the same way)? Conrad On 1/20/2015 4:16 PM, Oliver Clarke wrote: > Hi all - silly little feature suggestion, but I was wondering if it > would be possible to add an live-updating ?x % complete? or > ?estimated time to completion? entry in the status bar when running > Morph Conformations? > > When morphing two structures with very large numbers of atoms, morph > conformations can take a long time (hours) to complete, and it would > be handy to know whether it is nearly done or not (currently it just > shows ?computing interpolation 1? until it is finished). > > On a related note, is there any way to speed up morph conformations > for large structures? E.g calculating transformations using C-alpha > atoms only? > > Best, Oliver. _______________________________________________ > Chimera-users mailing list Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From moneterg at gmail.com Wed Jan 28 13:38:31 2015 From: moneterg at gmail.com (=?UTF-8?Q?Monete_Raj=C3=A3o_Gomes?=) Date: Wed, 28 Jan 2015 19:38:31 -0200 Subject: [Chimera-users] Question Message-ID: Hi, I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. Best, Monete -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: send.png Type: image/png Size: 145785 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Jan 28 15:55:24 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 28 Jan 2015 15:55:24 -0800 Subject: [Chimera-users] alignment of identical sequences In-Reply-To: References: Message-ID: Hi Monete, The short answer is that it does not matter for modeling, because all of the residues that are the same but not aligned in the sequence alignment are missing from the 3D structure of one or both of your two structures. Only the residues in the 3D structure(s) will be used for templating. The residues in the sequence are read from the SEQRES section of the PDB file, but some of those residues are often not visible in the 3D crystal structure, so they are not included in the atomic coordinates section of the PDB file. The residues missing from the 3D structure are shown in the red outlines. (Not the light orange boxes, only the red outline boxes.) The longer answer is to explain why they are missing: I am guessing you first used MatchMaker but then created the alignment with the next step mentioned in that earlier e-mail, Match->Align. Match->Align uses only 3D structure, not the sequence to create the alignment, and thus it will not align sequences that are not in both 3D structures. If you instead use the sequence alignment from the MatchMaker step, it will have all the identical residues aligned correctly. However, as mentioned above, this does not matter for any 3D comparative (homology) modeling you might do later that uses those 2 structures as templates. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 28, 2015, at 1:38 PM, Monete Raj?o Gomes wrote: > Hi, > I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. > > There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. > Best, > Monete From meng at cgl.ucsf.edu Wed Jan 28 16:02:51 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 28 Jan 2015 16:02:51 -0800 Subject: [Chimera-users] alignment of identical sequences In-Reply-To: References: Message-ID: <559D0AB2-F609-4CC4-A3F6-22022D7B9C73@cgl.ucsf.edu> On second thought, the unaligned parts might make the process harder, because when you align the sequence of your target with those templates, you would have to make sure the target residues are aligned with the template with 3D structure, instead of the one lacking those residues. Thus, in this case I recommend just using the MatchMaker alignment and skipping the Match->Align step. Turn on the option on the MatchMaker dialog to ?Show pairwise alignment(s)?, or if you are using the matchmaker command, use the ?show? option. The command could be something like: mm #0 #1 show true I hope this helps, Elaine On Jan 28, 2015, at 3:55 PM, Elaine Meng wrote: > Hi Monete, > The short answer is that it does not matter for modeling, because all of the residues that are the same but not aligned in the sequence alignment are missing from the 3D structure of one or both of your two structures. Only the residues in the 3D structure(s) will be used for templating. The residues in the sequence are read from the SEQRES section of the PDB file, but some of those residues are often not visible in the 3D crystal structure, so they are not included in the atomic coordinates section of the PDB file. The residues missing from the 3D structure are shown in the red outlines. (Not the light orange boxes, only the red outline boxes.) > > The longer answer is to explain why they are missing: > I am guessing you first used MatchMaker but then created the alignment with the next step mentioned in that earlier e-mail, Match->Align. Match->Align uses only 3D structure, not the sequence to create the alignment, and thus it will not align sequences that are not in both 3D structures. If you instead use the sequence alignment from the MatchMaker step, it will have all the identical residues aligned correctly. However, as mentioned above, this does not matter for any 3D comparative (homology) modeling you might do later that uses those 2 structures as templates. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 28, 2015, at 1:38 PM, Monete Raj?o Gomes wrote: > >> Hi, >> I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. >> >> There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. >> Best, >> Monete > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From ajn10d at fsu.edu Fri Jan 30 13:33:19 2015 From: ajn10d at fsu.edu (Noble, Alex) Date: Fri, 30 Jan 2015 21:33:19 +0000 Subject: [Chimera-users] Using Chimera to measure voxel densities Message-ID: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble From meng at cgl.ucsf.edu Fri Jan 30 14:36:06 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Jan 2015 14:36:06 -0800 Subject: [Chimera-users] Using Chimera to measure voxel densities In-Reply-To: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> References: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> Message-ID: <3F1CE6EC-E53E-4224-A53D-47F6E2437248@cgl.ucsf.edu> Hi Alex, Sure! There is a ?Values at Atom Positions? tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc. The tool is in the menu under Tools? Volume Data. Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below. The coloring could also be done with the ?rangecolor? command, and labeling with ?labelopt? (or menu Actions? Label? other). With labelopt you can specify a format so that you don?t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name: labelopt info %(value_name_of_map).3f I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 30, 2015, at 1:33 PM, Noble, Alex wrote: > Hi all, > I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? > Best, > -Alex Noble From meng at cgl.ucsf.edu Fri Jan 30 14:49:06 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Jan 2015 14:49:06 -0800 Subject: [Chimera-users] Using Chimera to measure voxel densities In-Reply-To: <3F1CE6EC-E53E-4224-A53D-47F6E2437248@cgl.ucsf.edu> References: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> <3F1CE6EC-E53E-4224-A53D-47F6E2437248@cgl.ucsf.edu> Message-ID: Just to clarify, after the ?labelopt? command you would still have to use ?label? to actually display the labels! Elaine On Jan 30, 2015, at 2:36 PM, Elaine Meng wrote: > Hi Alex, > Sure! There is a ?Values at Atom Positions? tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc. > > The tool is in the menu under Tools? Volume Data. > > > Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below. > > > > The coloring could also be done with the ?rangecolor? command, and labeling with ?labelopt? (or menu Actions? Label? other). With labelopt you can specify a format so that you don?t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name: > > labelopt info %(value_name_of_map).3f > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 30, 2015, at 1:33 PM, Noble, Alex wrote: > >> Hi all, >> I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? >> Best, >> -Alex Noble > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Fri Jan 30 14:43:32 2015 From: goddard at sonic.net (Tom Goddard) Date: Fri, 30 Jan 2015 14:43:32 -0800 Subject: [Chimera-users] Using Chimera to measure voxel densities In-Reply-To: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> References: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> Message-ID: Hi Alex, You could get the interpolated density each atom position with the Values at Atom Positions dialog (menu Tools / Volume Data). Usually this is used to color the atoms based on density value, but the values can be written out with the Render by Attribute dialog menu File / Save Attributes. It is not easy to see the positions of nearby grid points and those grid points can?t be selected. But if you really want to get at those values you might just display your map as a mesh and adjust the contour level by hand until you see the surface intersects a grid point (the contour lines in mesh mode lie in the grid planes so you may be able to visually see when the surface hits a grid point). Tom > On Jan 30, 2015, at 1:33 PM, Noble, Alex wrote: > > Hi all, > > I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? > > Best, > -Alex Noble > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From ajn10d at fsu.edu Fri Jan 30 18:41:06 2015 From: ajn10d at fsu.edu (Noble, Alex) Date: Sat, 31 Jan 2015 02:41:06 +0000 Subject: [Chimera-users] Using Chimera to measure voxel densities In-Reply-To: References: <23835417C9444B46BFA122E7B9CD3EB21C6DF521@fsu-exch-nwr03.fsu.edu> <3F1CE6EC-E53E-4224-A53D-47F6E2437248@cgl.ucsf.edu>, Message-ID: <23835417C9444B46BFA122E7B9CD3EB21C6DF555@fsu-exch-nwr03.fsu.edu> Wonderful! Thank you Elaine and Tom, much appreciated=) -Alex ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Friday, January 30, 2015 5:49 PM To: Noble, Alex Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Using Chimera to measure voxel densities Just to clarify, after the ?labelopt? command you would still have to use ?label? to actually display the labels! Elaine On Jan 30, 2015, at 2:36 PM, Elaine Meng wrote: > Hi Alex, > Sure! There is a ?Values at Atom Positions? tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc. > > The tool is in the menu under Tools? Volume Data. > > > Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below. > > > > The coloring could also be done with the ?rangecolor? command, and labeling with ?labelopt? (or menu Actions? Label? other). With labelopt you can specify a format so that you don?t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name: > > labelopt info %(value_name_of_map).3f > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 30, 2015, at 1:33 PM, Noble, Alex wrote: > >> Hi all, >> I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? >> Best, >> -Alex Noble > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >