From gregc at cgl.ucsf.edu Wed Mar 1 08:19:03 2017 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 1 Mar 2017 08:19:03 -0800 Subject: [Chimera-users] Segmentation fault when issuing chimera command In-Reply-To: References: <66917E2B-58D7-42E9-A0AC-9B5E2BFC8678@uw.edu> <59ab1f37-e666-71cc-a694-8df88d3050aa@cgl.ucsf.edu> <57ebd095-e6a6-9a41-54c2-e26035b8f8e0@cgl.ucsf.edu> Message-ID: <0b6a2aaa-a5ec-5caf-dbb0-b26292af3882@cgl.ucsf.edu> The glxinfo output looks good. I'll work with you off the mailing list on this. -- Greg On 2/28/2017 11:07 PM, Hui Shi wrote: > Hi Greg, > > Thanks again for your reply! I'm attaching a file of the glxinfo > result here, named glxinfo_output. > Hui > > On Tue, Feb 28, 2017 at 10:45 PM, Greg Couch > wrote: > > I am interested in the whole output. Not all of it is necessary > -- I'm mostly interested in the lines that start with OpenGL and > in the table at the end that describes the framebuffer > configurations that are supported. It's easier to just send the > whole thing. > > -- Greg > > > On 2/28/2017 6:37 PM, Hui Shi wrote: >> Hi Greg, >> >> Thank you for you reply! >> >> I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo >> command gave a very long list, for the first few lines, it gave this: >> >> name of display: :0 >> display: :0 screen: 0 >> direct rendering: Yes >> server glx vendor string: NVIDIA Corporation >> server glx version string: 1.4 >> >> Do you need the rest of the result? It is a really long one. I >> feel like it is better to keep it short in the mailing list. >> Hui >> >> On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch > > wrote: >> >> Most reported chimera bugs are due to faulty graphics >> drivers. So that is a good starting point. >> >> The first thing to try is to confirm that the graphics driver >> is installed properly. If you don't have the glxinfo program >> installed yet, install the glx-utils package. Then run >> glxinfo and send me the output. If it fails to run, then you >> need to fix the graphics driver installation. It it >> succeeds, then I'll have something to go by. >> >> HTH, >> >> Greg >> >> >> >> On 2/28/2017 4:55 PM, Hui Shi wrote: >> >> Hi there, >> >> Sorry for bothering you guys! I?m wondering if someone >> can help me to resolve the problem I have here. >> >> I?ve recently installed chimera-1.11.2 under CentOS 7 >> system. And I have a Nvidia GeForce TURBO-GTX1080 graphic >> card on my computer with NVIDIA driver Version 375.39 >> installed. >> >> But when I run issue the chimera command thought the >> terminal, an error message ?Segmentation fault (core >> dumped)? was thrown out. I googled this problem and found >> in a previous message of chimera-users that this should >> be a problem of driver issue. Also, on the ?benchmarks? >> link of chimera, GeForce GTX 1080 has been tested under >> Windows with NVIDIA 368.81 driver version. >> >> I could not find this driver version for 64-bit Linux >> system. Since I have already installed the newer driver >> version (375.39), I would think this should work. >> >> Any suggestions on how to deal with problem? Thanks a lot >> in advance! >> >> Hui >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> >> >> >> >> -- >> -------- >> Sincerely, >> Hui > > > > > -- > -------- > Sincerely, > Hui -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Mar 1 11:16:09 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Mar 2017 11:16:09 -0800 Subject: [Chimera-users] Error opening larger proteins In-Reply-To: References: Message-ID: Hi Catherine, It turns out that the singular value decomposition function that Chimera uses to get the eigenvectors and eigenvalues for the plane computation uses a lot of memory if you use a large number of atoms to define the plane (or axis for that matter). There is a non-default setting for that svd function that I just discovered that uses much less memory and seems to produce identical results, so I have switched Chimera to using that setting. The switched version will be available as the next daily build. Look for daily builds dated March 1 or newer. Also, you may be able to get your current version to work if you simply use less atoms to compute the plane. The selection you were using ? ?sel :.A,.B,.C,.D? ? will not only select all the protein but also all the waters, ligands, and ions. Perhaps just ?sel protein? would be more appropriate (depending on what you want the plane for) and might work in your current build. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 1, 2017, at 9:09 AM, Catherine Jenifer Rajam Rajendran wrote: > > Hello, > > When I try to open large protein in Chimera, and try to define plane for the protein, It is throwing me an error saying "Memory Error". Can you please help me with this error? > > Note: Attached a snapshot of the error. > > Thanks, > Catherine > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Mar 1 15:01:40 2017 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 1 Mar 2017 15:01:40 -0800 Subject: [Chimera-users] Segmentation fault when issuing chimera command In-Reply-To: <0b6a2aaa-a5ec-5caf-dbb0-b26292af3882@cgl.ucsf.edu> References: <66917E2B-58D7-42E9-A0AC-9B5E2BFC8678@uw.edu> <59ab1f37-e666-71cc-a694-8df88d3050aa@cgl.ucsf.edu> <57ebd095-e6a6-9a41-54c2-e26035b8f8e0@cgl.ucsf.edu> <0b6a2aaa-a5ec-5caf-dbb0-b26292af3882@cgl.ucsf.edu> Message-ID: Turns out the problem was trying to run the 32-bit version of chimera on a system where only the 64-bit OpenGL setup was completely installed. Switching to the 64-bit version of chimera solved the problem. -- Greg On 3/1/2017 8:19 AM, Greg Couch wrote: > > The glxinfo output looks good. I'll work with you off the mailing > list on this. > > -- Greg > > > On 2/28/2017 11:07 PM, Hui Shi wrote: >> Hi Greg, >> >> Thanks again for your reply! I'm attaching a file of the glxinfo >> result here, named glxinfo_output. >> Hui >> >> On Tue, Feb 28, 2017 at 10:45 PM, Greg Couch > > wrote: >> >> I am interested in the whole output. Not all of it is necessary >> -- I'm mostly interested in the lines that start with OpenGL and >> in the table at the end that describes the framebuffer >> configurations that are supported. It's easier to just send the >> whole thing. >> >> -- Greg >> >> >> On 2/28/2017 6:37 PM, Hui Shi wrote: >>> Hi Greg, >>> >>> Thank you for you reply! >>> >>> I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo >>> command gave a very long list, for the first few lines, it gave >>> this: >>> >>> name of display: :0 >>> display: :0 screen: 0 >>> direct rendering: Yes >>> server glx vendor string: NVIDIA Corporation >>> server glx version string: 1.4 >>> >>> Do you need the rest of the result? It is a really long one. I >>> feel like it is better to keep it short in the mailing list. >>> Hui >>> >>> On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch >> > wrote: >>> >>> Most reported chimera bugs are due to faulty graphics >>> drivers. So that is a good starting point. >>> >>> The first thing to try is to confirm that the graphics >>> driver is installed properly. If you don't have the glxinfo >>> program installed yet, install the glx-utils package. Then >>> run glxinfo and send me the output. If it fails to run, >>> then you need to fix the graphics driver installation. It >>> it succeeds, then I'll have something to go by. >>> >>> HTH, >>> >>> Greg >>> >>> >>> >>> On 2/28/2017 4:55 PM, Hui Shi wrote: >>> >>> Hi there, >>> >>> Sorry for bothering you guys! I?m wondering if someone >>> can help me to resolve the problem I have here. >>> >>> I?ve recently installed chimera-1.11.2 under CentOS 7 >>> system. And I have a Nvidia GeForce TURBO-GTX1080 >>> graphic card on my computer with NVIDIA driver Version >>> 375.39 installed. >>> >>> But when I run issue the chimera command thought the >>> terminal, an error message ?Segmentation fault (core >>> dumped)? was thrown out. I googled this problem and >>> found in a previous message of chimera-users that this >>> should be a problem of driver issue. Also, on the >>> ?benchmarks? link of chimera, GeForce GTX 1080 has been >>> tested under Windows with NVIDIA 368.81 driver version. >>> >>> I could not find this driver version for 64-bit Linux >>> system. Since I have already installed the newer driver >>> version (375.39), I would think this should work. >>> >>> Any suggestions on how to deal with problem? Thanks a >>> lot in advance! >>> >>> Hui >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> >>> Manage subscription: >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> >>> >>> >>> >>> -- >>> -------- >>> Sincerely, >>> Hui >> >> >> >> >> -- >> -------- >> Sincerely, >> Hui > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From klho98 at yahoo.com Fri Mar 3 00:54:08 2017 From: klho98 at yahoo.com (Ho Kok Lian) Date: Fri, 3 Mar 2017 16:54:08 +0800 Subject: [Chimera-users] move icosahedron surface to a model Message-ID: Hi All, I am a beginner of chimera. Sorry for the simple question. May I know how to move the icosahedron surface (see attached figure) to the model according to its symmetry? Many thanks. Kok-Lian -------------- next part -------------- A non-text attachment was scrubbed... Name: image1.png Type: image/png Size: 706892 bytes Desc: not available URL: From hklwork at googlemail.com Fri Mar 3 01:18:39 2017 From: hklwork at googlemail.com (KL Ho) Date: Fri, 3 Mar 2017 17:18:39 +0800 Subject: [Chimera-users] Moving icosahedron to model Message-ID: Dear All, I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. Best wishes, KokLian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image1.png Type: image/png Size: 706892 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Mar 3 08:46:38 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 3 Mar 2017 08:46:38 -0800 Subject: [Chimera-users] Moving icosahedron to model In-Reply-To: References: Message-ID: <05A839FA-66CE-46B8-A1A3-A5CEE3E1CAB0@cgl.ucsf.edu> Dear KokLian, I can?t think of a way to automatically move it to match the symmetry. However, when you create the icosahedron, if possible you should choose the orientation that is the same as the map data (the colored surface). Then only translation should be required to match them, so you wouldn?t have to rotate the icosahedron, only move it left-right-up-down. You can move objects separately with the mouse or with commands. If you want to save the current position first so that you can return to it if you mess up, use ?savepos? (e.g.: savepos p1). You can return to this position later in the same session with ?reset? (e.g.: reset p1). (A) With the mouse, you have to ?freeze? one model and move only the other. Remember to be careful if you only want to do translation (e.g. middle mouse button or Mac option-touchpad) and not rotation (e.g. left mouse button or touchpad without modifier key). You can freeze/unfreeze models using the ?A? buttons In the Model Panel (open from Favorites menu). (B) The command to translate is ?move? and you can use the ?models? option to specify moving only the icosahedron model. You can see which model is which number by looking in the Model Panel (open from Favorites menu). For example, if the map is #0 and the icosahedron is #1, you could move the icosahedron 10 angstroms to the right with command: move x 10 mod #1 If you also have to rotate the icosahedron, it can be done with the mouse and/or the ?turn? command, but it may be hard to see what the correct orientation should be. 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 Mar 3, 2017, at 1:18 AM, KL Ho wrote: > > Dear All, > I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. > > Best wishes, > KokLian > From goddard at sonic.net Fri Mar 3 10:31:44 2017 From: goddard at sonic.net (Tom Goddard) Date: Fri, 3 Mar 2017 10:31:44 -0800 Subject: [Chimera-users] Moving icosahedron to model In-Reply-To: References: Message-ID: Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. Tom > On Mar 3, 2017, at 1:18 AM, KL Ho wrote: > > Dear All, > I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. > > Best wishes, > KokLian > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Fri Mar 3 11:47:48 2017 From: goddard at sonic.net (Tom Goddard) Date: Fri, 3 Mar 2017 11:47:48 -0800 Subject: [Chimera-users] Moving icosahedron to model In-Reply-To: References: Message-ID: Hi David, I could not tell from the image if the surface was from a PDB or a density map. If it is from a PDB then the coordinate system is based on the crystal packing. That means the origin could be anywhere and the rotation can be arbitrary. So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv). In the hard cases there are various tricks. For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1") Tom > On Mar 3, 2017, at 11:12 AM, David Bhella wrote: > > Hi Tom > I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. > > Sent from my iPhone > >> On 3 Mar 2017, at 18:38, Tom Goddard wrote: >> >> Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. >> >> Tom >> >>> On Mar 3, 2017, at 1:18 AM, KL Ho wrote: >>> >>> Dear All, >>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. >>> >>> Best wishes, >>> KokLian >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From A.G.Lee at soton.ac.uk Fri Mar 3 05:24:51 2017 From: A.G.Lee at soton.ac.uk (Lee A.G.) Date: Fri, 3 Mar 2017 13:24:51 +0000 Subject: [Chimera-users] running DockPrep and Vina from python Message-ID: Hello I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) from DockPrep import prep model=Midas.open('4iaq.pdb') prep(model) modelname='4iaq.mol2' from WriteMol2 import writeMol2 writeMol2(model, modelname) #VinaRun OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don't have. Any help would be very gratefully received. Anthony -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 3 14:09:30 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 3 Mar 2017 14:09:30 -0800 Subject: [Chimera-users] running DockPrep and Vina from python In-Reply-To: References: Message-ID: <553C3288-4F46-4F75-A170-9A9A48469242@cgl.ucsf.edu> Hi Anthony, This is entirely befuddling, because to my knowledge the receptor.pdb file is literally the input to the script that makes the receptor.pdbqt file. In other words, I don?t see how the script could possibly access the unmodified data. However, the script may delete parts of the structure, see the ?Receptor options? settings in the manpage linked above. The receptor prep script is from AutoDock, for more details see: Besides setting the prep options appropriately, all I can say is to check the files very carefully, making sure to remove old files from previous runs. However, I don?t know python, so maybe the others will have some better insights. 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 Mar 3, 2017, at 5:24 AM, Lee A.G. wrote: > > Hello > I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) > from DockPrep import prep > model=Midas.open('4iaq.pdb') > prep(model) > modelname='4iaq.mol2' > from WriteMol2 import writeMol2 > writeMol2(model, modelname) > > #VinaRun > OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' > rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") > > The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. > The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. > The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. > > What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don?t have. > Any help would be very gratefully received. > Anthony From A.G.Lee at soton.ac.uk Mon Mar 6 05:20:19 2017 From: A.G.Lee at soton.ac.uk (Lee A.G.) Date: Mon, 6 Mar 2017 13:20:19 +0000 Subject: [Chimera-users] running DockPrep and Vina from python In-Reply-To: <553C3288-4F46-4F75-A170-9A9A48469242@cgl.ucsf.edu> References: , <553C3288-4F46-4F75-A170-9A9A48469242@cgl.ucsf.edu> Message-ID: Hi Elaine Many thanks for the rapid response. I have tracked down a mistake I was making, which was to already have a copy of the protein loaded into Chimera so that the Midas.open call created a model number #1 which was the copy that prep operated on, but the subsequent call to vina was to protein #0. All is now OK and you will be pleased to hear that the python calls give the same answer as running vina directly from Chimera. Thanks once again Anthony ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: 03 March 2017 22:09 To: Lee A.G. Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] running DockPrep and Vina from python Hi Anthony, This is entirely befuddling, because to my knowledge the receptor.pdb file is literally the input to the script that makes the receptor.pdbqt file. In other words, I don?t see how the script could possibly access the unmodified data. However, the script may delete parts of the structure, see the ?Receptor options? settings in the manpage linked above. The receptor prep script is from AutoDock, for more details see: Besides setting the prep options appropriately, all I can say is to check the files very carefully, making sure to remove old files from previous runs. However, I don?t know python, so maybe the others will have some better insights. 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 Mar 3, 2017, at 5:24 AM, Lee A.G. wrote: > > Hello > I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) > from DockPrep import prep > model=Midas.open('4iaq.pdb') > prep(model) > modelname='4iaq.mol2' > from WriteMol2 import writeMol2 > writeMol2(model, modelname) > > #VinaRun > OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' > rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") > > The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. > The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. > The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. > > What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don?t have. > Any help would be very gratefully received. > Anthony From meng at cgl.ucsf.edu Mon Mar 6 09:57:56 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 6 Mar 2017 09:57:56 -0800 Subject: [Chimera-users] [chimerax-users] animations In-Reply-To: References: Message-ID: <3A2961BD-3BFB-49DF-AA8B-9F3007B322FB@cgl.ucsf.edu> > On Mar 6, 2017, at 6:21 AM, Giorgio Luciano wrote: > > Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? > Giorgio Hi Giorgio, Chimera supports several export formats, see ?File? Export Scene? in the menu or the ?export? command. However, these are for individual conformations, not for a whole animation, so you?d have to export at each step. Although ChimeraX is in early development, currently the ?save? command formats include STL and X3D. The command ?save formats? lists all the formats that can be saved. These may be subject to the same limitations mentioned in the Chimera manual links above. 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 g.m.carstairs at dundee.ac.uk Tue Mar 7 08:32:51 2017 From: g.m.carstairs at dundee.ac.uk (Mungo Carstairs (Staff)) Date: Tue, 7 Mar 2017 16:32:51 +0000 Subject: [Chimera-users] Can you delete a residue attribute? Message-ID: Hi, I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html Is there any way to actually remove attributes after they have been set on residues? Thanks, Mungo [University of Dundee shield logo] Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org www.compbio.dundee.ac.uk g.m.carstairs at dundee.ac.uk [University of Dundee Facebook] [University of Dundee Twitter] [University of Dundee LinkedIn] [University of Dundee YouTube] [University of Dundee Instagram] [University of Dundee Snapchat] We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Mar 7 10:19:06 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 7 Mar 2017 10:19:06 -0800 Subject: [Chimera-users] Can you delete a residue attribute? In-Reply-To: References: Message-ID: <140B299C-9A3D-4ECE-9E66-A53B29230875@cgl.ucsf.edu> Hi Mungo, Yeah, the command language lacks any way to completely delete an attribute. I could enhance ~setattr to also allow deletion, but before I do that work, can you describe why you need to completely delete the attribute rather than set its value to None? Thanks. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 7, 2017, at 8:32 AM, Mungo Carstairs (Staff) wrote: > > Hi, > > I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). > Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. > https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html > > Is there any way to actually remove attributes after they have been set on residues? > > Thanks, > > Mungo > > > > > Mungo Carstairs > Jalview Computational Scientist > The Barton Group > Division of Computational Biology > School of Life Sciences > University of Dundee, Dundee, Scotland, UK > www.jalview.org > www.compbio.dundee.ac.uk > g.m.carstairs at dundee.ac.uk > > We're Scottish University of the Year again! > The Times / Sunday Times Good University Guide 2016 and 2017 > > The University of Dundee is a registered Scottish Charity, No: SC015096_______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Mar 8 13:16:32 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 8 Mar 2017 13:16:32 -0800 Subject: [Chimera-users] Can you delete a residue attribute? In-Reply-To: <140B299C-9A3D-4ECE-9E66-A53B29230875@cgl.ucsf.edu> References: <140B299C-9A3D-4ECE-9E66-A53B29230875@cgl.ucsf.edu> Message-ID: Okay, I have changed ~setattr in a non-backwards-compatible way. It now completely deletes the requested attributes in all objects of the requested type. It no longer takes an atom spec. Consequently, the normal setattr command has been enhanced to allow the value set to be ?none? (i.e. Python None), which is what ~setattr used to do. Available in the next daily build. ?Eric > On Mar 7, 2017, at 10:19 AM, Eric Pettersen wrote: > > Hi Mungo, > Yeah, the command language lacks any way to completely delete an attribute. I could enhance ~setattr to also allow deletion, but before I do that work, can you describe why you need to completely delete the attribute rather than set its value to None? Thanks. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Mar 7, 2017, at 8:32 AM, Mungo Carstairs (Staff) > wrote: >> >> Hi, >> >> I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). >> Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. >> https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html >> >> Is there any way to actually remove attributes after they have been set on residues? >> >> Thanks, >> >> Mungo >> >> >> >> >> Mungo Carstairs >> Jalview Computational Scientist >> The Barton Group >> Division of Computational Biology >> School of Life Sciences >> University of Dundee, Dundee, Scotland, UK >> www.jalview.org >> www.compbio.dundee.ac.uk >> g.m.carstairs at dundee.ac.uk >> >> We're Scottish University of the Year again! >> The Times / Sunday Times Good University Guide 2016 and 2017 >> >> The University of Dundee is a registered Scottish Charity, No: SC015096_______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 9 12:53:42 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Mar 2017 12:53:42 -0800 Subject: [Chimera-users] [chimerax-users] animations In-Reply-To: References: <3A2961BD-3BFB-49DF-AA8B-9F3007B322FB@cgl.ucsf.edu> Message-ID: Hi Giorgio, You would still have to use the ?export? command that exports one file at a time, but it can be run at every frame by combining it with the ?perframe? command. For example, in Chimera the following (should be all one line even though the Mail app may break it up): perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe ?where ~/temp is a directory that already exists, will make files 01.x3d ?. 50.x3d in that directory. In ChimeraX, there is a ?perframe? command and ?save? to export X3D, but no ?play wiggle? command. 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 Mar 9, 2017, at 11:44 AM, Giorgio Luciano wrote: > > Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? > Any help will be greatly appreciated :) > From olibclarke at gmail.com Thu Mar 9 15:16:03 2017 From: olibclarke at gmail.com (Oliver Clarke) Date: Thu, 9 Mar 2017 18:16:03 -0500 Subject: [Chimera-users] replay morph created with vop morph? Message-ID: Hi all, Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? I have a sequential morph of multiple different conformations (which I can?t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). Example command: vop morph #1,2,3,4,5 interpolateColors false constantVolume true Cheers Oli From goddard at sonic.net Thu Mar 9 15:32:45 2017 From: goddard at sonic.net (Tom Goddard) Date: Thu, 9 Mar 2017 15:32:45 -0800 Subject: [Chimera-users] replay morph created with vop morph? In-Reply-To: References: Message-ID: <4B972F36-15B1-4CEB-8D70-7F1DC3EA21F0@sonic.net> Hi Oliver, The vop morph command creates a new volume. So you can do vop morph #1,2,3,4,5 interpolateColors false constantVolume true volume #6 style mesh color pink vop morph #1,2,3,4,5 interpolateColors false constantVolume true model #6 If you specify the model number than it replays that morph instead of creating a new volume model. Tom > On Mar 9, 2017, at 3:16 PM, Oliver Clarke wrote: > > Hi all, > > Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? > > I have a sequential morph of multiple different conformations (which I can?t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). > > Example command: > > vop morph #1,2,3,4,5 interpolateColors false constantVolume true > > Cheers > Oli > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From olibclarke at gmail.com Thu Mar 9 16:18:32 2017 From: olibclarke at gmail.com (Oliver Clarke) Date: Thu, 9 Mar 2017 19:18:32 -0500 Subject: [Chimera-users] replay morph created with vop morph? In-Reply-To: <4B972F36-15B1-4CEB-8D70-7F1DC3EA21F0@sonic.net> References: <4B972F36-15B1-4CEB-8D70-7F1DC3EA21F0@sonic.net> Message-ID: Hi Tom, thanks that?s very helpful! But it doesn?t seem to work for solid representations, which do work with the GUI tool Cheers Oli > On Mar 9, 2017, at 6:32 PM, Tom Goddard wrote: > > Hi Oliver, > > The vop morph command creates a new volume. So you can do > > vop morph #1,2,3,4,5 interpolateColors false constantVolume true > volume #6 style mesh color pink > vop morph #1,2,3,4,5 interpolateColors false constantVolume true model #6 > > If you specify the model number than it replays that morph instead of creating a new volume model. > > Tom > > >> On Mar 9, 2017, at 3:16 PM, Oliver Clarke wrote: >> >> Hi all, >> >> Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? >> >> I have a sequential morph of multiple different conformations (which I can?t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). >> >> Example command: >> >> vop morph #1,2,3,4,5 interpolateColors false constantVolume true >> >> Cheers >> Oli >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From goddard at sonic.net Thu Mar 9 16:31:33 2017 From: goddard at sonic.net (Tom Goddard) Date: Thu, 9 Mar 2017 16:31:33 -0800 Subject: [Chimera-users] replay morph created with vop morph? In-Reply-To: References: <4B972F36-15B1-4CEB-8D70-7F1DC3EA21F0@sonic.net> Message-ID: <55814D31-C7AE-4724-B847-77FA3C96B551@sonic.net> Works fine for solid style display for me, Chimera 1.11.2. vop morph #1,2,3,4,5 interpolateColors false constantVolume true volume #6 style solid vop morph #1,2,3,4,5 interpolateColors false constantVolume true model #6 Although I?m not sure if the constantVolume does anything in that case since that relates to choosing the surface contour level to make enclosed volume constant. Tom > On Mar 9, 2017, at 4:18 PM, Oliver Clarke wrote: > > Hi Tom, thanks that?s very helpful! But it doesn?t seem to work for solid representations, which do work with the GUI tool > > Cheers > Oli >> On Mar 9, 2017, at 6:32 PM, Tom Goddard wrote: >> >> Hi Oliver, >> >> The vop morph command creates a new volume. So you can do >> >> vop morph #1,2,3,4,5 interpolateColors false constantVolume true >> volume #6 style mesh color pink >> vop morph #1,2,3,4,5 interpolateColors false constantVolume true model #6 >> >> If you specify the model number than it replays that morph instead of creating a new volume model. >> >> Tom >> >> >>> On Mar 9, 2017, at 3:16 PM, Oliver Clarke wrote: >>> >>> Hi all, >>> >>> Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? >>> >>> I have a sequential morph of multiple different conformations (which I can?t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). >>> >>> Example command: >>> >>> vop morph #1,2,3,4,5 interpolateColors false constantVolume true >>> >>> Cheers >>> Oli >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > From wurtz at igbmc.fr Fri Mar 10 02:16:26 2017 From: wurtz at igbmc.fr (Jean-Marie WURTZ) Date: Fri, 10 Mar 2017 10:16:26 +0000 Subject: [Chimera-users] chimera 1.11.2 interlaced stereo Message-ID: <01d56b11-417c-459b-cea0-5c5a7aa2b1f3@igbmc.fr> Hi, I am a long time user of chimera and had never such a problem. I would like to use the interlaced stereo with a zalman monitor but I get the following error : Unable to turn on stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. My configuration: Dell M4500 precision Windows 10 Quadro FX 1800M driver 342.01 What can I do to get it working? Thanks for your help. Best regards -- Jean-Marie Wurtz Professeur de Bioinformatique T?l : +33 (0)3 69 48 51 04 Fax : +33 (0)3 88 65 32 76 jm.wurtz at unistra.fr wurtz at igbmc.fr IGBMC-CEBGS D?partement de Biologie et de G?nomique Structurales Equipe de Biologie Structurales de Cibles Epig?n?tiques Parc d'Innovation, 1 rue Laurent Fries BP 10142 F - 67404 ILLKIRCH CEDEX http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html [Universit?? de Strasbourg] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature-universite-02.png Type: image/png Size: 4609 bytes Desc: signature-universite-02.png URL: From meng at cgl.ucsf.edu Fri Mar 10 09:20:50 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 10 Mar 2017 09:20:50 -0800 Subject: [Chimera-users] question on MAV In-Reply-To: References: Message-ID: > On Mar 10, 2017, at 12:59 AM, Jacqueline Vitali wrote: > > Elaine, > I would appreciate it if you could let me know how to make specific residues bold in MAV. Not all of them but only specific residues. > Thank you so much for your help. > Jackie Vitali Hi Jackie, Sorry, MAV (Multalign Viewer) does not have the option to use different fonts for different residues? as you probably saw, the Preferences? Appearance options only change the font of all the residues. To highlight specific residues in MAV, you could draw a box around them to make a region, and then using the Region Browser, change region background color and/or outline color, ...or you could create a custom header to put a symbol above the column. 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 From goddard at sonic.net Fri Mar 10 10:35:04 2017 From: goddard at sonic.net (Tom Goddard) Date: Fri, 10 Mar 2017 10:35:04 -0800 Subject: [Chimera-users] chimera 1.11.2 interlaced stereo In-Reply-To: <01d56b11-417c-459b-cea0-5c5a7aa2b1f3@igbmc.fr> References: <01d56b11-417c-459b-cea0-5c5a7aa2b1f3@igbmc.fr> Message-ID: <9AE4391C-8584-4717-B744-ED2AC6E2892E@sonic.net> Hi Jean-Marie, Your problem is very likely that Windows 10 did on automatic graphics driver update on you and the driver is broken in some way so Chimera cannot do the Zalman rendering. You can rollback graphics driver updates on Windows 10 ? you?ll have to search online how to do that. Tom > On Mar 10, 2017, at 2:16 AM, Jean-Marie WURTZ wrote: > > Hi, > I am a long time user of chimera and had never such a problem. > I would like to use the interlaced stereo with a zalman monitor but I get the following error : > Unable to turn on stereo viewing (Unable to find hardware stereo support > (couldn't choose pixel format > Couldn't configure togl widget)). > > I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. > My configuration: > Dell M4500 precision > Windows 10 > Quadro FX 1800M driver 342.01 > > What can I do to get it working? > Thanks for your help. > Best regards > -- > Jean-Marie Wurtz > Professeur de Bioinformatique > T?l : +33 (0)3 69 48 51 04 > Fax : +33 (0)3 88 65 32 76 > > IGBMC-CEBGS > D?partement de Biologie et de G?nomique Structurales > Equipe de Biologie Structurales de Cibles Epig?n?tiques > Parc d'Innovation, > 1 rue Laurent Fries > BP 10142 > F - 67404 ILLKIRCH CEDEX > http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Mar 13 08:22:19 2017 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 13 Mar 2017 08:22:19 -0700 Subject: [Chimera-users] chimera 1.11.2 interlaced stereo In-Reply-To: <9AE4391C-8584-4717-B744-ED2AC6E2892E@sonic.net> References: <01d56b11-417c-459b-cea0-5c5a7aa2b1f3@igbmc.fr> <9AE4391C-8584-4717-B744-ED2AC6E2892E@sonic.net> Message-ID: <7d013310-dad4-582d-575a-53a1e7445a32@cgl.ucsf.edu> Hi Jean-Marie, If a Windows 10 graphics update, messed things up, then it would have broken other programs beside Chimera and you should reconfigure your graphics driver as described in option 2 below. But Chimera has builtin support for the Zalman monitors, so that is not needed. Option 1) Using the Chimera documentation, with the Help / Search Documentation dialog, and then typing in Zalman, it gives you a link to the documentation for the stereo command. And that says to use the "row stereo, right eye even" stereo mode. If that doesn't work, then your graphics driver is decades old and needs updating. Option 2) For systems with NVidia Quadro graphics, you can get "sequential stereo" to work (which is designed for active 3D glasses that some 3D stereo TVs have. where the graphics driver needs to output a special signal), by reconfiguring the Quadro graphics driver. I don't have a Quadro system in front of me right now, so double check this -- go to the 3D settings, *not* the stereoscopic settings, and (a) enable stereo and (b) choose the correct stereo mode for the Zalman. Then both "sequential stereo" and "row stereo, right eye even" will work. Salut et bonne chance, Greg On 3/10/2017 10:35 AM, Tom Goddard wrote: > Hi Jean-Marie, > > Your problem is very likely that Windows 10 did on automatic > graphics driver update on you and the driver is broken in some way so > Chimera cannot do the Zalman rendering. You can rollback graphics > driver updates on Windows 10 ? you?ll have to search online how to do > that. > > Tom > > >> On Mar 10, 2017, at 2:16 AM, Jean-Marie WURTZ wrote: >> >> Hi, >> I am a long time user of chimera and had never such a problem. >> I would like to use the interlaced stereo with a zalman monitor but I >> get the following error : >> Unable to turn on stereo viewing (Unable to find hardware stereo >> support >> (couldn't choose pixel format >> Couldn't configure togl widget)). >> >> I must say that VMD stereo is working. But I understood also that >> both programs work differently with regard to steero. >> My configuration: >> Dell M4500 precision >> Windows 10 >> Quadro FX 1800M driver 342.01 >> >> What can I do to get it working? >> Thanks for your help. >> Best regards >> -- >> >> Jean-Marie Wurtz >> Professeur de Bioinformatique >> T?l : +33 (0)3 69 48 51 04 >> Fax : +33 (0)3 88 65 32 76 >> >> IGBMC-CEBGS >> D?partement de Biologie et de G?nomique Structurales >> Equipe de Biologie Structurales de Cibles Epig?n?tiques >> Parc d'Innovation, >> 1 rue Laurent Fries >> BP 10142 >> F - 67404 ILLKIRCH CEDEX >> http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.maly at ujep.cz Mon Mar 13 08:59:09 2017 From: marek.maly at ujep.cz (Marek Maly) Date: Mon, 13 Mar 2017 16:59:09 +0100 Subject: [Chimera-users] possible Chimera bug - saving bonds in MOL2 format Message-ID: Hello, it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. If you open attached file "source.mol2" , Chimera reads/show perfectly all the bonds including those where is "Ru" atom present, but when you save it in MOL2 format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened in Chimera all bonds are visualized. Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also in MOL2->MOL2 case. Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ -------------- next part -------------- A non-text attachment was scrubbed... Name: source.mol2 Type: application/octet-stream Size: 10671 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Chimera_MOL2.mol2 Type: application/octet-stream Size: 9481 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Chimera_PDB.pdb Type: application/octet-stream Size: 10196 bytes Desc: not available URL: From giorgio.luciano at gmail.com Sun Mar 12 10:13:23 2017 From: giorgio.luciano at gmail.com (Giorgio Luciano) Date: Sun, 12 Mar 2017 17:13:23 +0000 Subject: [Chimera-users] [chimerax-users] animations In-Reply-To: References: <3A2961BD-3BFB-49DF-AA8B-9F3007B322FB@cgl.ucsf.edu> Message-ID: Hello Elaine, and thanks as always for your reply. I will give it a try tomorrow. I hope I will get a good animation and I will also post the making of. Giorgio Il giorno gio 9 mar 2017 alle ore 21:53 Elaine Meng ha scritto: > Hi Giorgio, > You would still have to use the ?export? command that exports one file at > a time, but it can be run at every frame by combining it with the > ?perframe? command. > > For example, in Chimera the following (should be all one line even though > the Mail app may break it up): > > perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 > 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe > > ?where ~/temp is a directory that already exists, will make files 01.x3d > ?. 50.x3d in that directory. > > In ChimeraX, there is a ?perframe? command and ?save? to export X3D, but > no ?play wiggle? command. > > > > 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 Mar 9, 2017, at 11:44 AM, Giorgio Luciano > wrote: > > > > Thanks for the info and sorry for my late reply. I generally export > using x3d what I was thinking about is, how can someone export the single > model for an animation ? As an example if I make wiggle a molecule play > (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export > in batch the molecules for the single frame ? > > Any help will be greatly appreciated :) > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Mar 13 17:50:27 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 13 Mar 2017 17:50:27 -0700 Subject: [Chimera-users] possible Chimera bug - saving bonds in MOL2 format In-Reply-To: References: Message-ID: Hi Marek, Thanks for the suggestion ? I guess I don?t see many metal complexes in Mol2 files so this got overlooked. I?ve implemented it now and it will be available in the next daily build. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 13, 2017, at 8:59 AM, Marek Maly wrote: > > Hello, > > it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. > > If you open attached file "source.mol2" , Chimera reads/show perfectly all > the bonds including those where is "Ru" atom present, but when you save it in MOL2 > format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted > and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. > > Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved > in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened > in Chimera all bonds are visualized. > > Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also > in MOL2->MOL2 case. > > Best wishes, > > Marek > > > > > > > > -- > Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/_______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.maly at ujep.cz Mon Mar 13 20:16:51 2017 From: marek.maly at ujep.cz (Marek Maly) Date: Tue, 14 Mar 2017 04:16:51 +0100 Subject: [Chimera-users] possible Chimera bug - saving bonds in MOL2 format In-Reply-To: References: Message-ID: Thanks a lot Eric ! Best wishes, Marek Dne Tue, 14 Mar 2017 01:50:27 +0100 Eric Pettersen napsal/-a: > Hi Marek, > Thanks for the suggestion ? I guess I don?t see many metal complexes in > Mol2 files so this got overlooked. I?ve implemented it now and it will > be available in the next daily build. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Mar 13, 2017, at 8:59 AM, Marek Maly wrote: >> >> Hello, >> >> it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 >> format. >> >> If you open attached file "source.mol2" , Chimera reads/show perfectly >> all >> the bonds including those where is "Ru" atom present, but when you save >> it in MOL2 >> format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the >> "Ru-x" bonds are omitted >> and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" >> bonds are shown. >> >> Interestingly, if the original MOL2 file "source.mol2" is opened in >> Chimera and then saved >> in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this >> PDB file is opened >> in Chimera all bonds are visualized. >> >> Would be nice if the perfect bond preservation which works in MOL2->PDB >> case worked also >> in MOL2->MOL2 case. >> >> Best wishes, >> >> Marek >> >> >> >> >> >> >> >> -- >> Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: >> http://www.opera.com/mail/_______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > __________ Informace od ESET NOD32 Antivirus, verze virove databaze > 15083 (20170313) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From Kelvin.Lau at unige.ch Tue Mar 14 02:37:30 2017 From: Kelvin.Lau at unige.ch (Kelvin Lau) Date: Tue, 14 Mar 2017 10:37:30 +0100 Subject: [Chimera-users] Selecting certain atoms with exception Message-ID: Dear Chimera users, I'm trying to do the following: -select all the atoms of a single residue (trp) -except for one (residue number 285) I am not sure how to use a negation command to leave out only 285. Any ideas? Cheers Kelvin -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau at unige.ch Phone: +41 22 379 3026 From meng at cgl.ucsf.edu Tue Mar 14 09:21:20 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 14 Mar 2017 09:21:20 -0700 Subject: [Chimera-users] Selecting certain atoms with exception In-Reply-To: References: Message-ID: <1FD09C0D-0839-4BBF-85D4-7423BCBC65C9@cgl.ucsf.edu> Hi Kelvin, You could do it in two commands, which may be easier conceptually: select :trp ~sel :285 To do it in a single command, you?d use something like this (logical ?and not?): select :trp & ~ :285 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 Mar 14, 2017, at 2:37 AM, Kelvin Lau wrote: > > Dear Chimera users, > I'm trying to do the following: > > -select all the atoms of a single residue (trp) > > -except for one (residue number 285) > > I am not sure how to use a negation command to leave out only 285. Any ideas? > Cheers > Kelvin From kelvin.lau at unige.ch Tue Mar 14 12:47:06 2017 From: kelvin.lau at unige.ch (Kelvin Lau) Date: Tue, 14 Mar 2017 19:47:06 +0000 Subject: [Chimera-users] Selecting certain atoms with exception In-Reply-To: <1FD09C0D-0839-4BBF-85D4-7423BCBC65C9@cgl.ucsf.edu> References: <1FD09C0D-0839-4BBF-85D4-7423BCBC65C9@cgl.ucsf.edu> Message-ID: Thanks for the commands. The latter works great! -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau at unige.ch Phone: +41 22 379 3026 _____________________________ From: Elaine Meng Sent: Tuesday, March 14, 2017 17:21 Subject: Re: [Chimera-users] Selecting certain atoms with exception To: Kelvin Lau Cc: Hi Kelvin, You could do it in two commands, which may be easier conceptually: select :trp ~sel :285 To do it in a single command, you?d use something like this (logical ?and not?): select :trp & ~ :285 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 Mar 14, 2017, at 2:37 AM, Kelvin Lau wrote: > > Dear Chimera users, > I'm trying to do the following: > > -select all the atoms of a single residue (trp) > > -except for one (residue number 285) > > I am not sure how to use a negation command to leave out only 285. Any ideas? > Cheers > Kelvin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Martin.Ashdale at hcps.org Thu Mar 16 07:12:25 2017 From: Martin.Ashdale at hcps.org (Ashdale, Martin) Date: Thu, 16 Mar 2017 14:12:25 +0000 Subject: [Chimera-users] VPAT (Voluntary Product Accessibility Template) Message-ID: Good Morning, I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. Thanks, Martin Ashdale Biology Teacher Harford Technical High School 200 Thomas Run Road Bel Air, MD 21015 (410) 638-3804 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 16 11:08:18 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 16 Mar 2017 11:08:18 -0700 Subject: [Chimera-users] VPAT (Voluntary Product Accessibility Template) In-Reply-To: References: Message-ID: <6B9C9643-FEEC-4B9C-AF5B-39F139676F9C@cgl.ucsf.edu> Dear Martin, Sorry, we do not have a VPAT for UCSF Chimera or any other programs from our group. We do welcome your interest and hope that this will not disqualify Chimera from being used in your class. Chimera has been used in many courses. Most use is apparently at the college level, including undergraduate, but we?ve also heard from high school teachers before. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. here?s a recent publication from others (not our own group) about using Chimera in education: Using molecular visualization to explore protein structure and function and enhance student facility with computational tools. Terrell CR, Listenberger LL. Biochem Mol Biol Educ. 2017 Feb 1. doi: 10.1002/bmb.21040. [Epub ahead of print] https://www.ncbi.nlm.nih.gov/pubmed/?term=28145077 > On Mar 16, 2017, at 7:12 AM, Ashdale, Martin wrote: > > Good Morning, > I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. > Thanks, > > Martin Ashdale > Biology Teacher > Harford Technical High School > 200 Thomas Run Road > Bel Air, MD 21015 > (410) 638-3804 From goddard at sonic.net Thu Mar 16 11:28:27 2017 From: goddard at sonic.net (Tom Goddard) Date: Thu, 16 Mar 2017 11:28:27 -0700 Subject: [Chimera-users] Smoothing and binning volume data In-Reply-To: References: Message-ID: <76087DE4-8897-41FA-9CEB-C514F97BB63D@sonic.net> Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. To color ?solid? style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. Tom > On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: > > Dear Tom, > > How are you? > I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. > > Could you please send me some information on where I could look for this information? > > Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? > > I hope that I am not asking anything too strange. > Especially the first thing would help me greatly. > > Thank you, > Andrea > > -- > Andrea Fera, PhD ? [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > U?nit for Cytoskeletal Dynamics , NICHD, National Institute of Health > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Mar 16 12:08:32 2017 From: goddard at sonic.net (Tom Goddard) Date: Thu, 16 Mar 2017 12:08:32 -0700 Subject: [Chimera-users] Smoothing and binning volume data In-Reply-To: References: <76087DE4-8897-41FA-9CEB-C514F97BB63D@sonic.net> Message-ID: <8A1816DC-910E-4168-A129-71C66DCAEA82@sonic.net> Set "step 1? above the histogram in the Volume Viewer window to display the full resolution of the data. If step is 2 that means only every other density map grid point is shown along each axis. The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming?). The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options? , ?Adjust step to show at most [N] Mvoxels?. Tom > On Mar 16, 2017, at 11:41 AM, Andrea Fera wrote: > > Hi Tom! > > Tank you for your information. > Let me try to explain better what I asked. > > What I seem to have revised is that the virtual sections of my maps have a much higher resolution than the rendered images by Chimera. > This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. > Can you tell me how to do, or what to vary? > > Thank you for the tip about using two colors in the rendering. Going to try immediately. > Thanks, > Andrea > > > > > > > > > > -- > Andrea Fera, PhD ? [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > U?nit for Cytoskeletal Dynamics , NICHD, National Institute of Health > ?Email: andrea.fera at gmail.com > > > On 16 March 2017 at 14:28, Tom Goddard > wrote: > Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. > > To color ?solid? style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. > > Tom > > >> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: >> >> Dear Tom, >> >> How are you? >> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. >> >> Could you please send me some information on where I could look for this information? >> >> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? >> >> I hope that I am not asking anything too strange. >> Especially the first thing would help me greatly. >> >> Thank you, >> Andrea >> >> -- >> Andrea Fera, PhD ? [Senior Research Scientist] >> Advanced Molecular Imaging ; DUNS 824-XXX-XXX >> U?nit for Cytoskeletal Dynamics , NICHD, National Institute of Health -------------- next part -------------- An HTML attachment was scrubbed... URL: From xenonbat at ya.ru Thu Mar 16 18:03:10 2017 From: xenonbat at ya.ru (Vladyslav Dziuba) Date: Fri, 17 Mar 2017 04:03:10 +0300 Subject: [Chimera-users] Getting names of selected atoms and renaming Message-ID: <1001961489712590@web14g.yandex.ru> Dear Sir or Madam, I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? 2.Can I modify names of selected atoms? 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. Hope to receive a letter from you soon. Thanks in advance! Best regards, Vladislav Dziuba From meng at cgl.ucsf.edu Fri Mar 17 10:49:37 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Mar 2017 10:49:37 -0700 Subject: [Chimera-users] Getting names of selected atoms and renaming In-Reply-To: <1001961489712590@web14g.yandex.ru> References: <1001961489712590@web14g.yandex.ru> Message-ID: Dear Vladislav Dziuba, Chimera doesn?t have a tool to rename the atoms. It would probably be simplest to text-edit the input file to change the names directly, or write a script to do it. But maybe some of the following will make what you want to do possible without changing the names. You can write a list of the selected atoms with menu: Actions? Write List, or command ?writesel?. However, this list will give the atom names but not their serial numbers, so in your example it would give H27, not 100. In Chimera commands, you can actually specify atoms by serial number, for example: color blue @/serialNumber=12 select @/serialNumber>8 Serial number is an attribute of the atom, and although in general you can write a list of atoms with attribute values, this specific attribute is kept hidden. There is a tricky way to copy it to a new attribute and then write it out. First select the atoms you want, then: (1) open the Attribute Calculator tool (in menu under Tools? Structure Analysis) (2) in that dialog, enter Formula: atom.serialNumber (and whatever name you want for the new atom attribute in the entry field at the top, I just kept the default ?attributeName?) (3) check the 2nd and 5th boxes in dialog ?Restrict formula domain?? (to only include the selected atoms) and ?Save calculation results to file? (you can optionally check the 4th box to also show output in the Reply Log) (4) click OK or Apply and then specify output filename and location in the resulting dialog One stupid thing, however, is that it changes the integers (e.g. 10) to real numbers (e.g. 10.0) so you may still have to text-edit the results. This process might not be any easier than text-editing the atom names in the original input? your choice. 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 Mar 16, 2017, at 6:03 PM, Vladyslav Dziuba wrote: > > Dear Sir or Madam, > I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: > 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? > 2.Can I modify names of selected atoms? > 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. > Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. > Hope to receive a letter from you soon. > Thanks in advance! > Best regards, > Vladislav Dziuba > From pett at cgl.ucsf.edu Fri Mar 17 16:36:40 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 17 Mar 2017 16:36:40 -0700 Subject: [Chimera-users] Getting names of selected atoms and renaming In-Reply-To: References: <1001961489712590@web14g.yandex.ru> Message-ID: <044C0CED-1E6D-4428-BEB7-D4339F4619FA@cgl.ucsf.edu> Hi, You can change the names of selected atoms with the ?setattr? command, e.g.: setattr a name HX sel will change the name of all selected atoms to HX. You can?t easily modify an atom name though (i.e. add a character or number to the existing name) without using Python. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 17, 2017, at 10:49 AM, Elaine Meng wrote: > > Dear Vladislav Dziuba, > Chimera doesn?t have a tool to rename the atoms. It would probably be simplest to text-edit the input file to change the names directly, or write a script to do it. But maybe some of the following will make what you want to do possible without changing the names. > > You can write a list of the selected atoms with menu: Actions? Write List, or command ?writesel?. However, this list will give the atom names but not their serial numbers, so in your example it would give H27, not 100. > > In Chimera commands, you can actually specify atoms by serial number, for example: > > color blue @/serialNumber=12 > select @/serialNumber>8 > > Serial number is an attribute of the atom, and although in general you can write a list of atoms with attribute values, this specific attribute is kept hidden. There is a tricky way to copy it to a new attribute and then write it out. First select the atoms you want, then: > > (1) open the Attribute Calculator tool (in menu under Tools? Structure Analysis) > (2) in that dialog, enter Formula: atom.serialNumber > (and whatever name you want for the new atom attribute in the entry field at the top, I just kept the default ?attributeName?) > (3) check the 2nd and 5th boxes in dialog ?Restrict formula domain?? (to only include the selected atoms) and ?Save calculation results to file? > (you can optionally check the 4th box to also show output in the Reply Log) > (4) click OK or Apply and then specify output filename and location in the resulting dialog > > One stupid thing, however, is that it changes the integers (e.g. 10) to real numbers (e.g. 10.0) so you may still have to text-edit the results. This process might not be any easier than text-editing the atom names in the original input? your choice. > > 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 Mar 16, 2017, at 6:03 PM, Vladyslav Dziuba wrote: >> >> Dear Sir or Madam, >> I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: >> 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? >> 2.Can I modify names of selected atoms? >> 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. >> Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. >> Hope to receive a letter from you soon. >> Thanks in advance! >> Best regards, >> Vladislav Dziuba >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From wang.ying.jonathan at utexas.edu Mon Mar 20 00:30:56 2017 From: wang.ying.jonathan at utexas.edu (Jonathan Y Wang) Date: Mon, 20 Mar 2017 02:30:56 -0500 Subject: [Chimera-users] Looking at docked data with the receptor shows as surface Message-ID: To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Mar 20 10:52:24 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Mar 2017 10:52:24 -0700 Subject: [Chimera-users] Looking at docked data with the receptor shows as surface In-Reply-To: References: Message-ID: Hi Jonathan, Autodock Vina and the Autodock prep scripts it calls were developed by a different group, and Chimera just communicates with a web service to run the docking part. Thus I?m not an authority on the program, and for details you should probably consult the Autodock Vina website, publication, or its developers: Nevertheless, here are some thoughts as to how it works and what you should check. As I understand it, AutoDock Vina does not use the surface per se, but it takes into account the (nonhydrogen) receptor atoms, and should not give a good score when ligand atoms are too close to receptor atoms. One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered ?/location/name? as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.) >From the Chimera manual page : Output file - location and filename prefix for output files. If the prefix is name, the files generated by a successful run will be: ? name (or name.pdbqt if indicated in the file browser) - docking results in PDBQT format... ? name.receptor.pdb - receptor PDB file from Chimera, input to the AutoDock receptor preparation script ? name.receptor.pdbqt - processed receptor in PDBQT format, input to AutoDock Vina ? name.ligand.pdb - ligand PDB file from Chimera, input to the AutoDock ligand preparation script ? name.ligand.pdbqt - processed ligand in PDBQT format, input to AutoDock Vina ? name.conf - AutoDock Vina configuration file Another thought is that the calculation failed to find any positions of the ligand and it is just in the original position as input to docking. However, this would probably be fairly obvious. 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 Mar 20, 2017, at 12:30 AM, Jonathan Y Wang wrote: > > To whom it may concern, > > Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. > > My inquiry is this: Does AutodockVina take into account surface projections when performing docking? > > Thank you so much for your time, > Jonathan Wang From meng at cgl.ucsf.edu Mon Mar 20 11:06:40 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Mar 2017 11:06:40 -0700 Subject: [Chimera-users] Looking at docked data with the receptor shows as surface In-Reply-To: References: Message-ID: <1F8B9EB3-3A92-4081-88FE-F020D431F159@cgl.ucsf.edu> > On Mar 20, 2017, at 10:52 AM, Elaine Meng wrote: > > One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered ?/location/name? as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.) P.S. It may also depend on how you generated the trimer. In the Chimera dialog for AutoDock Vina, you have to specify a single model as the receptor. If you made the trimer from the monomer using the ?sym? command, for example, it could be more than one model, so you would have to combine them first. This could be done with the ?combine? command or with the ?copy/combine? function in the Model Panel. However, this is not relevant if your trimer was already a single model. Elaine From mohamed.noor at ul.ie Mon Mar 20 12:09:04 2017 From: mohamed.noor at ul.ie (Mohamed Noor) Date: Mon, 20 Mar 2017 19:09:04 +0000 Subject: [Chimera-users] Ensemble models Message-ID: <08d74120-c3b2-4427-a200-3a691173dafc@ul.ie> Hello. I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. Thanks. Mohamed From wang.ying.jonathan at utexas.edu Mon Mar 20 10:56:18 2017 From: wang.ying.jonathan at utexas.edu (Jonathan Y Wang) Date: Mon, 20 Mar 2017 12:56:18 -0500 Subject: [Chimera-users] Looking at docked data with the receptor shows as surface In-Reply-To: References: Message-ID: Thank you so much for your help and your timely response! I appreciated how clear your explanations were and your thoughts on how each might've occurred. Have a blessed day, Jonathan Wang On Mar 20, 2017 12:52 PM, "Elaine Meng" wrote: > Hi Jonathan, > Autodock Vina and the Autodock prep scripts it calls were developed by a > different group, and Chimera just communicates with a web service to run > the docking part. Thus I?m not an authority on the program, and for > details you should probably consult the Autodock Vina website, publication, > or its developers: > > > > Nevertheless, here are some thoughts as to how it works and what you > should check. > > As I understand it, AutoDock Vina does not use the surface per se, but it > takes into account the (nonhydrogen) receptor atoms, and should not give a > good score when ligand atoms are too close to receptor atoms. > > One thought is that maybe although the structure you are viewing is a > trimer, what was returned by the receptor-prep script and actually used in > the docking calculation was some smaller set of atoms, such as only the > monomer. If you entered ?/location/name? as the output file in the Chimera > dialog, then this prepared receptor file would be > /location/name.receptor.pdbqt. You should open this file in Chimera, and > verify that it contains the receptor atoms you expected. (I do not know if > this prep script handles multimers correctly.) > > From the Chimera manual page ContributedSoftware/vina/vina.html> : > > Output file - location and filename prefix for output files. If the prefix > is name, the files generated by a successful run will be: > ? name (or name.pdbqt if indicated in the file browser) - docking > results in PDBQT format... > ? name.receptor.pdb - receptor PDB file from Chimera, input to the > AutoDock receptor preparation script > ? name.receptor.pdbqt - processed receptor in PDBQT format, input > to AutoDock Vina > ? name.ligand.pdb - ligand PDB file from Chimera, input to the > AutoDock ligand preparation script > ? name.ligand.pdbqt - processed ligand in PDBQT format, input to > AutoDock Vina > ? name.conf - AutoDock Vina configuration file > > Another thought is that the calculation failed to find any positions of > the ligand and it is just in the original position as input to docking. > However, this would probably be fairly obvious. > > 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 Mar 20, 2017, at 12:30 AM, Jonathan Y Wang < > wang.ying.jonathan at utexas.edu> wrote: > > > > To whom it may concern, > > > > Hi! I recently docked a ligand onto a receptor using the AutodockVina > tool and when I opened the data the ligand seemed to be placed in the > middle of the trimer. I showed the receptor as surface and it seems as if > the ligand is too big to fit inside any of the holes surrounding the > trimer, but somehow it has placed itself inside. I additionally opened it > using PyMol to double check the file, but it also seems too small to fit > inside any of the holes. > > > > My inquiry is this: Does AutodockVina take into account surface > projections when performing docking? > > > > Thank you so much for your time, > > Jonathan Wang > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Mar 20 15:35:22 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Mar 2017 15:35:22 -0700 Subject: [Chimera-users] Ensemble models In-Reply-To: <08d74120-c3b2-4427-a200-3a691173dafc@ul.ie> References: <08d74120-c3b2-4427-a200-3a691173dafc@ul.ie> Message-ID: Hello Mohamed, (A) Saving/restoring the display. If you mean you want to be able to return to a specific display (what is shown, position, colors, style etc.), you can do that by saving a ?scene?, for example, with command: scene blah save (where ?blah? is whatever name you want to give that scene) ?then later as long as you haven?t deleted atoms or closed models, return to it with: scene blah reset Scenes are also saved in session files, although they will increase their size. There are also GUI ways of saving/restoring scenes. Actually the ?ribbons? preset (menu Presets? Interactive 1 (ribbons)) is quite similar to the default initial display, but some things like colors may be different. You could try that and if it is OK for your purposes, you wouldn?t need to save/restore a scene. You can also create your own custom presets. (B) RMSF, RMSD. Chimera can calculate RMSD per residue over the ensemble, which I think is equivalent to RMSF. The values can be written out, although not in CSV. Assuming your ensemble is read in from a single multi-model file (like an NMR ensemble from the PDB, e.g. 1G1P) or as multiple separate files, the steps would be: (1) open all the ensemble structures in Chimera (2) superimpose them as desired for the RMSD calculation, if they aren?t already (3) show Sequence of any one member of the ensemble (menu Favorites? Sequence) (4) associate all ensemble members with that one sequence (sequence window menu Structure? Associations) (5) in sequence window, show the RMSD histogram of interest (sequence window Headers menu: RMSD options are CA-only, backbone or full, but be aware ?full? only uses atom names and does not equivalence atoms within symmetric sidechain groups) (6) write out the corresponding residue attribute (main menu Tools? Structure Analysis? Render by Attribute, in the resulting dialog choose File? Save Attributes, specify that the attribute is for ?residues? not ?atoms? and then choose the corresponding RMSD attribute, e.g. ?mavRMSDbackbone") This will produce a text file listing the residues and the values, but you?d have to postprocess it further to convert to CSV. The file contents look something like this: attribute: mavRMSDbackbone recipient: residues :2.A 1.3780879732388507 :3.A 0.35308333821132976 :4.A 0.3016323720338901 :5.A 0.25425002410246056 :6.A 0.15787646490372187 :7.A 0.16093274470085253 :8.A 0.18328247884502627 :9.A 0.22521810279034554 :10.A 0.26080378520138037 [?etc?] 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 Mar 20, 2017, at 12:09 PM, Mohamed Noor wrote: > > Hello. > I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? > > Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. > Thanks. > Mohamed From persky at broadinstitute.org Wed Mar 22 12:44:29 2017 From: persky at broadinstitute.org (Nicole Persky) Date: Wed, 22 Mar 2017 15:44:29 -0400 Subject: [Chimera-users] Contact Maps (RRdistance Maps) questions: Message-ID: Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map. I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. ALSO: Anyone know of a way to map defined attributes onto a contact map? Thanks so much! Sincerely, Nicky -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Mar 22 19:05:58 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Mar 2017 19:05:58 -0700 Subject: [Chimera-users] Contact Maps (RRdistance Maps) questions: In-Reply-To: References: Message-ID: <3B14AA09-959B-4BBF-838C-C83E27CD30E0@cgl.ucsf.edu> Hi Nicky, Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with ?findclash? but that would entail some postprocessing, see the last part of this message. (A) Coloring applies across the whole value range, not just the unmasked part? e.g. even if you have masked everything above 6 A with some solid color (let?s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can?t really see any color differences?not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I?m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: (B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you?d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image. One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible. Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map. (C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn?t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs. (D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color. If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts? or the ?findclash? command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command: findclash #0 at ca test self overlap -2.3 save ~/Desktop/protein1.txt ? would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option ?bondsep 2? to include those as well. You can use ?log true? instead of (or in addition to) the ?save? option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command: findclash #0 at ca test self overlap -2.3 log true ? sends the following stuff to the Reply Log, primarily a list of the two atoms? identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: ------------------- Allowed overlap: -2.3 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 620 contacts atom1 atom2 overlap distance ARG 158.A CA GLY 116.A CA -0.203 3.963 LYS 189.A CA GLY 217.A CA -0.321 4.081 ARG 292.A CA THR 110.A CA -0.372 4.132 GLY 297.A CA VAL 254.A CA -0.453 4.213 THR 180.A CA LYS 147.A CA -0.460 4.220 VAL 235.A CA ASN 211.A CA -0.480 4.240 GLY 120.A CA VAL 162.A CA -0.493 4.253 LEU 196.A CA ALA 201.A CA -0.572 4.332 GLY 116.A CA VAL 162.A CA -0.663 4.423 MET 182.A CA GLY 148.A CA -0.668 4.428 THR 185.A CA GLY 217.A CA -0.697 4.457 ASN 256.A CA ASP 236.A CA -0.732 4.492 MET 182.A CA GLU 149.A CA -0.748 4.508 GLY 234.A CA ASP 212.A CA -0.794 4.554 [?. many lines ?] PHE 266.A CA LYS 270.A CA -2.269 6.029 ALA 155.A CA THR 159.A CA -2.274 6.034 ASN 302.A CA GLU 305.A CA -2.277 6.037 ILE 9.A CA SER 41.A CA -2.283 6.043 VAL 206.A CA ILE 204.A CA -2.285 6.045 LYS 92.A CA LEU 67.A CA -2.286 6.046 ALA 264.A CA LEU 268.A CA -2.286 6.046 LYS 270.A CA ASP 274.A CA -2.288 6.048 PRO 86.A CA ALA 105.A CA -2.289 6.049 ASN 130.A CA HIS 126.A CA -2.292 6.052 PHE 89.A CA TYR 106.A CA -2.293 6.053 ALA 251.A CA VAL 245.A CA -2.298 6.058 620 contacts --------------- So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn?t give a more convenient solution. 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 Mar 22, 2017, at 12:44 PM, Nicole Persky wrote: > > Hi All, > I've just found the RRdistance Map function on Chimera and > would like to compare between structures. > I would like to: > 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms > 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms > 3- compare these two contact maps using the colors available for the whole contact map. > > I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. > > Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. > > ALSO: > Anyone know of a way to map defined attributes onto a contact map? > > Thanks so much! > Sincerely, > Nicky From n.gandhiau at gmail.com Thu Mar 23 00:45:23 2017 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Thu, 23 Mar 2017 17:45:23 +1000 Subject: [Chimera-users] MD analysis outputting to file Message-ID: Dear Chimera support, I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. How can I write output per frame to a text file in Chimera? Your insight is appreciated. -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 23 09:23:58 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Mar 2017 09:23:58 -0700 Subject: [Chimera-users] MD analysis outputting to file In-Reply-To: References: Message-ID: <33C1F3A3-81C4-4E4F-B8FE-F3AF204B887A@cgl.ucsf.edu> Dear Neha Gandhi, I guess you want to measure this centroid-centroid distance at each frame of a trajectory that you are showing with the ?MD Movie? tool. First, figure out the Chimera commands to do the measurement at a single time point (for any single frame of the trajectory). The Command Line can be shown from the Favorites menu. You could use the ?define? command to calculate centroids, and the ?distance? command to measure the distance between the centroid objects or markers. For example (Tyr-1 to Phe-4 in 1plx, an NMR ensemble opened as a trajectory): define centroid radius 0.5 number 1 :1 at cg,cd1,cd2,ce1,ce2,cz define centroid radius 0.5 number 2 :4 at cg,cd1,cd2,ce1,ce2,cz distance c1 c2 Of course, you would need to use different residue numbers and atom names as appropriate for your own data. Once you have figured out the proper commands, you can enter them as a per-frame script to be run at each frame of the trajectory when you play through it in MD Movie (MD Movie menu: Per-Frame? Define script, enter the commands in that dialog). You could also echo frame number if that?s helpful, so total script could be echo frame define centroid radius 0.5 number 1 :1 at cg,cd1,cd2,ce1,ce2,cz define centroid radius 0.5 number 2 :4 at cg,cd1,cd2,ce1,ce2,cz distance c1 c2 If I click Apply or OK on the per-frame dialog (Apply leaves it up, OK makes it go away), that will execute at the current frame, and if I then play a few frames using the MD Movie controller, the Reply Log (open from Favorites menu) contains something like this: frame 21 centroid name, ID, center: centroid: c1 ( -2.746, 3.036, -0.904) centroid name, ID, center: centroid: c2 ( 2.165, -0.511, 1.683) Distance from c1 to c2 is 6.587 frame 22 centroid name, ID, center: centroid: c1 ( -2.429, 3.518, -0.332) centroid name, ID, center: centroid: c2 ( 1.489, -0.440, 1.981) Distance from c1 to c2 is 6.030 frame 23 centroid name, ID, center: centroid: c1 ( -2.665, 3.402, -0.915) centroid name, ID, center: centroid: c2 ( 1.831, -0.568, 1.777) Distance from c1 to c2 is 6.574 I would then Clear the Reply Log to get a fresh start and then play the whole trajectory from start to end one time (turn off looping), and then save the Reply Log to a text file using its Save button. 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 P.S. if you need to draw a dashed line between the centroids you have to use a slightly different method with ?measure center? instead of ?define?, as outlined in this previous post > On Mar 23, 2017, at 12:45 AM, Neha Gandhi wrote: > > Dear Chimera support, > > I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. > > How can I write output per frame to a text file in Chimera? > > Your insight is appreciated. From c.paulino at bioc.uzh.ch Thu Mar 23 09:37:09 2017 From: c.paulino at bioc.uzh.ch (Cristina Paulino) Date: Thu, 23 Mar 2017 17:37:09 +0100 Subject: [Chimera-users] Scripting commands for existing morph Message-ID: Dear all, I would like to create a movie from an existing morph between two pdb coordinates. I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. Can anyone help me out? I couldn't find any good description for this. Many thanks in advance Cristina From meng at cgl.ucsf.edu Thu Mar 23 10:13:03 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Mar 2017 10:13:03 -0700 Subject: [Chimera-users] Scripting commands for existing morph In-Reply-To: References: Message-ID: Hi Cristina, Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory. The playback part would be done with the ?coordset? command, and there are several additional movie-related commands, as listed in the ?making movies? page: Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them: (1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation) This should cover what you want to do, and more. 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 Mar 23, 2017, at 9:37 AM, Cristina Paulino wrote: > > Dear all, > I would like to create a movie from an existing morph between two pdb coordinates. > I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. > For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. > > Can anyone help me out? I couldn't find any good description for this. > Many thanks in advance > Cristina From meng at cgl.ucsf.edu Thu Mar 23 10:17:16 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Mar 2017 10:17:16 -0700 Subject: [Chimera-users] Scripting commands for existing morph In-Reply-To: References: Message-ID: P.S. the scripts are linked to the Animation Gallery entries, the full URLs given in my message. I see that the Mail tool made the script names ending in ?.com? look like links in my message, but they are not and won?t work if you click them. > On Mar 23, 2017, at 10:13 AM, Elaine Meng wrote: > > Hi Cristina, > Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory. The playback part would be done with the ?coordset? command, and there are several additional movie-related commands, as listed in the ?making movies? page: > > > Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them: > > (1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com > > > (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation) > > > This should cover what you want to do, and more. 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 Mar 23, 2017, at 9:37 AM, Cristina Paulino wrote: >> >> Dear all, >> I would like to create a movie from an existing morph between two pdb coordinates. >> I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. >> For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. >> >> Can anyone help me out? I couldn't find any good description for this. >> Many thanks in advance >> Cristina > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From persky at broadinstitute.org Thu Mar 23 14:31:52 2017 From: persky at broadinstitute.org (Nicole Persky) Date: Thu, 23 Mar 2017 17:31:52 -0400 Subject: [Chimera-users] Contact Maps (RRdistance Maps) questions: In-Reply-To: <3B14AA09-959B-4BBF-838C-C83E27CD30E0@cgl.ucsf.edu> References: <3B14AA09-959B-4BBF-838C-C83E27CD30E0@cgl.ucsf.edu> Message-ID: Oh Wow! Thanks so much Elaine! That command line was super helpful. I should definitely be able to work with this. Thank you so much! One quick followup question, you mentioned in (C) that there is an export button for giving value matrices for all pairs, where is that located? I wasn't able to locate it. Again, thank you so much for your help! It totally helped me get started. Sincerely, Nicky On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng wrote: > Hi Nicky, > Unfortunately the RR Dist Maps tool is limited in just the ways you > describe, so not that useful for what you want to do. A better way is with > ?findclash? but that would entail some postprocessing, see the last part > of this message. > > (A) Coloring applies across the whole value range, not just the unmasked > part? e.g. even if you have masked everything above 6 A with some solid > color (let?s say dark blue) and specified showing short-long distances with > a white-black gradient, white is 0 angstroms and black is longest > residue-residue distance in the protein, typically >50 A. So the unmasked > part of 0-6 A is only white to very light gray and you can?t really see any > color differences?not that helpful if you are only interested in smaller > differences between these shorter-range contacts. (I realize you > understand this problem, I?m just laying it out in case anybody else is > following along.) This problem is mentioned in the technical notes at the > bottom of the help page for this tool: > rrdistmaps/rrdistmaps.html> > > (B) Cannot show two RR Dist Maps dialogs at the same time. So to see two > maps side by side, you?d have to either run two Chimera sessions > concurrently or within a single session, do one calculation, save image, do > another, save image again or compare current dialog with previously saved > image. > > One way to compare the below-6-angstrom contacts only is to show > side-by-side images of the distance map calculated for each protein > separately with the distances >6 A masked out. However, this will only > show differences of where there is a contact <6A in one protein and not the > other, but because of the coloring issue, subtleties in different distances > within that range will not be perceptible. > > Another way is to compare the individual distance maps (or a single map of > average distance) with a difference map. However, it would be difficult to > tell exactly where the unmasked parts of the distance maps would be on the > difference map and only look at those latter areas of the difference map. > > (C) the Export button gives all the values of RR distance, and (if a > comparison) standard deviation in RR distance and difference in RR > distance. There isn?t an option to give only the residue IDs for contact > pairs within some distance; it only gives value matrices for all pairs. > > (D) RR DIst Maps visualization is also focused on those 3 quantities, not > attribute values. Chimera attributes are assigned to individual atoms, > residues, or models, not a pair of residues. The RR distance map shows > residue-pair values with color. > > If you want to use Chimera, for your purposes I think the best approach > would be to use "Find Clashes/Contacts? or the ?findclash? command to > measure (intraprotein) CA-CA distances, and then filter to list only the > pairs within 6 A. Then you could do that for the other protein as well, > then compare the two lists. For example, if you had one of your proteins > already open as #0, command: > > findclash #0 at ca test self overlap -2.3 save ~/Desktop/protein1.txt > > > > ? would save a text file listing all CA-CA pairs with VDW surfaces within > 2.3 angstroms. The distance from atom center to atom center will be > larger, but the output file will also give that distance and you can delete > the pairs for which it is >6 angstroms. I chose -2.3 because that should > give you all the pairs within 6 angstroms and only a few with larger > distances, using the VDW radii of CA atoms in structures without hydrogen > atoms. You may need to use a larger distance to get them all if your > protein has hydrogens, but in any case, you will be able to tell by looking > at the center-center distances included in the output. The list is sorted > by decreasing overlap so that longer distances willl be near the end. This > example command will automatically exclude residues that are adjacent in > sequence (separated by no more than 4 bonds), but you could add the > findclash command option ?bondsep 2? to include those as well. > > You can use ?log true? instead of (or in addition to) the ?save? option to > show the output in the Reply Log. For example, if I have PDB 2gbp open as > model #0, command: > > findclash #0 at ca test self overlap -2.3 log true > > ? sends the following stuff to the Reply Log, primarily a list of the two > atoms? identifiers, atom-atom VDW overlap (negative value = separation > between VDW surfaces of the two atoms), and atom-atom center-to-center > distance: > ------------------- > Allowed overlap: -2.3 > H-bond overlap reduction: 0.4 > Ignore contacts between atoms separated by 4 bonds or less > Detect intra-residue contacts: False > Detect intra-molecule contacts: True > > 620 contacts > atom1 atom2 overlap distance > ARG 158.A CA GLY 116.A CA -0.203 3.963 > LYS 189.A CA GLY 217.A CA -0.321 4.081 > ARG 292.A CA THR 110.A CA -0.372 4.132 > GLY 297.A CA VAL 254.A CA -0.453 4.213 > THR 180.A CA LYS 147.A CA -0.460 4.220 > VAL 235.A CA ASN 211.A CA -0.480 4.240 > GLY 120.A CA VAL 162.A CA -0.493 4.253 > LEU 196.A CA ALA 201.A CA -0.572 4.332 > GLY 116.A CA VAL 162.A CA -0.663 4.423 > MET 182.A CA GLY 148.A CA -0.668 4.428 > THR 185.A CA GLY 217.A CA -0.697 4.457 > ASN 256.A CA ASP 236.A CA -0.732 4.492 > MET 182.A CA GLU 149.A CA -0.748 4.508 > GLY 234.A CA ASP 212.A CA -0.794 4.554 > [?. many lines ?] > PHE 266.A CA LYS 270.A CA -2.269 6.029 > ALA 155.A CA THR 159.A CA -2.274 6.034 > ASN 302.A CA GLU 305.A CA -2.277 6.037 > ILE 9.A CA SER 41.A CA -2.283 6.043 > VAL 206.A CA ILE 204.A CA -2.285 6.045 > LYS 92.A CA LEU 67.A CA -2.286 6.046 > ALA 264.A CA LEU 268.A CA -2.286 6.046 > LYS 270.A CA ASP 274.A CA -2.288 6.048 > PRO 86.A CA ALA 105.A CA -2.289 6.049 > ASN 130.A CA HIS 126.A CA -2.292 6.052 > PHE 89.A CA TYR 106.A CA -2.293 6.053 > ALA 251.A CA VAL 245.A CA -2.298 6.058 > 620 contacts > --------------- > So, you would need to do some minor postprocessing to remove pairs with > distances >6 angstroms and probably the harder part would be figuring out > how to compare the two lists. Sorry I couldn?t give a more convenient > solution. > 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 Mar 22, 2017, at 12:44 PM, Nicole Persky > wrote: > > > > Hi All, > > I've just found the RRdistance Map function on Chimera and > > would like to compare between structures. > > I would like to: > > 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 > angstroms > > 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 > angstroms > > 3- compare these two contact maps using the colors available for the > whole contact map. > > > > I can only seem to compare the ENTIRE contact map of protein 1 to the > ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 > angstroms. > > > > Alternatively, if anyone knows of a way to export residue lists of > contacts from the contact map site I could just compare them that way. > > > > ALSO: > > Anyone know of a way to map defined attributes onto a contact map? > > > > Thanks so much! > > Sincerely, > > Nicky > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 23 15:24:35 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Mar 2017 15:24:35 -0700 Subject: [Chimera-users] Contact Maps (RRdistance Maps) questions: In-Reply-To: References: <3B14AA09-959B-4BBF-838C-C83E27CD30E0@cgl.ucsf.edu> Message-ID: Hi Nicky, Great! I worried that my reply included too many words before the actual solution. :-) There is an Export button near the bottom of the RR Distance Maps dialog, as shown in the image: If you don?t see this button in your Chimera, it must be an older version? according to the release notes, export was added sometime before the version 1.11 release. Either get the Chimera 1.11.2 production release or a 1.12 daily build to obtain this feature. Download: Best, Elaine > On Mar 23, 2017, at 2:31 PM, Nicole Persky wrote: > > Oh Wow! Thanks so much Elaine! That command line was super helpful. > I should definitely be able to work with this. Thank you so much! > One quick followup question, you mentioned in (C) that there is an export button for giving value matrices for all pairs, where is that located? I wasn't able to locate it. > Again, thank you so much for your help! It totally helped me get started. > Sincerely, > Nicky > > On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng wrote: > Hi Nicky, > Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with ?findclash? but that would entail some postprocessing, see the last part of this message. > > (A) Coloring applies across the whole value range, not just the unmasked part? e.g. even if you have masked everything above 6 A with some solid color (let?s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can?t really see any color differences?not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I?m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: > > > (B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you?d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image. > > One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible. > > Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map. > > (C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn?t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs. > > (D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color. > > If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts? or the ?findclash? command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command: > > findclash #0 at ca test self overlap -2.3 save ~/Desktop/protein1.txt > > > > ? would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option ?bondsep 2? to include those as well. > > You can use ?log true? instead of (or in addition to) the ?save? option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command: > > findclash #0 at ca test self overlap -2.3 log true > > ? sends the following stuff to the Reply Log, primarily a list of the two atoms? identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: > ------------------- > Allowed overlap: -2.3 > H-bond overlap reduction: 0.4 > Ignore contacts between atoms separated by 4 bonds or less > Detect intra-residue contacts: False > Detect intra-molecule contacts: True > > 620 contacts > atom1 atom2 overlap distance > ARG 158.A CA GLY 116.A CA -0.203 3.963 > LYS 189.A CA GLY 217.A CA -0.321 4.081 > ARG 292.A CA THR 110.A CA -0.372 4.132 > GLY 297.A CA VAL 254.A CA -0.453 4.213 > THR 180.A CA LYS 147.A CA -0.460 4.220 > VAL 235.A CA ASN 211.A CA -0.480 4.240 > GLY 120.A CA VAL 162.A CA -0.493 4.253 > LEU 196.A CA ALA 201.A CA -0.572 4.332 > GLY 116.A CA VAL 162.A CA -0.663 4.423 > MET 182.A CA GLY 148.A CA -0.668 4.428 > THR 185.A CA GLY 217.A CA -0.697 4.457 > ASN 256.A CA ASP 236.A CA -0.732 4.492 > MET 182.A CA GLU 149.A CA -0.748 4.508 > GLY 234.A CA ASP 212.A CA -0.794 4.554 > [?. many lines ?] > PHE 266.A CA LYS 270.A CA -2.269 6.029 > ALA 155.A CA THR 159.A CA -2.274 6.034 > ASN 302.A CA GLU 305.A CA -2.277 6.037 > ILE 9.A CA SER 41.A CA -2.283 6.043 > VAL 206.A CA ILE 204.A CA -2.285 6.045 > LYS 92.A CA LEU 67.A CA -2.286 6.046 > ALA 264.A CA LEU 268.A CA -2.286 6.046 > LYS 270.A CA ASP 274.A CA -2.288 6.048 > PRO 86.A CA ALA 105.A CA -2.289 6.049 > ASN 130.A CA HIS 126.A CA -2.292 6.052 > PHE 89.A CA TYR 106.A CA -2.293 6.053 > ALA 251.A CA VAL 245.A CA -2.298 6.058 > 620 contacts > --------------- > So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn?t give a more convenient solution. > 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 Mar 22, 2017, at 12:44 PM, Nicole Persky wrote: > > > > Hi All, > > I've just found the RRdistance Map function on Chimera and > > would like to compare between structures. > > I would like to: > > 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms > > 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms > > 3- compare these two contact maps using the colors available for the whole contact map. > > > > I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. > > > > Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. > > > > ALSO: > > Anyone know of a way to map defined attributes onto a contact map? > > > > Thanks so much! > > Sincerely, > > Nicky > From Zongli_Li at hms.harvard.edu Sun Mar 26 20:01:56 2017 From: Zongli_Li at hms.harvard.edu (Li, Zongli) Date: Mon, 27 Mar 2017 03:01:56 +0000 Subject: [Chimera-users] Create an entire virus from Octant In-Reply-To: References: Message-ID: Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Mar 27 09:49:58 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Mar 2017 09:49:58 -0700 Subject: [Chimera-users] Create an entire virus from Octant In-Reply-To: References: Message-ID: <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu> Hi Zongli, I believe you can use ?vop cover? to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: 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 Mar 26, 2017, at 8:01 PM, Li, Zongli wrote: > > Hello, > I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? > Thanks, > Zongli From Zongli_Li at hms.harvard.edu Mon Mar 27 12:51:51 2017 From: Zongli_Li at hms.harvard.edu (Li, Zongli) Date: Mon, 27 Mar 2017 19:51:51 +0000 Subject: [Chimera-users] Create an entire virus from Octant In-Reply-To: <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu> References: , <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you so much for the help. I look up the original post answered by Tom, as he pointed out, "The tricky part will be to assign the correct center of symmetry and icosahedron orientation for the asymmetric piece using the origin and symmetry options of the volume command". He is very right and I could not figured out the way to assign the correct center of the symmetry and icosahedron orientation for asymmetric piece with volume command while I am using "cop cover". The map I tried is EMD-5199 (rotavirus). Could you please help me out? Thanks again, Zongli ________________________________ From: Elaine Meng Sent: Monday, March 27, 2017 12:49:58 PM To: Li, Zongli Cc: chimera-users at cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Create an entire virus from Octant Hi Zongli, I believe you can use ?vop cover? to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: 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 Mar 26, 2017, at 8:01 PM, Li, Zongli wrote: > > Hello, > I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? > Thanks, > Zongli -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Mar 27 16:42:35 2017 From: goddard at sonic.net (Tom Goddard) Date: Mon, 27 Mar 2017 16:42:35 -0700 Subject: [Chimera-users] Create an entire virus from Octant In-Reply-To: <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu> References: <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu> Message-ID: Hi Zongli, Assign icosahedral symmetry to the map using the BIOMT matrices in the fit PDB coordinates then use vop cover to extend the octant map using that symmetry: open emdbID:5199 open 4v7q volume #0 symmetry #1 vop cover #0 ibox -499,-499,-499,499,499,499 cellsize 2000,2000,2000 The octant map is size 500,500,500 and I assume the 0,0,0 grid point is at the center of symmetry so the vop cover command says to cover grid points -499 to 499. The vop cover command is intended to be used with crystallography so I also tell it the unit cell is bigger than the full map (2000 instead of 1000) so it does not use periodicity of the map. The vop command took about 45 minutes to execute ? very slow. The result of this symmetric covering is not ideal because the edges of the octant map could introduce artifacts in the full map. Also it is interpolating the one octant at all symmetry equivalent points and averaging, and this trilinear interpolation is going to introduce a little bit of blurring. Unfortunately because of the symmetry you can?t simply put 8 copies of the octant map together to form a full virus. The x,y,z axes are 2-fold symmetry axes so the given octant can be mapped to 4 of the 8 octants with no grid interpolations, but the other four require other symmetry operators, not just 90 degree rotations. So you can?t reproduce the full virus map with complete fidelity. The only way to avoid the interpolation is to get a full map from the Harrison lab. It is unfortunate that only this inadequate octant map is what is in the EMDB. In the attached image I show the EMDB 5199 octant, and a neighbor octant which obviously is not just a rotated copy since the original octant has 9 spikes while the neighbor octant has only 6. Tom > On Mar 27, 2017, at 9:49 AM, Elaine Meng wrote: > > Hi Zongli, > I believe you can use ?vop cover? to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: > > > > 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 Mar 26, 2017, at 8:01 PM, Li, Zongli wrote: >> >> Hello, >> I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? >> Thanks, >> Zongli > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: 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: emd_5199.png Type: image/png Size: 378419 bytes Desc: not available URL: From Zongli_Li at hms.harvard.edu Mon Mar 27 20:18:03 2017 From: Zongli_Li at hms.harvard.edu (Li, Zongli) Date: Tue, 28 Mar 2017 03:18:03 +0000 Subject: [Chimera-users] Create an entire virus from Octant In-Reply-To: References: <85C3414E-EC75-4B21-A76B-1F27C36A880C@cgl.ucsf.edu>, Message-ID: Hi Tom, Thank you so much for your help, really appreciate. Best, Zongli ________________________________ From: Tom Goddard Sent: Monday, March 27, 2017 7:42:35 PM To: chimera-users at cgl.ucsf.edu BB Cc: Li, Zongli Subject: Re: [Chimera-users] Create an entire virus from Octant Hi Zongli, Assign icosahedral symmetry to the map using the BIOMT matrices in the fit PDB coordinates then use vop cover to extend the octant map using that symmetry: open emdbID:5199 open 4v7q volume #0 symmetry #1 vop cover #0 ibox -499,-499,-499,499,499,499 cellsize 2000,2000,2000 The octant map is size 500,500,500 and I assume the 0,0,0 grid point is at the center of symmetry so the vop cover command says to cover grid points -499 to 499. The vop cover command is intended to be used with crystallography so I also tell it the unit cell is bigger than the full map (2000 instead of 1000) so it does not use periodicity of the map. The vop command took about 45 minutes to execute ? very slow. The result of this symmetric covering is not ideal because the edges of the octant map could introduce artifacts in the full map. Also it is interpolating the one octant at all symmetry equivalent points and averaging, and this trilinear interpolation is going to introduce a little bit of blurring. Unfortunately because of the symmetry you can?t simply put 8 copies of the octant map together to form a full virus. The x,y,z axes are 2-fold symmetry axes so the given octant can be mapped to 4 of the 8 octants with no grid interpolations, but the other four require other symmetry operators, not just 90 degree rotations. So you can?t reproduce the full virus map with complete fidelity. The only way to avoid the interpolation is to get a full map from the Harrison lab. It is unfortunate that only this inadequate octant map is what is in the EMDB. In the attached image I show the EMDB 5199 octant, and a neighbor octant which obviously is not just a rotated copy since the original octant has 9 spikes while the neighbor octant has only 6. Tom [cid:FE798923-04E2-46DF-B9F1-CDE4D99131FF at cgl.ucsf.edu] On Mar 27, 2017, at 9:49 AM, Elaine Meng > wrote: Hi Zongli, I believe you can use ?vop cover? to expand the map if you can supply the needed symmetry information and box size. Please see this previous post: > 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 Mar 26, 2017, at 8:01 PM, Li, Zongli > wrote: Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: 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: emd_5199.png Type: image/png Size: 378419 bytes Desc: emd_5199.png URL: From 16110440015 at fudan.edu.cn Mon Mar 27 19:41:55 2017 From: 16110440015 at fudan.edu.cn (=?UTF-8?B?6auY5oyv6aOe?=) Date: Tue, 28 Mar 2017 10:41:55 +0800 (GMT+08:00) Subject: [Chimera-users] =?utf-8?b?5p2l6IeqIumrmOaMr+mjniIgPDE2MTEwNDQw?= =?utf-8?b?MDE1QGZ1ZGFuLmVkdS5jbj7nmoTpgq7ku7Y=?= Message-ID: Dear professor: I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. with my best regards yours sincerely Zhenfei Gao -- Zhenfei Gao(???) Department of Macromolecular Science Fudan University 310 Yuejin Hall 220 Handan Rd. Shanghai, China 200433 M: +86-18516637266 QQ: 7693692 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Mar 28 11:14:49 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 28 Mar 2017 11:14:49 -0700 Subject: [Chimera-users] =?utf-8?b?5p2l6IeqIumrmOaMr+mjniIgPDE2MTEwNDQw?= =?utf-8?b?MDE1QGZ1ZGFuLmVkdS5jbj7nmoTpgq7ku7Y=?= In-Reply-To: References: Message-ID: <55077D44-9198-4F80-A4AD-878CABFE7516@cgl.ucsf.edu> Dear Zhenfei Gao, I don?t know what you mean by ?can?t download it? ? as far as I know, you should not have problems downloading UCSF Chimera. Many others in China have downloaded it: If you meant the new program UCSF ChimeraX (different than Chimera), the download page was temporarily missing but it is now available. Best regards, 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 Mar 27, 2017, at 7:41 PM, ??? <16110440015 at fudan.edu.cn> wrote: > > Dear professor: > > I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. > > > with my best regards > > yours sincerely Zhenfei Gao > > > -- > Zhenfei Gao(???) > Department of Macromolecular Science > Fudan University > 310 Yuejin Hall > 220 Handan Rd. > Shanghai, China 200433 > M: +86-18516637266 > QQ: 7693692 From pett at cgl.ucsf.edu Tue Mar 28 12:41:39 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 28 Mar 2017 12:41:39 -0700 Subject: [Chimera-users] ChimeraX Alpha release Message-ID: <58652E49-2B85-4383-9BC0-E3DF5E35E387@cgl.ucsf.edu> Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn?t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ Download page: http://www.cgl.ucsf.edu/chimerax/download.html ?Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.paulino at bioc.uzh.ch Tue Mar 28 23:02:12 2017 From: c.paulino at bioc.uzh.ch (Cristina Paulino) Date: Wed, 29 Mar 2017 08:02:12 +0200 Subject: [Chimera-users] Scripting commands for existing morph In-Reply-To: References: Message-ID: <8EAE6629-C393-4B52-A10A-8D9A039AFFFE@bioc.uzh.ch> Dear Elaine, Thanks for the quick answer. Coordset was exactly was I was looking for! However, I?m missing the possibility of controlling how fast the morph trajectory goes as I cannot indicate how many frames it should take to get from frame #start to #end. I can indicate the step size, but the smallest is obviously 1 and this is still to quick for me. I guess I need to redo the morph and indicate to create the trajectory with the double amount of frames? On another note I have some trouble with the option loop [N] for the coordset command. I cannot get to loop smoothly back and forward. It instead goes from start to end and than instead of going backward it jumps back to start. Best, Cristina > On Mar 23, 2017, at 6:17 PM, Elaine Meng wrote: > > P.S. the scripts are linked to the Animation Gallery entries, the full URLs given in my message. I see that the Mail tool made the script names ending in ?.com? look like links in my message, but they are not and won?t work if you click them. > >> On Mar 23, 2017, at 10:13 AM, Elaine Meng wrote: >> >> Hi Cristina, >> Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory. The playback part would be done with the ?coordset? command, and there are several additional movie-related commands, as listed in the ?making movies? page: >> >> >> Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them: >> >> (1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com >> >> >> (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation) >> >> >> This should cover what you want to do, and more. 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 Mar 23, 2017, at 9:37 AM, Cristina Paulino wrote: >>> >>> Dear all, >>> I would like to create a movie from an existing morph between two pdb coordinates. >>> I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. >>> For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. >>> >>> Can anyone help me out? I couldn't find any good description for this. >>> Many thanks in advance >>> Cristina >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From meng at cgl.ucsf.edu Wed Mar 29 09:03:33 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Mar 2017 09:03:33 -0700 Subject: [Chimera-users] Scripting commands for existing morph In-Reply-To: <8EAE6629-C393-4B52-A10A-8D9A039AFFFE@bioc.uzh.ch> References: <8EAE6629-C393-4B52-A10A-8D9A039AFFFE@bioc.uzh.ch> Message-ID: Hi Cristina, (1) I don?t know if you mean it is too fast when it executes in Chimera, or in a saved movie file. Those are two different things. When you encode the movie there is an option for its playback frame rate. You could try setting that lower and see what you think. If you are using the Movie Recorder GUI it is in the Movie options. If using the command see ?movie encode? option ?framerate? (2) coordset ?loop? means to jump from the end to the start, not play it backwards. However, you would simply use coordset again to play backwards, for example: coordset #2 1,21; wait 21 coordset #2 21,1; wait 21 Or probably easier, just use the ?movie encode? option ?roundtrip true? (see link above). (In our new software ChimeraX the ?coordset? command now has a ?pause? option so that you can specify more image update frames per trajectory frame, but this program is still in early development, with many missing features.) 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 Mar 28, 2017, at 11:02 PM, Cristina Paulino wrote: > > Dear Elaine, > Thanks for the quick answer. > Coordset was exactly was I was looking for! > However, I?m missing the possibility of controlling how fast the morph trajectory goes as I cannot indicate how many frames it should take to get from frame #start to #end. I can indicate the step size, but the smallest is obviously 1 and this is still to quick for me. > > I guess I need to redo the morph and indicate to create the trajectory with the double amount of frames? > > On another note I have some trouble with the option loop [N] for the coordset command. > I cannot get to loop smoothly back and forward. It instead goes from start to end and than instead of going backward it jumps back to start. > > Best, > Cristina > >> On Mar 23, 2017, at 6:17 PM, Elaine Meng wrote: >> >> P.S. the scripts are linked to the Animation Gallery entries, the full URLs given in my message. I see that the Mail tool made the script names ending in ?.com? look like links in my message, but they are not and won?t work if you click them. >> >>> On Mar 23, 2017, at 10:13 AM, Elaine Meng wrote: >>> >>> Hi Cristina, >>> Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory. The playback part would be done with the ?coordset? command, and there are several additional movie-related commands, as listed in the ?making movies? page: >>> >>> >>> Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them: >>> >>> (1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com >>> >>> >>> (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation) >>> >>> >>> This should cover what you want to do, and more. 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 Mar 23, 2017, at 9:37 AM, Cristina Paulino wrote: >>>> >>>> Dear all, >>>> I would like to create a movie from an existing morph between two pdb coordinates. >>>> I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. >>>> For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. >>>> >>>> Can anyone help me out? I couldn't find any good description for this. >>>> Many thanks in advance >>>> Cristina >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Wed Mar 29 09:18:12 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Mar 2017 09:18:12 -0700 Subject: [Chimera-users] [chimera-dev] (no subject) In-Reply-To: References: Message-ID: <71888C1F-45F0-40C6-B9E5-8B95D30BD7E5@cgl.ucsf.edu> > On Mar 29, 2017, at 9:01 AM, Kavya Shankar wrote: > > Hi, > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > Thank you. > Regards, > Kavya Shankar Hi Kavya, Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either ?split? (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. After two models are superimposed, you can get the axis and rotation amount with command ?measure rotation? 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 P.S. seemed like a user question so I put it on the chimera-users list ? chimera-dev is more for programming issues From c.paulino at bioc.uzh.ch Wed Mar 29 09:18:52 2017 From: c.paulino at bioc.uzh.ch (Cristina Paulino) Date: Wed, 29 Mar 2017 18:18:52 +0200 Subject: [Chimera-users] Scripting commands for existing morph In-Reply-To: References: <8EAE6629-C393-4B52-A10A-8D9A039AFFFE@bioc.uzh.ch> Message-ID: <695C15ED-87C0-4091-847C-727403B6DD28@bioc.uzh.ch> Hi Elaine, > (1) I don?t know if you mean it is too fast when it executes in Chimera, or in a saved movie file. Those are two different things. I meant while saving the movie. Sorry for not being specific enough. > When you encode the movie there is an option for its playback frame rate. You could try setting that lower and see what you think. If you are using the Movie Recorder GUI it is in the Movie options. If using the command see ?movie encode? option ?framerate? > This will not help, as I just t change the speed of the trajectory to be slower and not in general for all the other commands in my script which I would otherwise have to change. I just help myself out by creating the morph new, but now being composed out of 61 instead of 21 frames. Does when using coordset later in my movie script it was 3 times slower then before :) > > (2) coordset ?loop? means to jump from the end to the start, not play it backwards. However, you would simply use coordset again to play backwards, for example: > coordset #2 1,21; wait 21 > coordset #2 21,1; wait 21 That is what I ended up doing. Thought there would be a ?loop? command option for scripting. In the movie encode gui there is the option of the loop for back and forth. > > Or probably easier, just use the ?movie encode? option ?roundtrip true? (see link above). > > (In our new software ChimeraX the ?coordset? command now has a ?pause? option so that you can specify more image update frames per trajectory frame, but this program is still in early development, with many missing features.) Looking forward to testing it :) Best, Cristina > > 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 Mar 28, 2017, at 11:02 PM, Cristina Paulino wrote: >> >> Dear Elaine, >> Thanks for the quick answer. >> Coordset was exactly was I was looking for! >> However, I?m missing the possibility of controlling how fast the morph trajectory goes as I cannot indicate how many frames it should take to get from frame #start to #end. I can indicate the step size, but the smallest is obviously 1 and this is still to quick for me. >> >> I guess I need to redo the morph and indicate to create the trajectory with the double amount of frames? >> >> On another note I have some trouble with the option loop [N] for the coordset command. >> I cannot get to loop smoothly back and forward. It instead goes from start to end and than instead of going backward it jumps back to start. >> >> Best, >> Cristina >> >>> On Mar 23, 2017, at 6:17 PM, Elaine Meng wrote: >>> >>> P.S. the scripts are linked to the Animation Gallery entries, the full URLs given in my message. I see that the Mail tool made the script names ending in ?.com? look like links in my message, but they are not and won?t work if you click them. >>> >>>> On Mar 23, 2017, at 10:13 AM, Elaine Meng wrote: >>>> >>>> Hi Cristina, >>>> Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory. The playback part would be done with the ?coordset? command, and there are several additional movie-related commands, as listed in the ?making movies? page: >>>> >>>> >>>> Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them: >>>> >>>> (1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com >>>> >>>> >>>> (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation) >>>> >>>> >>>> This should cover what you want to do, and more. 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 Mar 23, 2017, at 9:37 AM, Cristina Paulino wrote: >>>>> >>>>> Dear all, >>>>> I would like to create a movie from an existing morph between two pdb coordinates. >>>>> I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. >>>>> For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. >>>>> >>>>> Can anyone help me out? I couldn't find any good description for this. >>>>> Many thanks in advance >>>>> Cristina >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From meng at cgl.ucsf.edu Wed Mar 29 10:10:44 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Mar 2017 10:10:44 -0700 Subject: [Chimera-users] [chimera-dev] (no subject) In-Reply-To: References: <71888C1F-45F0-40C6-B9E5-8B95D30BD7E5@cgl.ucsf.edu> Message-ID: Hi Kavya, I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with ?measure rotation.? Elaine > On Mar 29, 2017, at 10:05 AM, Kavya Shankar wrote: > > Hi, > > To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. > > Thank you. > > Regards, > Kavya Shankar > > On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng wrote: > > > On Mar 29, 2017, at 9:01 AM, Kavya Shankar wrote: > > > > Hi, > > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > > Thank you. > > Regards, > > Kavya Shankar > > Hi Kavya, > Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either ?split? (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. > > > After two models are superimposed, you can get the axis and rotation amount with command ?measure rotation? > > > 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 > > P.S. seemed like a user question so I put it on the chimera-users list ? chimera-dev is more for programming issues > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev From meng at cgl.ucsf.edu Thu Mar 30 08:25:10 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Mar 2017 08:25:10 -0700 Subject: [Chimera-users] Chimera comparing homodimer with flipped homodimer In-Reply-To: References: <71888C1F-45F0-40C6-B9E5-8B95D30BD7E5@cgl.ucsf.edu> Message-ID: <79C9451C-8A99-465A-A82A-5602D4717804@cgl.ucsf.edu> Hi Kavya, I didn?t have a good example handy yesterday, but here is a more specific example, in commands: open 5hvp open 5hvp mm #0:.a:.b #1:.b:.a pair ss show :241.b measure rotation #0 #1 This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): Position of 5hvp (#1) relative to 5hvp (#0) coordinates: Matrix rotation and translation -0.32555997 0.82635225 -0.45951350 0.78339640 0.82635225 0.01248149 -0.56301524 15.06413576 -0.45951350 -0.56301524 -0.68692152 28.23994571 Axis 0.58070648 0.71150597 -0.39565040 Axis point -5.75571422 -0.00000000 18.30836454 Rotation angle (degrees) 180.00000000 Shift along axis 0.00000000 I also attach an image below. 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 Mar 29, 2017, at 10:10 AM, Elaine Meng wrote: > > Hi Kavya, > I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with ?measure rotation.? > Elaine > >> On Mar 29, 2017, at 10:05 AM, Kavya Shankar wrote: >> >> Hi, >> >> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >> >> Thank you. >> >> Regards, >> Kavya Shankar >> >> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng wrote: >> >>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar wrote: >>> >>> Hi, >>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>> Thank you. >>> Regards, >>> Kavya Shankar >> >> Hi Kavya, >> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either ?split? (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >> >> >> After two models are superimposed, you can get the axis and rotation amount with command ?measure rotation? >> >> >> 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 >> >> P.S. seemed like a user question so I put it on the chimera-users list ? chimera-dev is more for programming issues >> >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: flip-axis.png Type: image/png Size: 50745 bytes Desc: not available URL: From agszabo at outlook.com Thu Mar 30 11:28:26 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Thu, 30 Mar 2017 18:28:26 +0000 Subject: [Chimera-users] Stereo Message-ID: Is it possible to create a stereo view image from a single pdf image. I have colored different segments of the original pdf image. Thanks A G Szabo agszabo at outlook.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 30 11:52:42 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Mar 2017 11:52:42 -0700 Subject: [Chimera-users] Stereo In-Reply-To: References: Message-ID: Hi Arthur, No, certainly not with Chimera, if you really meant a PDF file. If you meant a structure that is open in Chimera (like from a PDB file), yes you can save it as a stereo image. The File? Save Image dialog has ?Image type? near the lower right with choices including: same as screen stereo pair wall-eye stereo pair You can either choose one of those ?stereo pair? options, or make the screen show stereo (e.g. with ?stereo? command ) and choose ?same as screen?. 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 Mar 30, 2017, at 11:28 AM, Arthur Szabo wrote: > > Is it possible to create a stereo view image from a single pdf image. I have colored different segments of the original pdf image. > > Thanks > > A G Szabo > > agszabo at outlook.com > From Theodor.Gescher at questu.ca Wed Mar 29 16:00:43 2017 From: Theodor.Gescher at questu.ca (Theodor Emil Gescher) Date: Wed, 29 Mar 2017 23:00:43 +0000 Subject: [Chimera-users] Collaboratory Message-ID: Dear Chimeramasters and mistresses, I'm having some serious difficulty starting a collaboratory session in UCSF Chimera on Mac. I have tried both an outdated version (build 40427) and the latest (build 41367). I can't find any mention within the program of collaboratory, and because of the Mac OS I don't think it's possible to start a hub from outside Chimera. Is there an additional extension that needs to be downloaded and installed seperately? Yours studiously, Theo -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 30 13:21:19 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Mar 2017 13:21:19 -0700 Subject: [Chimera-users] Collaboratory In-Reply-To: References: Message-ID: <19D1FB68-1014-4F10-9850-2AFFCDD448BD@cgl.ucsf.edu> Hi Theo, Sorry, Collaboratory is an obsolete feature that was removed from Chimera a long time ago, and we are no longer supporting it. Best wishes, 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 Mar 29, 2017, at 4:00 PM, Theodor Emil Gescher wrote: > > Dear Chimeramasters and mistresses, > > I'm having some serious difficulty starting a collaboratory session in UCSF Chimera on Mac. I have tried both an outdated version (build 40427) and the latest (build 41367). I can't find any mention within the program of collaboratory, and because of the MacOS I don't think it's possible to start a hub from outside Chimera. > > Is there an additional extension that needs to be downloaded and installed seperately? > > Yours studiously, Theo From ael355 at nyu.edu Thu Mar 30 14:38:55 2017 From: ael355 at nyu.edu (Abba E Leffler) Date: Thu, 30 Mar 2017 17:38:55 -0400 Subject: [Chimera-users] Get side-view model? Or, height of clipping planes? Message-ID: Dear All: I'm making a figure showing a ligand bound deeply in a cryptic pocket of a protein. To show it best, I've oriented the complex so that I am looking down directly on to it. Then, I adjust the hither and yon clipping planes to bracket the ligand so you get a cross-section through the protein containing the ligand and binding site. Is there a way to get the heights of the clipping planes, and then draw planes representing them? Better yet, can the image in the side view planning somehow be saved to high resolution with the yellow clipping planes indicated, but perhaps without the red field of view lines? Basically, for the figure I need some way of showing the viewer where the clipping planes are on the protein. This is critical because viewers need to know in a broad sense where the ligand is located. Thank you for your help -------------- next part -------------- An HTML attachment was scrubbed... URL: From agszabo at outlook.com Thu Mar 30 15:59:37 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Thu, 30 Mar 2017 22:59:37 +0000 Subject: [Chimera-users] file opening problem Message-ID: I had a major problem with my computer - too long a story - Needless to say a computer shop technician had to reinstall my operating system, Windows 7, install Microsoft Office 2016. Of course there were several other programs that had to be reinstalled. So recently I downloaded the latest version of Chimera and have been able to work with PDB files and do all the things that I am used to doing. However, I always save the sessions that I have worked on. They are saved to the desktop C:\users\user\desktop The session files are saved to the desktop. Now comes the problem. When I double click on the file I want [cid:image002.png at 01D2A987.C67BFFE0] I get the following message [cid:image001.png at 01D2A986.AAC7D360] If I right click on the file then in the menu window click on open with Another window opens with Chimera being the recommended program. Click on OK and the same window as above comes up. This happens even with a .py file that I worked on today. I am puzzled. Ideas will be appreciated. Arthur G. Szabo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 21304 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 10554 bytes Desc: image002.png URL: From meng at cgl.ucsf.edu Thu Mar 30 16:37:32 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Mar 2017 16:37:32 -0700 Subject: [Chimera-users] file opening problem In-Reply-To: References: Message-ID: <51D252EE-E76D-4ABD-AAD0-35E9CB8FC42D@cgl.ucsf.edu> Hi Arthur, I would start Chimera and then use its File? Restore Session (or File? Open) to open the session file. Maybe others know how to fix this double-click thing but I never use Windows so I couldn?t say. 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 Mar 30, 2017, at 3:59 PM, Arthur Szabo wrote: > > I had a major problem with my computer ? too long a story ? Needless to say a computer shop technician had to reinstall my operating system, Windows 7, install Microsoft Office 2016. Of course there were several other programs that had to be reinstalled. > > So recently I downloaded the latest version of Chimera and have been able to work with PDB files and do all the things that I am used to doing. > > However, I always save the sessions that I have worked on. They are saved to the desktop C:\users\user\desktop > > The session files are saved to the desktop. > > Now comes the problem. When I double click on the file I want > > > > I get the following message > > > If I right click on the file then in the menu window click on open with > > Another window opens with Chimera being the recommended program. > > Click on OK and the same window as above comes up. > > > This happens even with a .py file that I worked on today. > > I am puzzled. > > Ideas will be appreciated. > > Arthur G. Szabo > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Thu Mar 30 16:44:29 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Mar 2017 16:44:29 -0700 Subject: [Chimera-users] Get side-view model? Or, height of clipping planes? In-Reply-To: References: Message-ID: <68258617-1240-49DF-BC51-A270D648D621@cgl.ucsf.edu> Hi Abba, Here are some ideas, which are not exactly what you describe but may accomplish your goals. See the images attached below. (1) use per-model clipping plane in ?slab? mode, which can show a slice of any thickness at any angle (2) open the same structure again, but not clipped, and make it ghostly, like 80% transparent Then you can either show the slice on its own, at any angle, or with the ghostly representation of the whole protein, again at any angle. There are many options for display. I wasn?t sure whether you were showing the atoms/ribbons of the protein or a surface, but it can be done either way. In per-model clipping, the main things to understand are: - how to rotate and translate this slab of visibility on the protein - that you can slice the surface of a protein without slicing its atoms/ribbons and vice versa (surface and atoms are two separate models, and per-model clipping is per model, as the name suggests) - remember to turn off ?adjust clipping with mouse? in order to use those mouse buttons as you normally do to translate/zoom the view So I made some example images with 2gbp, with explanation of how I got them: open 2gbp ribbon; show ligand; repr sphere ligand [ then open Per-Model Clipping from under menu Tools? Depiction, enable clipping ?2gbp (#0)? , turn on slab mode, turn on adjust with mouse, then change slab thickness and use mouse to position/rotate the slab to your liking ] open 2gbp mcopy #0 #1 settings a transp 80 #1 set bg_color white [you can do more positioning/rotation of the slab and adjusting its thickness ] set silhouette setattr m silhouette false #1 ~set silhouette; ~ribbon; surf transp 80 #1 [? no visible change because model #0 surface is not clipped, only the atoms/ribbon ?] [ now in Per-Model Clipping, enable clip ?MSMS main surface of 2gbp #0?, slab mode, adjust with mouse the position and thickness of slab to your liking ] color green,a C repr bs ligand [ you can hide/show the ghostly one using the ?S? checkbox in the Model Panel] There are a lot of possibilities, I just tried to give you the flavor of it. 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 Mar 30, 2017, at 2:38 PM, Abba E Leffler wrote: > > Dear All: > > I'm making a figure showing a ligand bound deeply in a cryptic pocket of a protein. To show it best, I've oriented the complex so that I am looking down directly on to it. Then, I adjust the hither and yon clipping planes to bracket the ligand so you get a cross-section through the protein containing the ligand and binding site. > > > Is there a way to get the heights of the clipping planes, and then draw planes representing them? > > Better yet, can the image in the side view planning somehow be saved to high resolution with the yellow clipping planes indicated, but perhaps without the red field of view lines? > > Basically, for the figure I need some way of showing the viewer where the clipping planes are on the protein. This is critical because viewers need to know in a broad sense where the ligand is located. > > Thank you for your help -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex2.png Type: image/png Size: 117486 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex1.png Type: image/png Size: 121531 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex3.png Type: image/png Size: 248506 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex4.png Type: image/png Size: 46759 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex5.png Type: image/png Size: 189316 bytes Desc: not available URL: From 519198561 at 163.com Thu Mar 30 19:51:34 2017 From: 519198561 at 163.com (=?GBK?B?s8LB+Mfg?=) Date: Fri, 31 Mar 2017 10:51:34 +0800 (CST) Subject: [Chimera-users] =?gbk?q?Add_secondary_structure_or_symbols_to_hea?= =?gbk?q?ders_of_multalign_viewer_=28sequence=A3=A9?= Message-ID: <5cf4e879.49d1.15b22467648.Coremail.519198561@163.com> Dear all ! Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? thanks! Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 31 07:39:30 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 31 Mar 2017 07:39:30 -0700 Subject: [Chimera-users] Chimera comparing homodimer with flipped homodimer In-Reply-To: References: <71888C1F-45F0-40C6-B9E5-8B95D30BD7E5@cgl.ucsf.edu> <79C9451C-8A99-465A-A82A-5602D4717804@cgl.ucsf.edu> Message-ID: Hi Kavya, Your ?mm? command matched A to A and B to B, so there was no rotation between the two copies. It was hard to see if you entered exactly the same ?mm? command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently. I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build. Elaine > On Mar 31, 2017, at 6:55 AM, Kavya Shankar wrote: > > I have attached the screenshots. I have opened the same pdb file. > > Thank you. > > Regards, > Kavya Shankar > > On Fri, Mar 31, 2017 at 9:37 AM, Kavya Shankar wrote: > Thank you so much. When I do this I get a rotation angle of 0 degrees. Am I doing something wrong? > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng wrote: > Hi Kavya, > I didn?t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > 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 Mar 29, 2017, at 10:10 AM, Elaine Meng wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with ?measure rotation.? >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either ?split? (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command ?measure rotation? >>> >>> >>> 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 >>> >>> P.S. seemed like a user question so I put it on the chimera-users list ? chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > > > > From meng at cgl.ucsf.edu Fri Mar 31 08:00:40 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 31 Mar 2017 08:00:40 -0700 Subject: [Chimera-users] =?utf-8?q?Add_secondary_structure_or_symbols_to_h?= =?utf-8?q?eaders_of_multalign_viewer_=28sequence=EF=BC=89?= In-Reply-To: <5cf4e879.49d1.15b22467648.Coremail.519198561@163.com> References: <5cf4e879.49d1.15b22467648.Coremail.519198561@163.com> Message-ID: <678BE7B9-801B-4C77-8F2A-7C8DF99FB654@cgl.ucsf.edu> Dear Liuqing Chen, We don?t have secondary structure symbols, but there are other symbols as shown in the figure in this section of the manual page: The definition file format is fully described here, and it is a simple text file that you can easily make by typing into your favorite text-editing program. As it says, the shapes are circle, square, diamond and star. The only tricky thing is that the data lines have tabs in them, which is why I don?t just show a 3-line example file right in this e-mail. I attached one (simple.hdr) so you can see how simple it is. but you have to first open some sequence or alignment and then open this definition file ( sequence window menu: Headers? Load). It will show a blue star at the 3rd position of the sequence or alignment, as in the attached image. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: simple.hdr Type: application/octet-stream Size: 46 bytes Desc: not available URL: -------------- next part -------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: starheader.png Type: image/png Size: 70855 bytes Desc: not available URL: -------------- next part -------------- > On Mar 30, 2017, at 7:51 PM, ??? <519198561 at 163.com> wrote: > > Dear all ! > Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? > thanks! > Liuqing Chen From ael355 at nyu.edu Thu Mar 30 17:01:08 2017 From: ael355 at nyu.edu (Abba E Leffler) Date: Thu, 30 Mar 2017 20:01:08 -0400 Subject: [Chimera-users] Get side-view model? Or, height of clipping planes? In-Reply-To: <68258617-1240-49DF-BC51-A270D648D621@cgl.ucsf.edu> References: <68258617-1240-49DF-BC51-A270D648D621@cgl.ucsf.edu> Message-ID: That's perfect Elaine, thank you. I really appreciate your making the images as well. It's very analogous to the system I am modeling. I will play around with this and touch base if I have further questions. Thanks again for taking the time. On Thu, Mar 30, 2017 at 7:44 PM, Elaine Meng wrote: > Hi Abba, > Here are some ideas, which are not exactly what you describe but may > accomplish your goals. See the images attached below. > > (1) use per-model clipping plane in ?slab? mode, which can show a slice of > any thickness at any angle > > (2) open the same structure again, but not clipped, and make it ghostly, > like 80% transparent > > Then you can either show the slice on its own, at any angle, or with the > ghostly representation of the whole protein, again at any angle. There are > many options for display. I wasn?t sure whether you were showing the > atoms/ribbons of the protein or a surface, but it can be done either way. > In per-model clipping, the main things to understand are: > - how to rotate and translate this slab of visibility on the protein > - that you can slice the surface of a protein without slicing its > atoms/ribbons and vice versa (surface and atoms are two separate models, > and per-model clipping is per model, as the name suggests) > - remember to turn off ?adjust clipping with mouse? in order to use those > mouse buttons as you normally do to translate/zoom the view > > So I made some example images with 2gbp, with explanation of how I got > them: > > open 2gbp > ribbon; show ligand; repr sphere ligand > [ then open Per-Model Clipping from under menu Tools? Depiction, enable > clipping ?2gbp (#0)? , turn on slab mode, turn on adjust with mouse, then > change slab thickness and use mouse to position/rotate the slab to your > liking ] > open 2gbp > mcopy #0 #1 settings a > transp 80 #1 > set bg_color white > [you can do more positioning/rotation of the slab and adjusting its > thickness ] > > set silhouette > setattr m silhouette false #1 > ~set silhouette; ~ribbon; surf > transp 80 #1 > [? no visible change because model #0 surface is not clipped, only the > atoms/ribbon ?] > [ now in Per-Model Clipping, enable clip ?MSMS main surface of 2gbp #0?, > slab mode, adjust with mouse the position and thickness of slab to your > liking ] > color green,a C > repr bs ligand > [ you can hide/show the ghostly one using the ?S? checkbox in the Model > Panel] > There are a lot of possibilities, I just tried to give you the flavor of > it. > > 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 Mar 30, 2017, at 2:38 PM, Abba E Leffler wrote: > > Dear All: > > I'm making a figure showing a ligand bound deeply in a cryptic pocket of a > protein. To show it best, I've oriented the complex so that I am looking > down directly on to it. Then, I adjust the hither and yon clipping planes > to bracket the ligand so you get a cross-section through the protein > containing the ligand and binding site. > > > Is there a way to get the heights of the clipping planes, and then draw > planes representing them? > > Better yet, can the image in the side view planning somehow be saved to > high resolution with the yellow clipping planes indicated, but perhaps > without the red field of view lines? > > Basically, for the figure I need some way of showing the viewer where the > clipping planes are on the protein. This is critical because viewers need > to know in a broad sense where the ligand is located. > > Thank you for your help > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex1.png Type: image/png Size: 121531 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex2.png Type: image/png Size: 117486 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex4.png Type: image/png Size: 46759 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex5.png Type: image/png Size: 189316 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex3.png Type: image/png Size: 248506 bytes Desc: not available URL: From vk335 at cam.ac.uk Fri Mar 31 08:01:59 2017 From: vk335 at cam.ac.uk (Vasileios Kargas) Date: Fri, 31 Mar 2017 16:01:59 +0100 Subject: [Chimera-users] UCSF Chimera installation - library ubuntu 16.04 Message-ID: <83f510a707007db108f8aa26747c523d@cam.ac.uk> Dear Chimera developer, I am trying to install UCSF-Chimera and I have an issue with the libXext.so.6 library I 've installed the library package that contains this and I can locate it at: /usr/lib/x86_64-linux-gnu However I get this error: vk335 at hunter:~$ ./chimera-1.11.2-linux.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs at lists.wku.edu). Original path: '/home/vk335' inflating: chimera_install_L6RcLz/installer inflating: chimera_install_L6RcLz/chimera.bin Enter install location: ~/UCSF-Chimera-1.11.2 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/vk335/UCSF-Chimera-1.11.2' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org). Install desktop menu and icon? yes Traceback (most recent call last): File "/home/vk335/UCSF-Chimera-1.11.2/share/__main__.py", line 69, in value = chimeraInit.init(sys.argv) File "/home/vk335/UCSF-Chimera-1.11.2/share/chimeraInit.py", line 603, in init import chimera File "/home/vk335/UCSF-Chimera-1.11.2/share/chimera/__init__.py", line 16, in from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libXext.so.6: wrong ELF class: ELFCLASS64 ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_L6RcLz' Installation is done; press return. If I install it in the default Chimera directory without desktop icon it proceeds to the installation but I can not run chimera - taking the same error: ImportError: libXext.so.6: cannot open shared object file: No such file or directory Any suggestions how to solve it? Should this be linked to somewhere else in order the Chimera to find it? Thank you very much in advance. Best regards, Vas From janemei1210 at gmail.com Fri Mar 31 10:45:35 2017 From: janemei1210 at gmail.com (Kunrong Mei) Date: Fri, 31 Mar 2017 13:45:35 -0400 Subject: [Chimera-users] Residue information failed Message-ID: <5B539914-9525-4398-90E6-9F5D3455CA42@gmail.com> Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong From janemei1210 at gmail.com Fri Mar 31 09:51:17 2017 From: janemei1210 at gmail.com (Kunrong Mei) Date: Fri, 31 Mar 2017 12:51:17 -0400 Subject: [Chimera-users] Residue information failed Message-ID: Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong