From meng at cgl.ucsf.edu Tue Apr 1 13:27:54 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 1 Apr 2014 13:27:54 -0700 Subject: [Chimera-users] combining different chains In-Reply-To: References: Message-ID: Hello Faeze, I'm not sure what you mean by combine, but if you mean changing the relative positions, you can do that by freezing one in place and moving the other with the mouse, as described here: If you mean to put them in the same model, you can try the "copy/combine" function in the Model Panel (menu: Favorites? Model Panel) or the "combine" command, for example: combine #0,1 model #2 ? that example would copy both models #0 and #1 into a new model, #2. You would want to make the relative positions correct before combining them into a single model, however. Also, there isn't really a need to make a single model. You could just write a PDB file of one model that is in the correct position relative to the other, or just save the whole Chimera session. You can search the documentation for topics such as the word "combine" using the Chimera menu: Help? Search Documentation. 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 31, 2014, at 10:56 PM, faeze mohajer wrote: > good day > I have modeled heavy and light chains of myosin now I want to combine them through chimera, would you plz help me on that > > your faithfully > FAEZE SADAT MOHAJER > PhD Student > Faculty of Bioscience and Medical Engineering (FBME) > Universiti Teknologi Malaysia (UTM) From leonqli at gmail.com Wed Apr 2 12:10:47 2014 From: leonqli at gmail.com (Li, Leon) Date: Wed, 2 Apr 2014 15:10:47 -0400 Subject: [Chimera-users] Is there a way to save animation editing process? Message-ID: Dear all, I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. Thanks, Leon -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 2 12:22:31 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Apr 2014 12:22:31 -0700 Subject: [Chimera-users] Is there a way to save animation editing process? In-Reply-To: References: Message-ID: <0A54C2A3-C33E-4E57-974C-B55EEFEFEBEE@cgl.ucsf.edu> Hi Leon, The scenes and timeline should be saved in the session. If you are getting some kind of error message when you try to save a session, please use the button on the error dialog to report the bug (or use the Chimera menu: Help... Report a Bug). Please attach the session file if one was written, and include a short description of the problem and your email address if you would like to be updated about the bug status. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 2, 2014, at 12:10 PM, Li, Leon wrote: > Dear all, > I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. > Thanks, > Leon From jtk52 at cornell.edu Tue Apr 1 22:20:44 2014 From: jtk52 at cornell.edu (Jason Kaelber) Date: Wed, 2 Apr 2014 00:20:44 -0500 Subject: [Chimera-users] resampling maps Message-ID: Hi all, I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. Thanks, Jason Exception in Tk callback Function: > (type: ) Args: (,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand midas_text.makeCommand(cmdText) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd vop_command(cmdname, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command doExtensionFunc(func, fargs, specInfo = spec) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op boundingGrid, False, None, modelId) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation scale = scale[i]) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values : Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' ================================================ Event contents: char: delta: 36 height: ?? keycode: 36 keysym: Return keysym_num: 65293 num: ?? send_event: False serial: 39103 state: 16 time: 139539396 type: 2 widget: .59791048.661335648.802317088.802317376.802317448 width: ?? x: 159 x_root: 524 y: 9 y_root: 988 TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values See reply log for Python traceback. -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Apr 2 16:10:25 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 2 Apr 2014 16:10:25 -0700 Subject: [Chimera-users] resampling maps In-Reply-To: References: Message-ID: <519C06EB-B61E-404F-8A81-662C7022AE24@sonic.net> Hi Jason, This is a Chimera bug. Resampling a map with integer values on a new grid produces 32-bit floating point values because it uses trilinear interpolation. But the Chimera code makes the new resampled map have integer values of the same type as the input map, and converting the float values to integer is generating this error (I think because the Python numpy module changed at some point to not automatically cast float to integer). So I fixed the bug in tonight's Chimera daily build to cast the float values to the integer type of the original map. You can also avoid the error with the Chimera 1.8.1 that you are using by first converting your map to 32-bit float values using Chimera command vop scale #0 value float32 That will produce a new map (called #1) that has 32-bit float value and that can be resampled without errors in your Chimera. Thanks for reporting this bug. I'm surprised it was not reported earlier. Tom On Apr 1, 2014, at 10:20 PM, Jason Kaelber wrote: > Hi all, > > I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, > TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. > > Thanks, > Jason > > > > > > > Exception in Tk callback > Function: > (type: ) > Args: (,) > Event type: KeyPress (type num: 2) > Traceback (innermost last): > File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ > return apply(self.func, args) > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand > midas_text.makeCommand(cmdText) > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand > f(c, args) > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd > vop_command(cmdname, args) > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command > doExtensionFunc(func, fargs, specInfo = spec) > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op > boundingGrid, False, None, modelId) > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation > scale = scale[i]) > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values > m[:,:,:] += values > : Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > ================================================ > Event contents: > char: > delta: 36 > height: ?? > keycode: 36 > keysym: Return > keysym_num: 65293 > num: ?? > send_event: False > serial: 39103 > state: 16 > time: 139539396 > type: 2 > widget: .59791048.661335648.802317088.802317376.802317448 > width: ?? > x: 159 > x_root: 524 > y: 9 > y_root: 988 > > TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values > m[:,:,:] += values > > See reply log for Python traceback. > -- > National Center for Macromolecular Imaging, N420 > Baylor College of Medicine, MS BCM125 > 1 Baylor Plaza > Houston, TX, USA > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From g.whittaker at ed.ac.uk Thu Apr 3 02:48:12 2014 From: g.whittaker at ed.ac.uk (Gavin Whittaker) Date: Thu, 03 Apr 2014 10:48:12 +0100 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom Message-ID: <533D2E5C.7000303@ed.ac.uk> Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I /can/ now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin -------------- next part -------------- An HTML attachment was scrubbed... URL: From leonqli at gmail.com Thu Apr 3 07:01:28 2014 From: leonqli at gmail.com (Li, Leon) Date: Thu, 3 Apr 2014 10:01:28 -0400 Subject: [Chimera-users] Is there a way to save animation editing process? In-Reply-To: <0A54C2A3-C33E-4E57-974C-B55EEFEFEBEE@cgl.ucsf.edu> References: <0A54C2A3-C33E-4E57-974C-B55EEFEFEBEE@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks for your response. Yes, I met error when saving the scenes and timeline of animation. The errors have been submitted. I also enclosed the error here in case. Again thanks for the great work! Best, Leon ========================================== Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.8/share/chimera/triggerSet.py", line 83, in invoke self._funcData, triggerData) File "/opt/UCSF/Chimera64-1.8/share/Animate/Session.py", line 188, in sessionSave scPickle = pickled(scenes) File "/opt/UCSF/Chimera64-1.8/share/Animate/Session.py", line 173, in pickled objEncPickle = base64.b64encode(pickle.dumps(obj, protocol=2)) File "/opt/UCSF/Chimera64-1.8/share/Animate/SceneState.py", line 83, in __getstate__ pickleData['state'] = self.stateDump() File "/opt/UCSF/Chimera64-1.8/share/Animate/SceneState.py", line 1889, in stateDump modelID = modelsID[model] KeyError: On Wed, Apr 2, 2014 at 3:22 PM, Elaine Meng wrote: > Hi Leon, > The scenes and timeline should be saved in the session. > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.html > > > > If you are getting some kind of error message when you try to save a > session, please use the button on the error dialog to report the bug (or > use the Chimera menu: Help... Report a Bug). Please attach the session > file if one was written, and include a short description of the problem and > your email address if you would like to be updated about the bug status. > Thanks, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Apr 2, 2014, at 12:10 PM, Li, Leon wrote: > > > Dear all, > > I'm try to save all my editing of animation, it seems that 'save > session' can't save 'scenes', 'timelines', etc. I wonder is there a way to > save all the process, so that I can re-open it to edit. > > Thanks, > > Leon > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Apr 3 08:31:33 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 08:31:33 -0700 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <533D2E5C.7000303@ed.ac.uk> References: <533D2E5C.7000303@ed.ac.uk> Message-ID: <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> Hi Gavin, The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. Tom On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: > Dear all, > > I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? > > I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? > > thanks! > > Gavin > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From darrellh at niaid.nih.gov Thu Apr 3 09:18:38 2014 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Thu, 3 Apr 2014 16:18:38 +0000 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> References: <533D2E5C.7000303@ed.ac.uk> <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> Message-ID: Hi guys, I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find: Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon) File > Export without zooming: 4.2 MB X3D or 6.0 MB STL File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count! Great tip! Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard > Date: Thursday, April 3, 2014 11:31 AM To: Gavin Whittaker > Cc: "chimera-users at cgl.ucsf.edu BB" > Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom Hi Gavin, The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. Tom On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Thu Apr 3 11:32:08 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 11:32:08 -0700 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: References: <533D2E5C.7000303@ed.ac.uk> <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> Message-ID: <161BD64B-0BD1-49E4-8156-4BAB6110A350@sonic.net> Hi Darrell, Thanks for the test results! The scaling of the ribbon cross-section done by the Scaling tab of the Ribbon Style Editor (menu Tools / Depiction) should not change the size of the exported STL file at all. It only moves the vertices of the triangles, but you still get the same number of triangles. The STL file uses 48 bytes for each triangle (x,y,z coords for 3 vertices, plus nx,ny,nz normal vector for triangle, giving 12 floating point values each taking 4 bytes). That is rather inefficient. Chimera uses only 24 bytes per triangle in memory, and for 3d printing you don't need the normal vectors and 18 bytes per triangle would be possible. And if 16-bit precision on coordinates were adequate you could drop that to 9 bytes per triangle, about 5x smaller than STL files. But without a standard file format that can handle that format it doesn't help. Also the 3d printing software is probably not struggling with the size of the file, it is the large number of triangles that it has trouble with. The Catalyst 4.3 uPrint 3d printer software we use is very bad, usually crashing, sometimes just extremely slow (hours to process), with large files (100 Mbytes). I believe the job done by that software could be done 100 times more efficiently, but the 3d printer vendors probably aren't doing it because common uses don't produce such large files. Tom On Apr 3, 2014, at 9:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi guys, > > I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find: > > Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon) > > File > Export without zooming: 4.2 MB X3D or 6.0 MB STL > File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL > File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL > File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL > File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL > File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL > > When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count! > > Great tip! > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: Tom Goddard > > Date: Thursday, April 3, 2014 11:31 AM > To: Gavin Whittaker > > Cc: "chimera-users at cgl.ucsf.edu BB" > > Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom > > Hi Gavin, > > The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. > > The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. > > Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. > > Tom > > > On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: > > Dear all, > > I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? > > I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? > > thanks! > > Gavin > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From darrellh at niaid.nih.gov Thu Apr 3 13:06:15 2014 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Thu, 3 Apr 2014 20:06:15 +0000 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <161BD64B-0BD1-49E4-8156-4BAB6110A350@sonic.net> Message-ID: <624EEF8436486C438E2C9E71C4879E6E291532@MLBXV06.nih.gov> The differences in file size in my testing associated with ribbon scaling are likely just because of my imprecise zooming back and forth. But there certainly are file size reductions to be realized by zooming out and by simplifying the cross section. I can totally use this! Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office? 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ----- Original Message ----- From: Tom Goddard [mailto:goddard at sonic.net] Sent: Thursday, April 03, 2014 02:32 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: Gavin Whittaker ; chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom Hi Darrell, Thanks for the test results! The scaling of the ribbon cross-section done by the Scaling tab of the Ribbon Style Editor (menu Tools / Depiction) should not change the size of the exported STL file at all. It only moves the vertices of the triangles, but you still get the same number of triangles. The STL file uses 48 bytes for each triangle (x,y,z coords for 3 vertices, plus nx,ny,nz normal vector for triangle, giving 12 floating point values each taking 4 bytes). That is rather inefficient. Chimera uses only 24 bytes per triangle in memory, and for 3d printing you don't need the normal vectors and 18 bytes per triangle would be possible. And if 16-bit precision on coordinates were adequate you could drop that to 9 bytes per triangle, about 5x smaller than STL files. But without a standard file format that can handle that format it doesn't help. Also the 3d printing software is probably not struggling with the size of the file, it is the large number of triangles that it has trouble with. The Catalyst 4.3 uPrint 3d printer software we use is very bad, usually crashing, sometimes just extremely slow (hours to process), with large files (100 Mbytes). I believe the job done by that software could be done 100 times more efficiently, but the 3d printer vendors probably aren't doing it because common uses don't produce such large files. Tom On Apr 3, 2014, at 9:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi guys, > > I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find: > > Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon) > > File > Export without zooming: 4.2 MB X3D or 6.0 MB STL > File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL > File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL > File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL > File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL > File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL > > When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count! > > Great tip! > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: Tom Goddard > > Date: Thursday, April 3, 2014 11:31 AM > To: Gavin Whittaker > > Cc: "chimera-users at cgl.ucsf.edu BB" > > Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom > > Hi Gavin, > > The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. > > The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. > > Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. > > Tom > > > On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: > > Dear all, > > I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? > > I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? > > thanks! > > Gavin > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jtk52 at cornell.edu Wed Apr 2 23:30:50 2014 From: jtk52 at cornell.edu (Jason Kaelber) Date: Thu, 3 Apr 2014 01:30:50 -0500 Subject: [Chimera-users] resampling maps In-Reply-To: <519C06EB-B61E-404F-8A81-662C7022AE24@sonic.net> References: <519C06EB-B61E-404F-8A81-662C7022AE24@sonic.net> Message-ID: Just in case anybody else has a similar question and finds this thread in the mailing list archives, I wanted to follow up: I tried your suggestion of vop scale #0 value float32. Unfortunately this makes the map lose its orientation. But, your explanation told me that if I convert the map to 32-bit, it will resample OK. Therefore, I -saved the open session where I oriented all my models, -made a temp directory and moved all the models into it, -generated float32 version of the map with the same name, e.g. e2proc3d.py ./temp/model.mrc ./model.mrc -and reopened the Chimera session. Then I can resample and save all the maps! Tom, thanks a lot for helping me figure this out and also for fixing the bug in the new version. Sincerely, Jason On Wed, Apr 2, 2014 at 6:10 PM, Tom Goddard wrote: > Hi Jason, > > This is a Chimera bug. Resampling a map with integer values on a new > grid produces 32-bit floating point values because it uses trilinear > interpolation. But the Chimera code makes the new resampled map have > integer values of the same type as the input map, and converting the float > values to integer is generating this error (I think because the Python > numpy module changed at some point to not automatically cast float to > integer). > > So I fixed the bug in tonight's Chimera daily build to cast the float > values to the integer type of the original map. > > You can also avoid the error with the Chimera 1.8.1 that you are using > by first converting your map to 32-bit float values using Chimera command > > vop scale #0 value float32 > > That will produce a new map (called #1) that has 32-bit float value and > that can be resampled without errors in your Chimera. > > Thanks for reporting this bug. I'm surprised it was not reported > earlier. > > Tom > > > On Apr 1, 2014, at 10:20 PM, Jason Kaelber wrote: > > > Hi all, > > > > I decided to do a rough alignment of density maps manually and resample > onto a common coordinate system to feed the output mrc files into my fine > aligner. But, when I vop resample #1 onGrid #0, I get, > > TypeError: Cannot cast ufunc add output from dtype('float32') to > dtype('uint8') with casting rule 'same_kind' > > > > What might I be doing wrong to get this error? As far as I know, all the > maps should be uint8 since they were most recently operated on by David > Mastronarde's newstack command which outputs them as unsigned bytes. > > > > Thanks, > > Jason > > > > > > > > > > > > > > Exception in Tk callback > > Function: > (type: 'instancemethod'>) > > Args: (,) > > Event type: KeyPress (type num: 2) > > Traceback (innermost last): > > File > "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", > line 1747, in __call__ > > return apply(self.func, args) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in > processCommand > > midas_text.makeCommand(cmdText) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, > in makeCommand > > f(c, args) > > File > "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line > 24, in vop_cmd > > vop_command(cmdname, args) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", > line 91, in vop_command > > doExtensionFunc(func, fargs, specInfo = spec) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, > in doExtensionFunc > > extFunc(*tuple(processedArgs), **kw) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", > line 553, in resample_op > > boundingGrid, False, None, modelId) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", > line 168, in add_operation > > scale = scale[i]) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line > 1535, in add_interpolated_values > > m[:,:,:] += values > > : Cannot cast ufunc add output from > dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > > > ================================================ > > Event contents: > > char: > > delta: 36 > > height: ?? > > keycode: 36 > > keysym: Return > > keysym_num: 65293 > > num: ?? > > send_event: False > > serial: 39103 > > state: 16 > > time: 139539396 > > type: 2 > > widget: .59791048.661335648.802317088.802317376.802317448 > > width: ?? > > x: 159 > > x_root: 524 > > y: 9 > > y_root: 988 > > > > TypeError: Cannot cast ufunc add output from dtype('float32') to > dtype('uint8') with casting rule 'same_kind' > > > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line > 1535, in add_interpolated_values > > m[:,:,:] += values > > > > See reply log for Python traceback. > > -- > > National Center for Macromolecular Imaging, N420 > > Baylor College of Medicine, MS BCM125 > > 1 Baylor Plaza > > Houston, TX, USA > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From Hugo.J.Bohorquez at FIDIC.org.co Thu Apr 3 11:31:21 2014 From: Hugo.J.Bohorquez at FIDIC.org.co (Hugo J Bohorquez) Date: Thu, 3 Apr 2014 13:31:21 -0500 Subject: [Chimera-users] ellipsoid main axis alignment ? Message-ID: Hi, I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. Every ellipsoid should be positioned at a specific location *P* = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-*A*, *B*, *C*. However, when I create an ellipsoid with shape_command it gets located correctly at *P* but it is aligned with the global axis. I can't find a general way to reorient an object so its original axes point along the vectors *A*, *B*, and *C*. I will appreciate any suggestion how to do it. -- Hugo J Boh?rquez , PhD *Investigador* Grupo de Biof?sica Fundaci?n Instituto de Inmunolog?a de Colombia TEL. +57 +1 -3158920 Ext. 122 CEL. +57 315-6169069 *The Pauli energy grows exponentially with the electronic localisation * -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Apr 3 14:45:39 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 3 Apr 2014 14:45:39 -0700 Subject: [Chimera-users] ellipsoid main axis alignment ? In-Reply-To: References: Message-ID: <1EBD71EC-E719-4BDB-AE70-0D382DCD4BAD@cgl.ucsf.edu> Hi Hugo, There is a Thermal Ellipsoids tool (and "aniso" command) that shows anisotropic B-factors from the ANISOU records of a PDB file: ? so one way would be to generate a PDB file with ANISOU records describing your ellipsoids instead of anisotropic B-factors, ...and then read it into Chimera and use this tool. However, it might be difficult to figure out the correct numbers to put into such records, and also they do not directly specify the size. The size would be chosen indirectly as a probability level in the Thermal Ellipsoids tool. Somebody else may be able to suggest a more direct or efficient way to do what you want. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2014, at 11:31 AM, Hugo J Bohorquez wrote: > Hi, > I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. > > Every ellipsoid should be positioned at a specific location P = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-A, B, C. > > However, when I create an ellipsoid with shape_command it gets located correctly at P but it is aligned with the global axis. > I can't find a general way to reorient an object so its original axes point along the vectors A, B, and C. > I will appreciate any suggestion how to do it. > > -- > Hugo J Boh?rquez, PhD > Investigador > Grupo de Biof?sica > Fundaci?n Instituto de Inmunolog?a de Colombia > TEL. +57 +1 -3158920 Ext. 122 > CEL. +57 315-6169069 From goddard at sonic.net Thu Apr 3 15:46:52 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 15:46:52 -0700 Subject: [Chimera-users] resampling maps In-Reply-To: References: <519C06EB-B61E-404F-8A81-662C7022AE24@sonic.net> Message-ID: <4A169A34-C7BE-4264-AD53-9A543C0BE869@sonic.net> Hi Jason, Ugh. Sorry Chimera is causing you so many troubles. That "vop scale" is not aligning the new volume with the one you scaled is a bug. I've fixed that in tonight's daily build. The trouble was that the code forgot to set the the position of the new scaled map to match the original map. So it used Chimera's default rule when creating a new map or molecule which is to align it with the currently open model which has the lowest id number (e.g. id #0). Apparently in your session that lowest id model was moved relative to the map you were scaling so its positioning transform was different. This is fixed so the new scaled map will always align with the original map. To work around this in your current Chimera after you do "vop scale #5 value float32" and it creates the new scaled map as say #6 (if that is the next available id number), then you can fix its alignment with "matrixcopy #5 #6". I hope you don't find more bugs, but if you do, tell me and I will fix them. Tom On Apr 2, 2014, at 11:30 PM, Jason Kaelber wrote: > Just in case anybody else has a similar question and finds this thread in the mailing list archives, I wanted to follow up: > > I tried your suggestion of vop scale #0 value float32. Unfortunately this makes the map lose its orientation. > > But, your explanation told me that if I convert the map to 32-bit, it will resample OK. Therefore, I > -saved the open session where I oriented all my models, > -made a temp directory and moved all the models into it, > -generated float32 version of the map with the same name, e.g. e2proc3d.py ./temp/model.mrc ./model.mrc > -and reopened the Chimera session. Then I can resample and save all the maps! > > Tom, thanks a lot for helping me figure this out and also for fixing the bug in the new version. > Sincerely, > Jason > > > > On Wed, Apr 2, 2014 at 6:10 PM, Tom Goddard wrote: > Hi Jason, > > This is a Chimera bug. Resampling a map with integer values on a new grid produces 32-bit floating point values because it uses trilinear interpolation. But the Chimera code makes the new resampled map have integer values of the same type as the input map, and converting the float values to integer is generating this error (I think because the Python numpy module changed at some point to not automatically cast float to integer). > > So I fixed the bug in tonight's Chimera daily build to cast the float values to the integer type of the original map. > > You can also avoid the error with the Chimera 1.8.1 that you are using by first converting your map to 32-bit float values using Chimera command > > vop scale #0 value float32 > > That will produce a new map (called #1) that has 32-bit float value and that can be resampled without errors in your Chimera. > > Thanks for reporting this bug. I'm surprised it was not reported earlier. > > Tom > > > On Apr 1, 2014, at 10:20 PM, Jason Kaelber wrote: > > > Hi all, > > > > I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, > > TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > > > What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. > > > > Thanks, > > Jason > > > > > > > > > > > > > > Exception in Tk callback > > Function: > (type: ) > > Args: (,) > > Event type: KeyPress (type num: 2) > > Traceback (innermost last): > > File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ > > return apply(self.func, args) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand > > midas_text.makeCommand(cmdText) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand > > f(c, args) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd > > vop_command(cmdname, args) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command > > doExtensionFunc(func, fargs, specInfo = spec) > > File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc > > extFunc(*tuple(processedArgs), **kw) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op > > boundingGrid, False, None, modelId) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation > > scale = scale[i]) > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values > > m[:,:,:] += values > > : Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > > > ================================================ > > Event contents: > > char: > > delta: 36 > > height: ?? > > keycode: 36 > > keysym: Return > > keysym_num: 65293 > > num: ?? > > send_event: False > > serial: 39103 > > state: 16 > > time: 139539396 > > type: 2 > > widget: .59791048.661335648.802317088.802317376.802317448 > > width: ?? > > x: 159 > > x_root: 524 > > y: 9 > > y_root: 988 > > > > TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' > > > > File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values > > m[:,:,:] += values > > > > See reply log for Python traceback. > > -- > > National Center for Macromolecular Imaging, N420 > > Baylor College of Medicine, MS BCM125 > > 1 Baylor Plaza > > Houston, TX, USA > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > National Center for Macromolecular Imaging, N420 > Baylor College of Medicine, MS BCM125 > 1 Baylor Plaza > Houston, TX, USA > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Apr 3 15:59:00 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 15:59:00 -0700 Subject: [Chimera-users] ellipsoid main axis alignment ? In-Reply-To: <1EBD71EC-E719-4BDB-AE70-0D382DCD4BAD@cgl.ucsf.edu> References: <1EBD71EC-E719-4BDB-AE70-0D382DCD4BAD@cgl.ucsf.edu> Message-ID: Hi Hugo, Chimera has no command for specifying a coordinate system as 3 axes A,B,C. But you can specify it as a rotation axis and angle that takes the unit vectors (1,0,0), (0,1,0) and (0,0,1) to your A,B,C. For instance if your A,B,C is a rotation about the z axis by 45 degrees and you want to place an ellipsoid with those primary axes use command shape ellipsoid radius 2,3,5 rotation 0,0,1,45 coord #1 The "rotation" argument takes the 3 components of the axis to rotate about and the rotation angle in degrees, and this will be in the coordinate system of already opened model #1. If the A,B,C vectors are unit vectors then making those the columns of a 3 by 3 matrix produces a rotation matrix and you simply want to use the axis and angle for that rotation matrix. Of course that requires some computation. I don't know now you are computing A,B,C but perhaps that code can instead output a rotation axis and angle and you can use the above technique. Tom On Apr 3, 2014, at 2:45 PM, Elaine Meng wrote: > Hi Hugo, > There is a Thermal Ellipsoids tool (and "aniso" command) that shows anisotropic B-factors from the ANISOU records of a PDB file: > > > ? so one way would be to generate a PDB file with ANISOU records describing your ellipsoids instead of anisotropic B-factors, > > > ...and then read it into Chimera and use this tool. However, it might be difficult to figure out the correct numbers to put into such records, and also they do not directly specify the size. The size would be chosen indirectly as a probability level in the Thermal Ellipsoids tool. > > Somebody else may be able to suggest a more direct or efficient way to do what you want. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Apr 3, 2014, at 11:31 AM, Hugo J Bohorquez wrote: > >> Hi, >> I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. >> >> Every ellipsoid should be positioned at a specific location P = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-A, B, C. >> >> However, when I create an ellipsoid with shape_command it gets located correctly at P but it is aligned with the global axis. >> I can't find a general way to reorient an object so its original axes point along the vectors A, B, and C. >> I will appreciate any suggestion how to do it. >> >> -- >> Hugo J Boh?rquez, PhD >> Investigador >> Grupo de Biof?sica >> Fundaci?n Instituto de Inmunolog?a de Colombia >> TEL. +57 +1 -3158920 Ext. 122 >> CEL. +57 315-6169069 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Thu Apr 3 16:02:28 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 16:02:28 -0700 Subject: [Chimera-users] ellipsoid main axis alignment ? In-Reply-To: References: <1EBD71EC-E719-4BDB-AE70-0D382DCD4BAD@cgl.ucsf.edu> Message-ID: <1BA2A747-1BA7-4836-97BD-45DE243B3162@sonic.net> Hi Hugo, Your question has come up before. If it is not convenient to use the rotation axis / angle solution I suggested, I can add an option to the shape command so that you can specify your principle axes A,B,C and the code will simply apply that transform to the shape (ie. multiply the 3 by 3 matrix which has A,B,C vectors as the 3 columns). Let me know if you want that. Tom On Apr 3, 2014, at 3:59 PM, Tom Goddard wrote: > Hi Hugo, > > Chimera has no command for specifying a coordinate system as 3 axes A,B,C. But you can specify it as a rotation axis and angle that takes the unit vectors (1,0,0), (0,1,0) and (0,0,1) to your A,B,C. For instance if your A,B,C is a rotation about the z axis by 45 degrees and you want to place an ellipsoid with those primary axes use command > > shape ellipsoid radius 2,3,5 rotation 0,0,1,45 coord #1 > > The "rotation" argument takes the 3 components of the axis to rotate about and the rotation angle in degrees, and this will be in the coordinate system of already opened model #1. If the A,B,C vectors are unit vectors then making those the columns of a 3 by 3 matrix produces a rotation matrix and you simply want to use the axis and angle for that rotation matrix. Of course that requires some computation. I don't know now you are computing A,B,C but perhaps that code can instead output a rotation axis and angle and you can use the above technique. > > Tom > > > > On Apr 3, 2014, at 2:45 PM, Elaine Meng wrote: > >> Hi Hugo, >> There is a Thermal Ellipsoids tool (and "aniso" command) that shows anisotropic B-factors from the ANISOU records of a PDB file: >> >> >> ? so one way would be to generate a PDB file with ANISOU records describing your ellipsoids instead of anisotropic B-factors, >> >> >> ...and then read it into Chimera and use this tool. However, it might be difficult to figure out the correct numbers to put into such records, and also they do not directly specify the size. The size would be chosen indirectly as a probability level in the Thermal Ellipsoids tool. >> >> Somebody else may be able to suggest a more direct or efficient way to do what you want. >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Apr 3, 2014, at 11:31 AM, Hugo J Bohorquez wrote: >> >>> Hi, >>> I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. >>> >>> Every ellipsoid should be positioned at a specific location P = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-A, B, C. >>> >>> However, when I create an ellipsoid with shape_command it gets located correctly at P but it is aligned with the global axis. >>> I can't find a general way to reorient an object so its original axes point along the vectors A, B, and C. >>> I will appreciate any suggestion how to do it. >>> >>> -- >>> Hugo J Boh?rquez, PhD >>> Investigador >>> Grupo de Biof?sica >>> Fundaci?n Instituto de Inmunolog?a de Colombia >>> TEL. +57 +1 -3158920 Ext. 122 >>> CEL. +57 315-6169069 >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From g.whittaker at ed.ac.uk Fri Apr 4 02:31:24 2014 From: g.whittaker at ed.ac.uk (Gavin Whittaker) Date: Fri, 04 Apr 2014 10:31:24 +0100 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <624EEF8436486C438E2C9E71C4879E6E291532@MLBXV06.nih.gov> References: <624EEF8436486C438E2C9E71C4879E6E291532@MLBXV06.nih.gov> Message-ID: <533E7BEC.2030009@ed.ac.uk> Darrell, Tom, VERY many thanks for the advice, information and really useful handles on how to minimise the file size. I think I'm most surprised by the effect of zooming, although it /does/ explain why I found .stl files from the same protein, taken at different times, were slightly different in size (75Mb v. 82Mb, for example) for no obvious reason; clearly the slight difference in zooming was enough to effect this difference. It's (almost!) obvious in hindsight... One thing the zooming certainly improves on, relative to lowering the resolution post-Chimera, is the rendering of spheres. My ribbon model included some metal atoms, and lowering resolution outside Chimera meant that they ended up looking like icosahedra and needing repair in CAD software... Anyway, thanks again - you've been /incredibly/ helpful! Best wishes, Gavin On 03/04/2014 21:06, Hurt, Darrell (NIH/NIAID) [E] wrote: > The differences in file size in my testing associated with ribbon scaling are likely just because of my imprecise zooming back and forth. But there certainly are file size reductions to be realized by zooming out and by simplifying the cross section. I can totally use this! > > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > > Office 301-402-0095 > Mobile 301-758-3559 > http://bioinformatics.niaid.nih.gov (Within NIH) > http://exon.niaid.nih.gov (Public) > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > ----- Original Message ----- > From: Tom Goddard [mailto:goddard at sonic.net] > Sent: Thursday, April 03, 2014 02:32 PM > To: Hurt, Darrell (NIH/NIAID) [E] > Cc: Gavin Whittaker ; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom > > Hi Darrell, > > Thanks for the test results! > > The scaling of the ribbon cross-section done by the Scaling tab of the Ribbon Style Editor (menu Tools / Depiction) should not change the size of the exported STL file at all. It only moves the vertices of the triangles, but you still get the same number of triangles. > > The STL file uses 48 bytes for each triangle (x,y,z coords for 3 vertices, plus nx,ny,nz normal vector for triangle, giving 12 floating point values each taking 4 bytes). That is rather inefficient. Chimera uses only 24 bytes per triangle in memory, and for 3d printing you don't need the normal vectors and 18 bytes per triangle would be possible. And if 16-bit precision on coordinates were adequate you could drop that to 9 bytes per triangle, about 5x smaller than STL files. But without a standard file format that can handle that format it doesn't help. Also the 3d printing software is probably not struggling with the size of the file, it is the large number of triangles that it has trouble with. The Catalyst 4.3 uPrint 3d printer software we use is very bad, usually crashing, sometimes just extremely slow (hours to process), with large files (100 Mbytes). I believe the job done by that software could be done 100 times more efficiently, but the 3d printer vendors probably aren't doing it because common uses don't produce such large files. > > Tom > > > On Apr 3, 2014, at 9:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > >> Hi guys, >> >> I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find: >> >> Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon) >> >> File > Export without zooming: 4.2 MB X3D or 6.0 MB STL >> File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL >> File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL >> File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL >> File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL >> File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL >> >> When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count! >> >> Great tip! >> >> Thanks, >> Darrell >> >> -- >> Darrell Hurt, Ph.D. >> Section Head, Computational Biology >> Bioinformatics and Computational Biosciences Branch (BCBB) >> OCICB/OSMO/OD/NIAID/NIH >> >> 31 Center Drive, Room 3B62B, MSC 2135 >> Bethesda, MD 20892-2135 >> Office: 301-402-0095 >> Mobile: 301-758-3559 >> Web: BCBB Home Page >> Twitter: @niaidbioit >> >> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. >> >> From: Tom Goddard > >> Date: Thursday, April 3, 2014 11:31 AM >> To: Gavin Whittaker > >> Cc: "chimera-users at cgl.ucsf.edu BB" > >> Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom >> >> Hi Gavin, >> >> The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. >> >> The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. >> >> Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. >> >> Tom >> >> >> On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: >> >> Dear all, >> >> I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? >> >> I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? >> >> thanks! >> >> Gavin >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From ingvar at ebi.ac.uk Fri Apr 4 02:53:26 2014 From: ingvar at ebi.ac.uk (ingvar) Date: Fri, 04 Apr 2014 10:53:26 +0100 Subject: [Chimera-users] Surprising "measure symmetry" result Message-ID: Hello, I fetched entry EMD-2463 from EMDB and issued: measure symmetry #0 nMax 24 and got the result "Symmetry emd_2463.map: C13, center 64 64 37" Increasing the number of sampling points does not change the result, but if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. Also if I change the contour level to 0.05, the author recommended level, I get C12 again. Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. Kind Regards, Ingvar Lagerstedt -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533 From bhaskarbagchi at gmail.com Fri Apr 4 08:33:42 2014 From: bhaskarbagchi at gmail.com (Bhaskar Bagchi) Date: Fri, 4 Apr 2014 21:03:42 +0530 Subject: [Chimera-users] query Message-ID: Respected Sir I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. Thanking you Yours faithfully, Bhaskar Bagchi Research Scholar Raiganj University College Email: bhaskarbagchi at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Apr 4 10:10:16 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Apr 2014 10:10:16 -0700 Subject: [Chimera-users] surface area calculations In-Reply-To: References: Message-ID: <743A98E6-4DA5-44A2-9D35-EAAFC6902295@cgl.ucsf.edu> Dear Bhaskar, As explained in more detail here: ...when you show a molecular surface in Chimera (e.g. menu: Actions... Surface... show) it will automatically calculate solvent-accessible surface (SAS) and solvent-excluded surface (SES) areas. The total is reported in the Reply Log (in Favorites menu), but also per each atom and each residue. The per-atom and per-residue area values are attributes named areaSAS and areaSES. In the Render/Select by Attribute tool (menu "Select... By Attribute Value" or "Tools... Depiction... Render by Attribute"), you can: see a histogram of the values, select or color atoms by the values, or (using its File menu) write a text file with the values. Or, to report per-atom values in the Reply Log instead of writing a file, you could use the "list atoms" command, for example: list atoms attribute areaSAS More about attributes here: There is also an attributes tutorial: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 4, 2014, at 8:33 AM, Bhaskar Bagchi wrote: > Respected Sir > I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. From goddard at sonic.net Thu Apr 3 08:36:39 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Apr 2014 08:36:39 -0700 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> References: <533D2E5C.7000303@ed.ac.uk> <63170005-2DB1-4788-BA19-FBEA3A90CC38@sonic.net> Message-ID: <3E91E147-F869-4DBE-AB60-50AD08BC2891@sonic.net> Hi Gavin, The subdivision setting and zooming effect ribbons, atom spheres, ball and stick, and sticks (bonds). It does not effect molecular surface or density map display fineness (ie number of triangles composing the rendering). For molecular surfaces there is a ?vertex density? parameter that controls fineness, and for density map contour surfaces the grid ?step? set in the volume viewer dialog controls the fineness (e.g. step 2 using every other density map grid point along each axis). Tom On Apr 3, 2014, at 8:31 AM, Tom Goddard wrote: > Hi Gavin, > > The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. > > The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. > > Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. > > Tom > > > On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: > >> Dear all, >> >> I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? >> >> I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? >> >> thanks! >> >> Gavin >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Apr 4 11:13:03 2014 From: goddard at sonic.net (Tom Goddard) Date: Fri, 4 Apr 2014 11:13:03 -0700 Subject: [Chimera-users] Surprising "measure symmetry" result In-Reply-To: References: Message-ID: <3CD3F34D-39C8-4A7F-AFD7-681395094131@sonic.net> Hi Ingvar, The basic trouble is that this map is so close to being cylindrically symmetric, ie identical at any rotation angle about z, that the ?measure symmetry? command makes the wrong choice. I put a print statement in the measure symmetry code and here are the correlation values it found for the map with a rotated copy of itself for cyclic n-fold symmetry with n = 2, 3, ?, 24: > measure sym #0 nmax 24 Symmetry emd_2463.map: C13, center 64 64 37 2 0.999913062795 3 0.999864979563 4 0.999949744672 5 0.991690288767 6 0.999886369722 7 0.994690864511 8 0.991400840587 9 0.992535268321 10 0.995822490928 11 0.999002374601 12 0.999904810469 13 0.999346674071 14 0.998135913568 15 0.996806980709 16 0.99559228476 17 0.994463541105 18 0.993546515874 19 0.992755122912 20 0.992182861668 21 0.99181103327 22 0.991574006772 23 0.991460398423 24 0.991401690757 Now the default correlation threshold for ?measure symmetry? to recognize a symmetry is 0.99. So the above table shows that with that criteria this map could be cyclic n-fold symmetric for any n = 2, ?, 24. So you might say let?s take the highest correlation value. Looking at the table that is for n = 4, 4-fold symmetry. The measure symmetry command doesn?t choose that wrong answer. The map is C4 symmetric. But a C12 map is automatically C6, C4, C3 and C2 symmetric since 6, 4, 3, and 2 divides evenly into 12. So the measure symmetry command eliminates the choices for n that are divisors of another choice of n that has correlation > 0.99. This is where C12 gets eliminated. Because you see C24 has correlation of 0.991 and so C12 is eliminated because measure symmetry prefers to say the maps is C24. Once you eliminate lower order symmetries the choices left are C13 through C24 and C13 has the highest correlation of those choices! There are various ways you can get the right answer C12. Using "measure sym #0 nmax 23? to exclude 24-fold symmetry which is causing C12 to be knocked out the competition works. Or setting a higher correlation threshold works since again C24 then gets eliminated because it doesn?t meet the correlation threshold. Or changing the contour levels changes all the correlation values since it only considers grid points within the contour level when computing correlation. The fundamental difficulty is that every choice of n for n-fold symmetry gives a correlation value greater than 0.99. Maybe smarter code would not use a fixed cutoff value. Instead it would look at the correlation values it finds, and choose a cutoff based on those. But there is no easy answer. If you look at the table of numbers above C4 symmetry has correlation 0.99994 while C12 has only 0.99990. Why don?t I say the map has C4 symmetry and just happens to be very close to cylindrical so C12 is also high? I guess you could look at the variance of the correlation values. I see C8 is only 0.991, so clearly the map isn?t cylindrically symmetric at the 0.9999 level. So some vary nuanced code could probably get the right answer. I have no sound suggestion as to how to get the right answer consistently. These EM maps were computed with an imposed symmetry, and the fundamental problem is that EMDB didn?t collect that information from the person who deposited the map. And now it is very tricky to deduce what the symmetry the author used was in an automated way. The solution is to collect this information from the author when they deposit the map ? as this is very important information about the map. Tom On Apr 4, 2014, at 2:53 AM, ingvar wrote: > Hello, > > I fetched entry EMD-2463 from EMDB and issued: > measure symmetry #0 nMax 24 > and got the result "Symmetry emd_2463.map: C13, center 64 64 37" > > Increasing the number of sampling points does not change the result, but > if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. > Also if I change the contour level to 0.05, the author recommended level, I get C12 again. > > Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. > > Kind Regards, > Ingvar Lagerstedt > -- > Ingvar Lagerstedt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > > Tel: +44 (0)1223 492533 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Fri Apr 4 11:22:39 2014 From: goddard at sonic.net (Tom Goddard) Date: Fri, 4 Apr 2014 11:22:39 -0700 Subject: [Chimera-users] Resolution of .stl file of ribbon representatiom In-Reply-To: <533E7BEC.2030009@ed.ac.uk> References: <624EEF8436486C438E2C9E71C4879E6E291532@MLBXV06.nih.gov> <533E7BEC.2030009@ed.ac.uk> Message-ID: <90E5D638-B47A-4D2B-8670-D52850DDBDF0@sonic.net> Hi Gavin, Yes zoom level can make a huge difference in STL file size with atoms shown as spheres. If you are zoomed in so an atom sphere is big on the screen it will be drawn using about 1000 triangles. If you are zoomed out so each atom is only a few pixels on the screen, it is drawn with only 8 triangles, more than 100 times fewer triangles and the STL file size will be more than 100 times smaller. This level-of-detail with zooming is to give you the best graphics performance. When you export the model as STL what fineness should Chimera use? It has no way of knowing what your requirements are, so it simply uses what it is using on your display. One solution is to have the Chimera Export dialog show an option ?Output resolution in Angstroms? with some default value filled in based on your current zoom level or maybe 1/1000 times the maximum x,y,z extent of your models. We don?t have that option now. Tom On Apr 4, 2014, at 2:31 AM, Gavin Whittaker wrote: > > Darrell, Tom, > > VERY many thanks for the advice, information and really useful handles on how to minimise the file size. I think I'm most surprised by the effect of zooming, although it does explain why I found .stl files from the same protein, taken at different times, were slightly different in size (75Mb v. 82Mb, for example) for no obvious reason; clearly the slight difference in zooming was enough to effect this difference. It's (almost!) obvious in hindsight... > > One thing the zooming certainly improves on, relative to lowering the resolution post-Chimera, is the rendering of spheres. My ribbon model included some metal atoms, and lowering resolution outside Chimera meant that they ended up looking like icosahedra and needing repair in CAD software... > > Anyway, thanks again - you've been incredibly helpful! > > Best wishes, > > Gavin > > > On 03/04/2014 21:06, Hurt, Darrell (NIH/NIAID) [E] wrote: >> The differences in file size in my testing associated with ribbon scaling are likely just because of my imprecise zooming back and forth. But there certainly are file size reductions to be realized by zooming out and by simplifying the cross section. I can totally use this! >> >> Darrell Hurt, Ph.D. >> Section Head, Computational Biology >> Bioinformatics and Computational Biosciences Branch (BCBB) >> OCICB/OSMO/OD/NIAID/NIH >> >> 31 Center Drive, Room 3B62B, MSC 2135 >> Bethesda, MD 20892-2135 >> >> Office 301-402-0095 >> Mobile 301-758-3559 >> http://bioinformatics.niaid.nih.gov (Within NIH) >> http://exon.niaid.nih.gov (Public) >> >> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. >> >> ----- Original Message ----- >> From: Tom Goddard [mailto:goddard at sonic.net] >> Sent: Thursday, April 03, 2014 02:32 PM >> To: Hurt, Darrell (NIH/NIAID) [E] >> Cc: Gavin Whittaker ; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom >> >> Hi Darrell, >> >> Thanks for the test results! >> >> The scaling of the ribbon cross-section done by the Scaling tab of the Ribbon Style Editor (menu Tools / Depiction) should not change the size of the exported STL file at all. It only moves the vertices of the triangles, but you still get the same number of triangles. >> >> The STL file uses 48 bytes for each triangle (x,y,z coords for 3 vertices, plus nx,ny,nz normal vector for triangle, giving 12 floating point values each taking 4 bytes). That is rather inefficient. Chimera uses only 24 bytes per triangle in memory, and for 3d printing you don't need the normal vectors and 18 bytes per triangle would be possible. And if 16-bit precision on coordinates were adequate you could drop that to 9 bytes per triangle, about 5x smaller than STL files. But without a standard file format that can handle that format it doesn't help. Also the 3d printing software is probably not struggling with the size of the file, it is the large number of triangles that it has trouble with. The Catalyst 4.3 uPrint 3d printer software we use is very bad, usually crashing, sometimes just extremely slow (hours to process), with large files (100 Mbytes). I believe the job done by that software could be done 100 times more efficiently, but the 3d printer vendors pr! >> obably a >> ren't doing it because common uses don't produce such large files. >> >> Tom >> >> >> On Apr 3, 2014, at 9:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: >> >>> Hi guys, >>> >>> I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find: >>> >>> Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon) >>> >>> File > Export without zooming: 4.2 MB X3D or 6.0 MB STL >>> File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL >>> File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL >>> File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL >>> File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL >>> File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL >>> >>> When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count! >>> >>> Great tip! >>> >>> Thanks, >>> Darrell >>> >>> -- >>> Darrell Hurt, Ph.D. >>> Section Head, Computational Biology >>> Bioinformatics and Computational Biosciences Branch (BCBB) >>> OCICB/OSMO/OD/NIAID/NIH >>> >>> 31 Center Drive, Room 3B62B, MSC 2135 >>> Bethesda, MD 20892-2135 >>> Office: 301-402-0095 >>> Mobile: 301-758-3559 >>> Web: BCBB Home Page >>> Twitter: @niaidbioit >>> >>> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. >>> >>> From: Tom Goddard > >>> Date: Thursday, April 3, 2014 11:31 AM >>> To: Gavin Whittaker > >>> Cc: "chimera-users at cgl.ucsf.edu BB" > >>> Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom >>> >>> Hi Gavin, >>> >>> The ?subdivision? setting under ?graphics quality? in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh. Actually it only controls the subdivisions along the ribbon. I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is. So you may still need to use an external program to reduce the fineness. >>> >>> The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially. >>> >>> Aha, there is more to it. The level of subdivision is intended to maintain good quality appearance on your display. So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser. I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes! So siimply zooming out before you export will control fineness. Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed. When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place. >>> >>> Tom >>> >>> >>> On Apr 3, 2014, at 2:48 AM, Gavin Whittaker wrote: >>> >>> Dear all, >>> >>> I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? >>> >>> I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? >>> >>> thanks! >>> >>> Gavin >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingvar at ebi.ac.uk Sun Apr 6 06:26:33 2014 From: ingvar at ebi.ac.uk (ingvar) Date: Sun, 06 Apr 2014 14:26:33 +0100 Subject: [Chimera-users] Surprising "measure symmetry" result In-Reply-To: <3CD3F34D-39C8-4A7F-AFD7-681395094131@sonic.net> References: <3CD3F34D-39C8-4A7F-AFD7-681395094131@sonic.net> Message-ID: <491c2fe90d1e443e40bd1828625a0ec1@ebi.ac.uk> Hi Tom, Thank you for the thorough answer. It was really useful to see all the correlation coefficients. EMDB has started to collect any imposed symmetry in the image processing, but most entries in the archive do not have that info. One idea is to try remediate the older entries with the symmetries reported by Chimera, and I picked this entry as a spot check. For this volume the authors reported that they imposed C12 symmetry, so I wanted to see if that was what Chimera reported. When I viewed the volume it looked to me that there were some features that was C4 rather then C12, so it was nice to see that the cc for C4 was higher than C12, but not massively so. I agree that just taking the highest cc is likely to not be the best choice. One could device a significance score, maybe log(1-cc) and say that the lower symmetry is the relevant one if the difference is larger than log(2). (There may be a better value than log(2), possibly based on the symmetry multiples between the two cases.) With these rules C12 would be favoured over C24 and also just pip C4, but a larger sampling set would be needed to see if this actually works. This type of score would only apply in a relatively narrow band, we are only interested if the correlation is high enough, > 0.99, and there will be an upper limit were the values of a handful of voxels would be all decisive. Another observation is that the cc is quite large for both C11 and C13. I think that is probably the case for any large n, if the cc for Cn is high then the cc's for both Cn-1 and Cn+1 are likely to also be quite high. All the best, Ingvar On 2014-04-04 19:13, Tom Goddard wrote: > Hi Ingvar, > > The basic trouble is that this map is so close to being > cylindrically symmetric, ie identical at any rotation angle about z, > that the ?measure symmetry? command makes the wrong choice. I put a > print statement in the measure symmetry code and here are the > correlation values it found for the map with a rotated copy of itself > for cyclic n-fold symmetry with n = 2, 3, ?, 24: > >> measure sym #0 nmax 24 > Symmetry emd_2463.map: C13, center 64 64 37 > 2 0.999913062795 > 3 0.999864979563 > 4 > 5 0.991690288767 > 6 0.999886369722 > 7 0.994690864511 > 8 0.991400840587 > 9 0.992535268321 > 10 0.995822490928 > 11 0.999002374601 > 12 0.999904810469 > 13 0.999346674071 > 14 0.998135913568 > 15 0.996806980709 > 16 0.99559228476 > 17 0.994463541105 > 18 0.993546515874 > 19 0.992755122912 > 20 0.992182861668 > 21 0.99181103327 > 22 0.991574006772 > 23 0.991460398423 > 24 0.991401690757 > > Now the default correlation threshold for ?measure symmetry? to > recognize a symmetry is 0.99. So the above table shows that with that > criteria this map could be cyclic n-fold symmetric for any n = 2, ?, > 24. > > So you might say let?s take the highest correlation value. Looking > at the table that is for n = 4, 4-fold symmetry. The measure symmetry > command doesn?t choose that wrong answer. The map is C4 symmetric. > But a C12 map is automatically C6, C4, C3 and C2 symmetric since 6, 4, > 3, and 2 divides evenly into 12. So the measure symmetry command > eliminates the choices for n that are divisors of another choice of n > that has correlation > 0.99. This is where C12 gets eliminated. > Because you see C24 has correlation of 0.991 and so C12 is eliminated > because measure symmetry prefers to say the maps is C24. Once you > eliminate lower order symmetries the choices left are C13 through C24 > and C13 has the highest correlation of those choices! > > There are various ways you can get the right answer C12. Using > "measure sym #0 nmax 23? to exclude 24-fold symmetry which is causing > C12 to be knocked out the competition works. Or setting a higher > correlation threshold works since again C24 then gets eliminated > because it doesn?t meet the correlation threshold. Or changing the > contour levels changes all the correlation values since it only > considers grid points within the contour level when computing > correlation. > > The fundamental difficulty is that every choice of n for n-fold > symmetry gives a correlation value greater than 0.99. Maybe smarter > code would not use a fixed cutoff value. Instead it would look at the > correlation values it finds, and choose a cutoff based on those. But > there is no easy answer. If you look at the table of numbers above C4 > symmetry has correlation 0.99994 while C12 has only 0.99990. Why > don?t I say the map has C4 symmetry and just happens to be very close > to cylindrical so C12 is also high? I guess you could look at the > variance of the correlation values. I see C8 is only 0.991, so > clearly the map isn?t cylindrically symmetric at the 0.9999 level. So > some vary nuanced code could probably get the right answer. > > I have no sound suggestion as to how to get the right answer > consistently. These EM maps were computed with an imposed symmetry, > and the fundamental problem is that EMDB didn?t collect that > information from the person who deposited the map. And now it is very > tricky to deduce what the symmetry the author used was in an automated > way. The solution is to collect this information from the author when > they deposit the map ? as this is very important information about the > map. > > Tom > > > On Apr 4, 2014, at 2:53 AM, ingvar wrote: > >> Hello, >> >> I fetched entry EMD-2463 from EMDB and issued: >> measure symmetry #0 nMax 24 >> and got the result "Symmetry emd_2463.map: C13, center 64 64 37" >> >> Increasing the number of sampling points does not change the result, >> but >> if I increase the correlation criteria a little, to say 0.992, I get >> the expected C12 symmetry. >> Also if I change the contour level to 0.05, the author recommended >> level, I get C12 again. >> >> Looking at the volume at several different contour levels, it is >> difficult to see how it could be considered C13, and also how it would >> go from C13 to C12. >> >> Kind Regards, >> Ingvar Lagerstedt >> -- >> Ingvar Lagerstedt >> European Bioinformatics Institute (EMBL-EBI) >> European Molecular Biology Laboratory >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> >> Tel: +44 (0)1223 492533 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533 From sun at ntnu.edu.tw Sun Apr 6 07:16:36 2014 From: sun at ntnu.edu.tw (Ying-Chieh Sun) Date: Sun, 6 Apr 2014 22:16:36 +0800 Subject: [Chimera-users] presets-interactive 3-hydrophobicity surface- those water molecules stay! Message-ID: <003901cf51a2$d237ae50$76a70af0$@ntnu.edu.tw> Hi, I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine 'crystal (or say, ordered) water molecules'. This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. Thank you for your help. Ying-chieh Ying-Chieh Sun, Professor of Computational Chemistry Chemistry Department National Taiwan Normal University Taipei, Taiwan 11617 Tel: +886-2-7734-6215 Fax: +886-2-2932-4249 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sun Apr 6 08:40:09 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 6 Apr 2014 08:40:09 -0700 Subject: [Chimera-users] presets-interactive 3-hydrophobicity surface- those water molecules stay! In-Reply-To: <003901cf51a2$d237ae50$76a70af0$@ntnu.edu.tw> References: <003901cf51a2$d237ae50$76a70af0$@ntnu.edu.tw> Message-ID: <45AE4ABE-26BB-4582-9DA6-5D0105F63ACE@cgl.ucsf.edu> Hi Ying-chieh, The "hydrophobicity surface" refers to the surface coloring only: blue for the most hydrophilic amino amino acids, orange-red for the most hydrophobic. I would not give special meaning to which water molecules are displayed. The preset may display atomic detail including water molecules near a ligand, but only based on a simple distance cutoff from ligand atoms, like the "ribbons" interactive preset. The presets are described here: One idea for trying to find more tightly bound water molecules is to use the "MD Movie" tool (in menu under Tools... MD/Ensemble Analysis) to view your Amber trajectory and to calculate an occupancy map for water atoms relative to parts of the protein. This might or might not be useful depending on the protein flexibility and on which parts of the protein are held steady for the calculations. MD Movie, see the "occupancy analysis" section: There is also a tutorial on MD Movie with occupancy calculations: 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 Apr 6, 2014, at 7:16 AM, Ying-Chieh Sun wrote: > Hi, > I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. > > When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. > > I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine ?crystal (or say, ordered) water molecules?. > > This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. > Thank you for your help. > Ying-chieh From aldosegura at gmail.com Sun Apr 6 15:12:03 2014 From: aldosegura at gmail.com (Aldo Segura) Date: Sun, 6 Apr 2014 18:12:03 -0400 Subject: [Chimera-users] presets-interactive 3-hydrophobicity surface- those water molecules stay! In-Reply-To: <45AE4ABE-26BB-4582-9DA6-5D0105F63ACE@cgl.ucsf.edu> References: <003901cf51a2$d237ae50$76a70af0$@ntnu.edu.tw> <45AE4ABE-26BB-4582-9DA6-5D0105F63ACE@cgl.ucsf.edu> Message-ID: Hi, You should try to perform a RMSF analysis focused on the water molecules in your trajectory and identify those with low fluctuation values. Best, Aldo 2014-04-06 11:40 GMT-04:00 Elaine Meng : > Hi Ying-chieh, > The "hydrophobicity surface" refers to the surface coloring only: blue for > the most hydrophilic amino amino acids, orange-red for the most hydrophobic. > > I would not give special meaning to which water molecules are displayed. > The preset may display atomic detail including water molecules near a > ligand, but only based on a simple distance cutoff from ligand atoms, like > the "ribbons" interactive preset. The presets are described here: > > > One idea for trying to find more tightly bound water molecules is to use > the "MD Movie" tool (in menu under Tools... MD/Ensemble Analysis) to view > your Amber trajectory and to calculate an occupancy map for water atoms > relative to parts of the protein. This might or might not be useful > depending on the protein flexibility and on which parts of the protein are > held steady for the calculations. > > MD Movie, see the "occupancy analysis" section: > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html > > > > There is also a tutorial on MD Movie with occupancy calculations: > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2 > > > > 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 Apr 6, 2014, at 7:16 AM, Ying-Chieh Sun wrote: > > > Hi, > > I did a simulation using Amber package and saved a snapshot into its pdb > file, and use Chimera to open it. The pdb file contains a protein-ligand > complex plus a box of about 20000 TIP3P water molecules. > > > > When I pressed presets-interactive 3-hydrophobicity surface, there are 8 > water molecules stayed close to the ligand binding site. > > > > I am wondering how these 8 water molecules were determined? The reason I > ask is because we are trying to find a way to determine 'crystal (or say, > ordered) water molecules'. > > > > This presets-interactive 3-hydrophobicity surface seems to perform this > function in some way. > > Thank you for your help. > > Ying-chieh > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- ========================================= Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera at cchmc.org ; aldosegura at gmail.com ========================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.rogue at gmail.com Mon Apr 7 08:44:01 2014 From: jaime.rogue at gmail.com (=?ISO-8859-1?Q?Jaime_Rodr=EDguez=2DGuerra?=) Date: Mon, 7 Apr 2014 17:44:01 +0200 Subject: [Chimera-users] Calculating SAS and SES with Chimera-MSMS wrap Message-ID: Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Apr 7 14:30:56 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 7 Apr 2014 14:30:56 -0700 Subject: [Chimera-users] Reaction Mechanism Movie In-Reply-To: References: Message-ID: <10A0EF8E-8CD2-455C-8B06-2064225B0558@cgl.ucsf.edu> On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote: > Dear Dr. Pettersen, > I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. Hi Moses, It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do. The simplest method is to decide which frame# you want the bond to start existing and use the "Define script?" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame. For example, if you wanted a bond between :337.A at P and :338.A at O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script: #53 bond :337.A at P :338.A at O3' There is also a hidden capability in Chimera to compute all bonds on a per-frame basis. I can tell you how to access that if it turns out you really need it. However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you. I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file?" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other. There are some values at the top of the script that you can edit to make it work best in your situation. There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0). There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames). Let me know if you need more help than this. Hmmm, this all assumes you have a trajectory of the reaction. You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: varbond.py Type: text/x-python-script Size: 779 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Apr 7 17:34:59 2014 From: goddard at sonic.net (Tom Goddard) Date: Mon, 7 Apr 2014 17:34:59 -0700 Subject: [Chimera-users] Calculating SAS and SES with Chimera-MSMS wrap In-Reply-To: References: Message-ID: <41CDCF49-1764-4DA0-B499-BD40E1916F6B@sonic.net> Hi Jaime, Your Chimera code for reporting SES and SAS areas looks almost right. It appears you have reversed SES and SAS though. My look at the Chimera measure.py code says atom_areas[i,0] is SES area and atom_areas[i,1] is SAS area for atom i where atom_areas = surfaces[3]. You print them out switched. Also I ran your code and SAS should be larger for most atoms, but it is smaller for most when using your code. Also be aware that your code completely ignores all non-selected atoms. You are not getting the exposed areas of the selected atoms within the entire molecule. Instead what your code calculates is the exposed area assuming all the non-selected atoms were deleted. If instead you want the exposed areas taking into account the area buried by unselected atoms, then you need to do the atom_xyzr() call with all the atoms, and then just pick out the exposed areas for the selected atoms. Tom On Apr 7, 2014, at 8:44 AM, Jaime Rodr?guez-Guerra wrote: > Dear Chimera dev team, > > I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. > > Here is my current procedure: > > ``` > import chimera, Measure, MoleculeSurface > atoms = chimera.selection.currentAtoms() > xyzr_data = Measure.measure.atom_xyzr(atoms) > surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) > > for i, a in enumerate(atoms): > print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) > > ``` > > Is this OK? I don't know how to handle all that output that MSMS is giving back! > > Thanks in advance, > Jaime. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From swong18 at terpmail.umd.edu Tue Apr 8 07:17:35 2014 From: swong18 at terpmail.umd.edu (Sook Wong) Date: Tue, 8 Apr 2014 10:17:35 -0400 Subject: [Chimera-users] Docking ligands and protein using Chimera Message-ID: Good morning, I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? Looking forward to hear from you. Thank you so much! Sincerely, Sook Y Wong Chemical and Biomolecular Engineering '14 A. James Clark School of Engineering University of Maryland, College Park, MD 20742 swong18 at terpmail.umd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 8 09:23:35 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 8 Apr 2014 09:23:35 -0700 Subject: [Chimera-users] Docking ligands and protein using Chimera In-Reply-To: References: Message-ID: Good morning, Chimera itself does not do docking. It has a tool that connects to an AutoDock Vina web service, but it is quite limited: you can only dock ONE ligand molecule per calculation, and only a small number of output positions can be saved (menu: Tools? Surface/Binding Analysis? AutoDock Vina). I believe you will need to use some other program outside of Chimera to do the docking. After that, you can view and analyze the docking results with Chimera (menu: Tools? Surface/Binding Analysis? ViewDock). What docking program to use? Possibilities include DOCK, AutoDock, AutoDock Vina, GOLD ? there are links to the websites of these programs in the ViewDock manual page linked above. Some are free for academic use, and downloads and tutorials are available on their websites. There are also some web servers (so you wouldn't have to download another program), but they may limit your options. I haven't tried them, but a couple that I know of are: Dock Blaster SwissDock 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 Apr 8, 2014, at 7:17 AM, Sook Wong wrote: > Good morning, > I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? > Looking forward to hear from you. > Thank you so much! > Sincerely, > Sook Y Wong > Chemical and Biomolecular Engineering '14 > A. James Clark School of Engineering > University of Maryland, College Park, MD 20742 > swong18 at terpmail.umd.edu From goddard at sonic.net Tue Apr 8 12:19:33 2014 From: goddard at sonic.net (Tom Goddard) Date: Tue, 8 Apr 2014 12:19:33 -0700 Subject: [Chimera-users] Surprising "measure symmetry" result In-Reply-To: <491c2fe90d1e443e40bd1828625a0ec1@ebi.ac.uk> References: <3CD3F34D-39C8-4A7F-AFD7-681395094131@sonic.net> <491c2fe90d1e443e40bd1828625a0ec1@ebi.ac.uk> Message-ID: Hi Ingvar, Glad to hear that the EMDB is collecting the map symmetry information. This will make the maps more valuable for further research. Before creating weird heuristics for guessing the symmetry in ambiguous cases, it is important to understand why we don?t get correlation values equal to 1 for a map that has been symmetrized. The map we have been talking about, EMDB 2463, is said to have been created by imposing 12-fold symmetry as described in the article Structure, adsorption to host, and infection mechanism of virulent lactococcal phage p2. Bebeacua C, Tremblay D, Farenc C, Chapot-Chartier MP, Sadovskaya I, van Heel M, Veesler D, Moineau S, Cambillau C. J Virol. 2013 Nov;87(22):12302-12. doi: 10.1128/JVI.02033-13. Epub 2013 Sep 11. Chimera reports the center of symmetry of the 128 by 128 by 128 grid point map to be at grid point 64,64,any-z-index. Is this right? The ?measure symmetry? command only considers symmetry axes passing through a grid point, or midway between grid points. In other words it assumes the grid index i,j,k that the symmetry axis passes through has integer or half-integer values. That doesn?t appear to be the case for this map. The first sign that raises some suspicion is that the C4 correlation values is not 1.0. If the map has C12 symmetry then it also has C4 symmetry, and C4 symmetry is just rotation by 90 degrees. If the center is at a grid point (i=j=64) then the 90 degree rotation maps each grid point exactly to another grid point. So the map values should be identical at symmetry equivalent grid points (i,j,k), (-j,i,k), (-i,-j,k), (j,-i,k). If I make two copies of the map and rotate one by 90 degrees and subtract, the result should be exactly zero at each grid point. So why does Chimera report the C4 correlation as 0.99995 instead of 1.0? In these cases I like to visually look at two copies of the map, with one copy rotated about the presumed symmetry axis. I?ve attached an image emdb_2463_r180_64.jpg showing the result. The yellow map was rotated by 180 degrees about the z-axis through grid point 64,64,64. It doesn?t align with the gray copy of the map ? it appears shifted to the left, indicating that the x grid index for the center is wrong. The second image emdb_2463_r180_64.2.jpg shows the result if I rotate about grid point 64.2,64,64 ? it is misaligned in the opposite direction. Using rotation center 64.08,64,64 gives a resonable superposition, image emdb_2463_r180_64.08.jpg. The surfaces don?t match exactly because rotation by 180 degrees is not mapping a grid point to a grid point because the center is not an integer grid index. The surfaces are computed using grids that are shifted relative to one another and will not be identical since the surface triangulation is based on the grid (using marching cubes algorithm). Unfortunately the problems with the symmetry of this map are not as simple as the above explanation that the center is not at a grid point. The previous images used the contour level 0.05. But if I now switch to contour level 0.08 then 64.08,64,64 does not appear to be the correct center of rotation as show in image emdb_2463_r180_64.08_lev0.08.jpg. For level 0.08 the correct center seems close to 64.02,64,64. But then the base (low z) and tube (high z) portions of the map appear to be shifted in opposite directions, as if the symmetry axis is not really exactly along z, but tilted slightly in the xz plane. My conclusion is that something very weird was done in the symmetrization of this map. It is perhaps not surprising since the biological structure is a 12-fold symmetric portal crammed into a 5-fold symmetric virus capsid vertex. It is difficult to handle the symmetry mismatch in such reconstructions and that probably plays a role in why this map does not appear to have C12 symmetry. Its deviations from C12 symmetry are more than just limited floating point precision (32-bit float values have about 7 digits of precision). Although we could cook up some ?rules? to make Chimera choose C12 symmetry for this map, it would not make sense. Your efforts to guess the map symmetry are bound to run into hard cases like this. Obviously the right solution is to have the depositor tell you the answer, and then you should verify it when the map is deposited. I don?t think days of work on this one map would lead to an understanding of what was done to ?impose 12-fold symmetry?. I think one improvement that should be made to Chimera ?measure symmetry? is it should not just give you the ?best guess?. It should report the other high correlation guesses so you can see when the assignment is ambiguous. Tom On Apr 6, 2014, at 6:26 AM, ingvar wrote: > Hi Tom, > > Thank you for the thorough answer. It was really useful to see all the correlation coefficients. > > EMDB has started to collect any imposed symmetry in the image processing, but most entries in the archive do not have that info. One idea is to try remediate the older entries with the symmetries reported by Chimera, and I picked this entry as a spot check. For this volume the authors reported that they imposed C12 symmetry, so I wanted to see if that was what Chimera reported. When I viewed the volume it looked to me that there were some features that was C4 rather then C12, so it was nice to see that the cc for C4 was higher than C12, but not massively so. > > I agree that just taking the highest cc is likely to not be the best choice. One could device a significance score, maybe log(1-cc) and say that the lower symmetry is the relevant one if the difference is larger than log(2). (There may be a better value than log(2), possibly based on the symmetry multiples between the two cases.) With these rules C12 would be favoured over C24 and also just pip C4, but a larger sampling set would be needed to see if this actually works. > This type of score would only apply in a relatively narrow band, we are only interested if the correlation is high enough, > 0.99, and there will be an upper limit were the values of a handful of voxels would be all decisive. > > Another observation is that the cc is quite large for both C11 and C13. I think that is probably the case for any large n, if the cc for Cn is high then the cc's for both Cn-1 and Cn+1 are likely to also be quite high. > > All the best, > Ingvar > > On 2014-04-04 19:13, Tom Goddard wrote: >> Hi Ingvar, >> The basic trouble is that this map is so close to being >> cylindrically symmetric, ie identical at any rotation angle about z, >> that the ?measure symmetry? command makes the wrong choice. I put a >> print statement in the measure symmetry code and here are the >> correlation values it found for the map with a rotated copy of itself >> for cyclic n-fold symmetry with n = 2, 3, ?, 24: >>> measure sym #0 nmax 24 >> Symmetry emd_2463.map: C13, center 64 64 37 >> 2 0.999913062795 >> 3 0.999864979563 >> 4 >> 5 0.991690288767 >> 6 0.999886369722 >> 7 0.994690864511 >> 8 0.991400840587 >> 9 0.992535268321 >> 10 0.995822490928 >> 11 0.999002374601 >> 12 0.999904810469 >> 13 0.999346674071 >> 14 0.998135913568 >> 15 0.996806980709 >> 16 0.99559228476 >> 17 0.994463541105 >> 18 0.993546515874 >> 19 0.992755122912 >> 20 0.992182861668 >> 21 0.99181103327 >> 22 0.991574006772 >> 23 0.991460398423 >> 24 0.991401690757 >> Now the default correlation threshold for ?measure symmetry? to >> recognize a symmetry is 0.99. So the above table shows that with that >> criteria this map could be cyclic n-fold symmetric for any n = 2, ?, >> 24. >> So you might say let?s take the highest correlation value. Looking >> at the table that is for n = 4, 4-fold symmetry. The measure symmetry >> command doesn?t choose that wrong answer. The map is C4 symmetric. >> But a C12 map is automatically C6, C4, C3 and C2 symmetric since 6, 4, >> 3, and 2 divides evenly into 12. So the measure symmetry command >> eliminates the choices for n that are divisors of another choice of n >> that has correlation > 0.99. This is where C12 gets eliminated. >> Because you see C24 has correlation of 0.991 and so C12 is eliminated >> because measure symmetry prefers to say the maps is C24. Once you >> eliminate lower order symmetries the choices left are C13 through C24 >> and C13 has the highest correlation of those choices! >> There are various ways you can get the right answer C12. Using >> "measure sym #0 nmax 23? to exclude 24-fold symmetry which is causing >> C12 to be knocked out the competition works. Or setting a higher >> correlation threshold works since again C24 then gets eliminated >> because it doesn?t meet the correlation threshold. Or changing the >> contour levels changes all the correlation values since it only >> considers grid points within the contour level when computing >> correlation. >> The fundamental difficulty is that every choice of n for n-fold >> symmetry gives a correlation value greater than 0.99. Maybe smarter >> code would not use a fixed cutoff value. Instead it would look at the >> correlation values it finds, and choose a cutoff based on those. But >> there is no easy answer. If you look at the table of numbers above C4 >> symmetry has correlation 0.99994 while C12 has only 0.99990. Why >> don?t I say the map has C4 symmetry and just happens to be very close >> to cylindrical so C12 is also high? I guess you could look at the >> variance of the correlation values. I see C8 is only 0.991, so >> clearly the map isn?t cylindrically symmetric at the 0.9999 level. So >> some vary nuanced code could probably get the right answer. >> I have no sound suggestion as to how to get the right answer >> consistently. These EM maps were computed with an imposed symmetry, >> and the fundamental problem is that EMDB didn?t collect that >> information from the person who deposited the map. And now it is very >> tricky to deduce what the symmetry the author used was in an automated >> way. The solution is to collect this information from the author when >> they deposit the map ? as this is very important information about the >> map. >> Tom >> On Apr 4, 2014, at 2:53 AM, ingvar wrote: >>> Hello, >>> I fetched entry EMD-2463 from EMDB and issued: >>> measure symmetry #0 nMax 24 >>> and got the result "Symmetry emd_2463.map: C13, center 64 64 37" >>> Increasing the number of sampling points does not change the result, but >>> if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. >>> Also if I change the contour level to 0.05, the author recommended level, I get C12 again. >>> Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. >>> Kind Regards, >>> Ingvar Lagerstedt >>> -- >>> Ingvar Lagerstedt >>> European Bioinformatics Institute (EMBL-EBI) >>> European Molecular Biology Laboratory >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD >>> Tel: +44 (0)1223 492533 >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- > Ingvar Lagerstedt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > > Tel: +44 (0)1223 492533 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emdb_2463_r180_64.jpg Type: image/jpg Size: 34450 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emdb_2463_r180_64.2.jpg Type: image/jpg Size: 35694 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emdb_2463_r180_64.08.jpg Type: image/jpg Size: 39965 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emdb_2463_r180_64.08_lev0.08.jpg Type: image/jpg Size: 38340 bytes Desc: not available URL: From geniouschemist26 at gmail.com Tue Apr 8 05:07:53 2014 From: geniouschemist26 at gmail.com (MUHAMMAD RAMZAN MANWAR) Date: Tue, 8 Apr 2014 15:07:53 +0300 Subject: [Chimera-users] Request for guidance Message-ID: Dear Dr. Ferrin, Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. With regards Hussain MR PACER-HD, KAU, KSA -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 8 14:59:23 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 8 Apr 2014 14:59:23 -0700 Subject: [Chimera-users] mutating residues In-Reply-To: References: Message-ID: <120CFF10-D59F-4350-9C14-BB94617D8545@cgl.ucsf.edu> Dear Hussain MR, The chimera-users at cgl.ucsf.edu address (not the others) is recommended for asking questions about using Chimera. To change an amino acid in a protein structure, you can use the Rotamers tool (in menu under Tools? Structure Editing) or the "swapaa" command. Please see the manual: There are "swapaa" examples in the link above, and examples of using Rotamers in the "Structure Analysis and Comparison Tutorial": You can find tutorials and search the documentation using the Help menu in Chimera. 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 Apr 8, 2014, at 5:07 AM, MUHAMMAD RAMZAN MANWAR wrote: > Dear Dr. Ferrin, > Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. > With regards > Hussain MR > PACER-HD, KAU, KSA From gtzotzos at me.com Thu Apr 10 11:14:06 2014 From: gtzotzos at me.com (George Tzotzos) Date: Thu, 10 Apr 2014 15:14:06 -0300 Subject: [Chimera-users] Structure editing: addH Message-ID: <809A298A-C860-4402-B4D1-66C6A0AA3863@me.com> Hi everybody, I?ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. I?m attaching the ligand.pdb for easy reference. I?d appreciate any suggestions regarding this behavior Best regards George -------------- next part -------------- A non-text attachment was scrubbed... Name: docking.result_6_2.pdb Type: application/octet-stream Size: 714 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Apr 10 13:40:56 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 10 Apr 2014 13:40:56 -0700 Subject: [Chimera-users] Structure editing: addH In-Reply-To: <809A298A-C860-4402-B4D1-66C6A0AA3863@me.com> References: <809A298A-C860-4402-B4D1-66C6A0AA3863@me.com> Message-ID: Hi George, Chimera tries to make the protonation reasonable for near-neutral pH, so in general carboxylates would not be protonated. However, if you want to force protonation of such groups, it can be done by changing the atom type of one of the oxygens first. Choosing menu item "Actions? Labels? IDATM Type" shows the atom types, which are described here: Type "O2-" is not going to get protonated. You could change one of the carboxylate oxygens to type O3, which would be protonated. For example, select (Ctrl-click) the oxygen you want to become protonated, then change the type with command: setattr a idatmType O3 sel (you would have to re-label for the label to change, but the type has changed)? then add hydrogens. Having one oxygen with type O3 and the other with type O2- is inconsistent, so you could change the other to type O2, but it isn't necessary if all you care about is the protonation state. Another possibility is to just get this compound from Pub3D, which already has carboxyl groups protonated, e.g. with the Chimera command: open pubchem:543977 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 Apr 10, 2014, at 11:14 AM, George Tzotzos wrote: > Hi everybody, > I?ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. > I?m attaching the ligand.pdb for easy reference. > I?d appreciate any suggestions regarding this behavior > Best regards > George From wagner at mail.sysu.edu.cn Thu Apr 10 19:27:38 2014 From: wagner at mail.sysu.edu.cn (Christian Wagner) Date: Fri, 11 Apr 2014 10:27:38 +0800 (CST) Subject: [Chimera-users] Structure editing: addH In-Reply-To: Message-ID: <1126615985.3605211.1397183258059.JavaMail.root@mail.sysu.edu.cn> Hi George, You could also try using Avogadro, which allows protonation according to a user defined pH: http://avogadro.cc/wiki/Main_Page Best regards, Chris Wagner ----- Original Message ----- > From: "Elaine Meng" > To: "George Tzotzos" > Cc: "chimera-users at cgl.ucsf.edu BB" > Sent: Friday, April 11, 2014 4:40:56 AM > Subject: Re: [Chimera-users] Structure editing: addH > Hi George, > Chimera tries to make the protonation reasonable for near-neutral pH, > so in general carboxylates would not be protonated. However, if you > want to force protonation of such groups, it can be done by changing > the atom type of one of the oxygens first. > Choosing menu item "Actions? Labels? IDATM Type" shows the atom > types, which are described here: > > Type "O2-" is not going to get protonated. You could change one of > the carboxylate oxygens to type O3, which would be protonated. For > example, select (Ctrl-click) the oxygen you want to become > protonated, then change the type with command: > setattr a idatmType O3 sel > > (you would have to re-label for the label to change, but the type has > changed)? then add hydrogens. Having one oxygen with type O3 and the > other with type O2- is inconsistent, so you could change the other > to type O2, but it isn't necessary if all you care about is the > protonation state. > Another possibility is to just get this compound from Pub3D, which > already has carboxyl groups protonated, e.g. with the Chimera > command: > open pubchem:543977 > > 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 Apr 10, 2014, at 11:14 AM, George Tzotzos wrote: > > Hi everybody, > > I?ve been trying to add hydrogens to a ligand (7-octenoic acid) > > obtained from docking. Hydrogens are added but not on the carboxyl > > group. > > I?m attaching the ligand.pdb for easy reference. > > I?d appreciate any suggestions regarding this behavior > > Best regards > > George > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From aabisoye-ogunniyan4879 at mytu.tuskegee.edu Tue Apr 15 14:34:24 2014 From: aabisoye-ogunniyan4879 at mytu.tuskegee.edu (Ogunniyan, Abisola) Date: Tue, 15 Apr 2014 16:34:24 -0500 Subject: [Chimera-users] Relevant interacting amino acids between molecules Message-ID: Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 15 15:28:01 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 15 Apr 2014 15:28:01 -0700 Subject: [Chimera-users] Relevant interacting amino acids between molecules In-Reply-To: References: Message-ID: <03AD021F-7A39-4DFE-A2ED-05D4069C44CD@cgl.ucsf.edu> Dear Abisola, You can use the "Find Clashes/Contacts" tool or just a simple distance cutoff to find all the amino acid residues in one protein that are close to another molecule, which could be a small ligand, or another protein, DNA, etc. There is an example of using "FindHBond" and "Find Clashes/Contacts" to identify amino acids interacting with a ligand molecule in the "Structure Analysis and Comparison" tutorial: It would be very similar to find the H-bonds and contacts between amino acids and some other kind of molecule (such as another protein), you would just need to select that other molecule instead of the ligand molecule. I think it will be clearer if you try that tutorial. Or, for simple cutoff you can first select one molecule and then use menu: Select... Zone to also select the nearby residues. Once they are selected, you can do other stuff with the Actions menu like labeling them, or getting a list of them as in the tutorial mentioned above. How to select: There is a more advanced example of using findclash (the command version of Find Clashes/Contacts) to color the atoms involved in a protein-protein interaction in the "Opened Interface" image tutorial: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote: > Hi, > My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. > I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. > Please, I will really appreciate it if this is made clearer to me. > Thank You. > Best Regards, > Abisola Abisoye-Ogunniyan. From aabisoye-ogunniyan4879 at mytu.tuskegee.edu Tue Apr 15 18:04:00 2014 From: aabisoye-ogunniyan4879 at mytu.tuskegee.edu (Ogunniyan, Abisola) Date: Tue, 15 Apr 2014 20:04:00 -0500 Subject: [Chimera-users] Relevant interacting amino acids between molecules In-Reply-To: <03AD021F-7A39-4DFE-A2ED-05D4069C44CD@cgl.ucsf.edu> References: <03AD021F-7A39-4DFE-A2ED-05D4069C44CD@cgl.ucsf.edu> Message-ID: Dear Elaine, Thank you for the prompt response. I will go through the tutorials and I am sure it will be of great help. Thank you. Best Regards, Abisola Abisoye-Ogunniyan On Tue, Apr 15, 2014 at 5:28 PM, Elaine Meng wrote: > Dear Abisola, > You can use the "Find Clashes/Contacts" tool or just a simple distance > cutoff to find all the amino acid residues in one protein that are close to > another molecule, which could be a small ligand, or another protein, DNA, > etc. > > There is an example of using "FindHBond" and "Find Clashes/Contacts" to > identify amino acids interacting with a ligand molecule in the "Structure > Analysis and Comparison" tutorial: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html > > > > It would be very similar to find the H-bonds and contacts between amino > acids and some other kind of molecule (such as another protein), you would > just need to select that other molecule instead of the ligand molecule. I > think it will be clearer if you try that tutorial. > > Or, for simple cutoff you can first select one molecule and then use menu: > Select... Zone to also select the nearby residues. Once they are selected, > you can do other stuff with the Actions menu like labeling them, or getting > a list of them as in the tutorial mentioned above. How to select: > > > There is a more advanced example of using findclash (the command version > of Find Clashes/Contacts) to color the atoms involved in a protein-protein > interaction in the "Opened Interface" image tutorial: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote: > > > Hi, > > My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate > student in Tuskegee University. I got to learn about the use of Chimera in > my Biochemistry Class. > > I have been having difficulty in trying to determine the relevant > interacting amino acids between molecules. > > Please, I will really appreciate it if this is made clearer to me. > > Thank You. > > Best Regards, > > Abisola Abisoye-Ogunniyan. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From njosyu2 at uic.edu Tue Apr 15 19:29:32 2014 From: njosyu2 at uic.edu (Navya Shilpa Josyula) Date: Tue, 15 Apr 2014 21:29:32 -0500 Subject: [Chimera-users] Working with several proteins Message-ID: Hi, I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following 1. atomic areaSAS 2. atomic B-factor values 3. CASTp identified pocket residues and 4. CASTp identified pocket volumes for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. Thank you in advance for your help. Regards, Navya -------------- next part -------------- An HTML attachment was scrubbed... URL: From garg.80 at buckeyemail.osu.edu Tue Apr 15 22:22:07 2014 From: garg.80 at buckeyemail.osu.edu (Garg, Ayush A.) Date: Wed, 16 Apr 2014 05:22:07 +0000 Subject: [Chimera-users] Doubts regarding building a structure using Build Structure option Message-ID: <11b065375c36425fbbdc4108a8304c69@BY2PR01MB441.prod.exchangelabs.com> Dear Developer I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. Thank and Regards Ayush Arpit Garg Graduate Student Ohio State University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: detailed query.doc Type: application/msword Size: 390144 bytes Desc: detailed query.doc URL: From meng at cgl.ucsf.edu Wed Apr 16 15:16:07 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 16 Apr 2014 15:16:07 -0700 Subject: [Chimera-users] Working with several proteins In-Reply-To: References: Message-ID: Dear Navya, This would require Python programming because not all of these tasks can be done with Chimera commands. See the Chimera programmer's guide: You did not say if your structures are from the PDB database or whether you generated them somehow (for example, from a simulation). If they are in the PDB database, it is possible they are also in the CASTp database, in which case you could open each with a Chimera command something like: open castp:2gbp CASTp finds a lot of pockets for one structure, and each pocket would have a separate volume value and list of residues. If the structures are not in the CASTp database, you would have to upload them individually for a calculation at the CASTp web server, and this cannot be done from inside Chimera. After you got the CASTp results by email, you could open them in Chimera. Even if the structure is already in CASTp, it might just be better to get the CASTp results files directly from their website and not use Chimera. If showing CASTp results in Chimera, you would then have to use python to write out the desired information to a file anyway. CASTp search at their website: CASTp upload for new structure calculation: For bfactor, again you can just get the values directly from the text of the PDB files, no need to go through Chimera. Just like for CASTp, it may be simpler to write your own scripts to get the values from these files. Back to Chimera: To calculate areaSAS you have to show the surface (for example, command: surface). Attribute values can be written out to a file using the File menu of the Render by Attribute tool (in menu under Tools? Depiction), ...but again to process many structures instead of using the GUI, you would have to use python scripting because there isn't a command. There is a similar script attached to this previous post (get the writeAttr.py attachment using the URL near the bottom, unfortunately it will be named attachment.bin but it is really a text file containing the script): 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 Apr 15, 2014, at 7:29 PM, Navya Shilpa Josyula wrote: > Hi, > > I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following > ? atomic areaSAS > ? atomic B-factor values > ? CASTp identified pocket residues and > ? CASTp identified pocket volumes > for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. > > Thank you in advance for your help. > Regards, > Navya From meng at cgl.ucsf.edu Wed Apr 16 15:32:48 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 16 Apr 2014 15:32:48 -0700 Subject: [Chimera-users] Doubts regarding building a structure using Build Structure option In-Reply-To: <11b065375c36425fbbdc4108a8304c69@BY2PR01MB441.prod.exchangelabs.com> References: <11b065375c36425fbbdc4108a8304c69@BY2PR01MB441.prod.exchangelabs.com> Message-ID: <3D21EB3E-093C-419E-AEB1-337BFA389709@cgl.ucsf.edu> Hi Ayush, The main question is "why would you want to do this??!" Build Structure is not meant for such a task, and there is no reason to regenerate a structure that you can already get from the Protein Databank. In my opinion it would be extremely difficult, if not impossible, to do this. To create exactly the same structure with building in Chimera, you would have to know ALL of the bond lengths, bond angles, and torsional angles of the original protein, and then set them painstakingly. You would have to measure each of those things in the original structure. Then in the copy, you couldn't just set the entire secondary structure phi/psi angles to the suggested values, either. Instead you would have to enter exactly the phi and psi measured for each residue in the original structure for the corresponding residue in the new structure. Even that would only be a tiny starting point, because you would still have to adjust all the sidechain torsion angles, and every single bond length and bond angle as well. Build Structure does allow creating peptides of defined sequence and changing torsion angles, bond lengths, and bond angles to exactly the values you specify. Thus it should be possible in principle, but I think infeasible in practice, even if using commands where available (adjust, rotation). So my best advice is "don't even try it!" 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 Apr 15, 2014, at 10:22 PM, "Garg, Ayush A." wrote: > Dear Developer > > I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. > > Thank and Regards > Ayush Arpit Garg > Graduate Student > Ohio State University From klexa at umich.edu Wed Apr 16 17:58:20 2014 From: klexa at umich.edu (Katrina Lexa) Date: Wed, 16 Apr 2014 17:58:20 -0700 Subject: [Chimera-users] call file-> open gui popup from script ? Message-ID: Hello All, I?m wondering if there is a way to call the file->open popup within chimera when running a python script? I know that it?s possible to run the script on the command line and read the desired arguments in that way, and obviously the files I want could be coded in and then changed every time I want to look at something new, but I?m not seeing an obvious option from the mailing list or in the runCommand list for writing in a mid-script call for the user to select a file. Is such a thing possible? Thanks for your help, --? Katrina? -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Thu Apr 17 08:54:07 2014 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Thu, 17 Apr 2014 08:54:07 -0700 Subject: [Chimera-users] call file-> open gui popup from script ? In-Reply-To: References: Message-ID: <534FF91F.2020107@cgl.ucsf.edu> You can use the "open" command with no arguments to pop up the open dialog. Chimera should wait until you select a file (or cancel) before continuing to the next command (either on the same line or the next line in a script). Conrad On 4/16/2014 5:58 PM, Katrina Lexa wrote: > Hello All, > > I?m wondering if there is a way to call the file->open popup within > chimera when running a python script? I know that it?s possible to run > the script on the command line and read the desired arguments in that > way, and obviously the files I want could be coded in and then changed > every time I want to look at something new, but I?m not seeing an > obvious option from the mailing list or in the runCommand list for > writing in a mid-script call for the user to select a file. Is such a > thing possible? > > Thanks for your help, > -- > Katrina > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From pett at cgl.ucsf.edu Thu Apr 17 10:41:16 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 17 Apr 2014 10:41:16 -0700 Subject: [Chimera-users] call file-> open gui popup from script ? In-Reply-To: <534FF91F.2020107@cgl.ucsf.edu> References: <534FF91F.2020107@cgl.ucsf.edu> Message-ID: If the file is something that your script needs to read itself (a list of residue IDs or something) then instead of the "open" command you would do this to get the file path: from OpenSave import OpenModal from chimera.tkgui import app pathsAndTypes = OpenModal(title="Input for script").run(app) 'pathsAndTypes' is a list of 2-tuples. The 2-tuples are the path and file type. So assuming you only want one file, you would get the file path with: path = pathsAndTypes[0][0] --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 17, 2014, at 8:54 AM, Conrad Huang wrote: > You can use the "open" command with no arguments to pop up the open dialog. Chimera should wait until you select a file (or cancel) before continuing to the next command (either on the same line or the next line in a script). > > Conrad > > On 4/16/2014 5:58 PM, Katrina Lexa wrote: >> Hello All, >> >> I?m wondering if there is a way to call the file->open popup within >> chimera when running a python script? I know that it?s possible to run >> the script on the command line and read the desired arguments in that >> way, and obviously the files I want could be coded in and then changed >> every time I want to look at something new, but I?m not seeing an >> obvious option from the mailing list or in the runCommand list for >> writing in a mid-script call for the user to select a file. Is such a >> thing possible? >> >> Thanks for your help, >> -- >> Katrina >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From klexa at umich.edu Thu Apr 17 11:24:34 2014 From: klexa at umich.edu (Katrina Lexa) Date: Thu, 17 Apr 2014 11:24:34 -0700 Subject: [Chimera-users] call file-> open gui popup from script ? In-Reply-To: References: <534FF91F.2020107@cgl.ucsf.edu> Message-ID: Terrific! Thanks Eric and Conrad. On April 17, 2014 at 10:41:21 AM, Eric Pettersen (pett at cgl.ucsf.edu) wrote: If the file is something that your script needs to read itself (a list of residue IDs or something) then instead of the "open" command you would do this to get the file path: from OpenSave import OpenModal from chimera.tkgui import app pathsAndTypes = OpenModal(title="Input for script").run(app) 'pathsAndTypes' is a list of 2-tuples. The 2-tuples are the path and file type. So assuming you only want one file, you would get the file path with: path = pathsAndTypes[0][0] --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 17, 2014, at 8:54 AM, Conrad Huang wrote: > You can use the "open" command with no arguments to pop up the open dialog. Chimera should wait until you select a file (or cancel) before continuing to the next command (either on the same line or the next line in a script). > > Conrad > > On 4/16/2014 5:58 PM, Katrina Lexa wrote: >> Hello All, >> >> I?m wondering if there is a way to call the file->open popup within >> chimera when running a python script? I know that it?s possible to run >> the script on the command line and read the desired arguments in that >> way, and obviously the files I want could be coded in and then changed >> every time I want to look at something new, but I?m not seeing an >> obvious option from the mailing list or in the runCommand list for >> writing in a mid-script call for the user to select a file. Is such a >> thing possible? >> >> Thanks for your help, >> -- >> Katrina >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From adenaike at sas.upenn.edu Wed Apr 16 23:15:46 2014 From: adenaike at sas.upenn.edu (Moses Adenaike) Date: Thu, 17 Apr 2014 02:15:46 -0400 Subject: [Chimera-users] morphs Message-ID: Hello Chimera users, Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. Moses -------------- next part -------------- An HTML attachment was scrubbed... URL: From prasanth.311994 at gmail.com Thu Apr 17 04:32:09 2014 From: prasanth.311994 at gmail.com (Prasanth Kumar) Date: Thu, 17 Apr 2014 17:02:09 +0530 Subject: [Chimera-users] Chimera-crashing-ubuntu Message-ID: Dear Sir/Madam, I have been using chimera for past 3 months. In the past two days, when i load my saved sessions (.py files), chimera is getting hanged and my ubuntu 12.04 OS is also getting hanged. So please help me on how to fix the problem. Chimera has been a really useful tool in my research. Waiting for your reply. Thank you, Yours Truly, *PRASANTH*, Undergraduate Department, Indian Institute of Science, Bangalore-560012. Contact:- prasanth.311994 at gmail.com, prasanth at ug.iisc.in. -------------- next part -------------- An HTML attachment was scrubbed... URL: From geirrseach at gmail.com Thu Apr 17 11:19:51 2014 From: geirrseach at gmail.com (Rebecca Swett) Date: Thu, 17 Apr 2014 14:19:51 -0400 Subject: [Chimera-users] Rendering into 3d Message-ID: Hey All, I'm looking at rendering some movies output from chimera as a 3d movie for viewing with nvidia 3d vision pro glasses. From everything I've read as long as the left/right eye frames are sequential, making the movie with ffmpeg should work fine. The problem I'm having is that ffmpeg has no way to alternate between 0-left.ppm 0-right.ppm 1-left.ppm 1-right.ppm, which is how chimera saves images when recording movies in stereo mode. If those same images were named 1.ppm 2.ppm 3.ppm 4.ppm, there would be no problem. Is there a quick fix that can be inserted to change the naming of the recorded frames? Any other suggestions? Rebecca Swett -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Apr 17 15:06:51 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Apr 2014 15:06:51 -0700 Subject: [Chimera-users] morphs In-Reply-To: References: Message-ID: <0A527B8D-E7AD-42BC-8438-BE8DA2908DED@cgl.ucsf.edu> Hello Moses, It is not necessary to have the same number of atoms (or residues), the method takes care of that. You can even morph between different but related proteins as long as their sequences are similar enough to align easily. However, the models *must* have the same number of chains. You can still display the "extra" chain(s) by simply opening an additional copy of the structure that has more chains. More specifically, in the case you mentioned: (1) open structure of enzyme (2) open structure of enzyme+DNA as another model, but delete the DNA part so that these first two models will have the same number of chains (3) use those first two models for morphing (4) open another copy of the structure of enzyme+DNA, use to display DNA (can hide or delete the rest) You can script making the DNA appear at a specific frame in playback of the morph trajectory or fade in gradually (see MD Movie per-frame scripting or "coordset","transparency" commands). 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 Apr 16, 2014, at 11:15 PM, Moses Adenaike wrote: > Hello Chimera users, > Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. > Moses From goddard at sonic.net Thu Apr 17 17:51:58 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 17 Apr 2014 17:51:58 -0700 Subject: [Chimera-users] Rendering into 3d In-Reply-To: References: Message-ID: <55F36EE9-9E40-4704-904E-A03E7F693DF1@sonic.net> Hi Rebecca, I didn?t even know Chimera wrote out two image files when you save an image in stereo mode. The way I have made stereo movies is by recording a left-eye movie (there is a Chimera "stereo left eye? camera mode) and then recording a right eye movie. Then I hand the two movie files to a stereo player, I use Bino, and it does the job. I have not made single file stereo movies. The typical formats for that use a single large frame with the left (or right) image stacked above the right (or left) image, called top/bottom stereo, and there is a blank band between the two images. Another stereo format uses side-by-side images in a single frame. Both these formats require meta-data in the movie file to say that it is a stereo format, and at least a few months ago ffmpeg discussions suggestions said that ffmpeg could not do that. I have not heard of a player that uses a left image then a right image sequentially, although I would not be surprised if some player can do that. Which player are you using? There is a serious problem with that format in that movie formats do compression based on each image differing little from the previous image. By alternating left and right eye images you are going to make the compression work horribly ? it will need a very high bit rate or the artifacts will be ugly. If you still want to renumber the Chimera movie images I think the easiest way is to write some script to rename your files. Chimera is putting the frame number in the image file names and the frame number is the same for left and right eye images. It would be as complicated in Chimera to renumber these images as it is in a separate script. Since I don?t think it serves most Chimera users I suggest you use a script. Tom On Apr 17, 2014, at 11:19 AM, Rebecca Swett wrote: > Hey All, > I'm looking at rendering some movies output from chimera as a 3d movie for viewing with nvidia 3d vision pro glasses. From everything I've read as long as the left/right eye frames are sequential, making the movie with ffmpeg should work fine. The problem I'm having is that ffmpeg has no way to alternate between 0-left.ppm 0-right.ppm 1-left.ppm 1-right.ppm, which is how chimera saves images when recording movies in stereo mode. If those same images were named 1.ppm 2.ppm 3.ppm 4.ppm, there would be no problem. Is there a quick fix that can be inserted to change the naming of the recorded frames? Any other suggestions? > > Rebecca Swett > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Thu Apr 17 18:01:19 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 17 Apr 2014 18:01:19 -0700 Subject: [Chimera-users] Chimera-crashing-ubuntu In-Reply-To: References: Message-ID: <9153E24C-DA6B-41C8-B09B-F39BFB65030C@sonic.net> Chimera and Linux hanging very likely is because of a graphics driver bug. Probably your Ubuntu 12.04 graphics driver got updated a few days ago. The solution is to install a working graphics driver. Greg Couch in our lab might have a recommendation about which driver will work. He would probably need to know your graphics card (Nvidia? AMD? Intel?) Tom On Apr 17, 2014, at 4:32 AM, Prasanth Kumar wrote: > Dear Sir/Madam, > I have been using chimera for past 3 months. In the past two days, when i load my saved sessions (.py files), chimera is getting hanged and my ubuntu 12.04 OS is also getting hanged. > > So please help me on how to fix the problem. Chimera has been a really useful tool in my research. > > Waiting for your reply. > > Thank you, > Yours Truly, > PRASANTH, > Undergraduate Department, > Indian Institute of Science, > Bangalore-560012. > Contact:- prasanth.311994 at gmail.com, > prasanth at ug.iisc.in. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtzotzos at me.com Fri Apr 18 04:28:19 2014 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 18 Apr 2014 08:28:19 -0300 Subject: [Chimera-users] Structure editing: add charge In-Reply-To: References: Message-ID: In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same. Apologies for bothering you with this question. A good weekend to you all George On Apr 18, 2014, at 8:03 AM, George Tzotzos wrote: > Hi everybody, > > I?m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. > Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. > > Is there a way to force the charge on the ligand to be +1.000? > > Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). > > Regards > > George > From gtzotzos at me.com Fri Apr 18 04:03:19 2014 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 18 Apr 2014 08:03:19 -0300 Subject: [Chimera-users] Structure editing: add charge Message-ID: Hi everybody, I?m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. Is there a way to force the charge on the ligand to be +1.000? Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). Regards George From meng at cgl.ucsf.edu Fri Apr 18 10:05:30 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Apr 2014 10:05:30 -0700 Subject: [Chimera-users] Structure editing: add charge In-Reply-To: References: Message-ID: <5B9D0DA8-DA32-48E9-AB71-423127D01D06@cgl.ucsf.edu> Hi George, The calculation of charges for nonstandard residues is done by the Antechamber package included with Chimera, rather than Chimera directly. I'm guessing that small (e.g. 0.001) deviations from integer total charges are fairly common and are caused by rounding of the per-atom values. I don't know of any way to prevent that (maybe the amber list people would have comments?), but once you see the total you can manually edit the charges, either in the output file (as you did) or directly in Chimera with the "setattr" command. You would still have to decide which charges to adjust and how much to adjust them yourself, however, so I'm not sure if you would consider changing them in Chimera to be more intelligent. It might be easier just to edit the output file. Nevertheless, an example with neutral octenoic acid fetched from Pub3D. Commands: open pubchem:543977 addcharge ... this reports net charge 0.001. So I show the charge values as labels and can change one or more, for example: labelopt info charge label setattr a charge -.488 @o1 label But now I wonder why your octenoic acid charge was close to 1. Shouldn't it be close to -1, or 0 if you are using the protonated form? Sorry I don't have a better answer about enforcing integral charge. Wishing you a good weekend too, 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 Apr 18, 2014, at 4:28 AM, George Tzotzos wrote: > In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same. > > Apologies for bothering you with this question. > > A good weekend to you all > > George > > On Apr 18, 2014, at 8:03 AM, George Tzotzos wrote: > >> Hi everybody, >> >> I?m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. >> Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. >> >> Is there a way to force the charge on the ligand to be +1.000? >> >> Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). >> >> Regards >> George From gtzotzos at me.com Fri Apr 18 11:13:08 2014 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 18 Apr 2014 15:13:08 -0300 Subject: [Chimera-users] Structure editing: add charge In-Reply-To: <5B9D0DA8-DA32-48E9-AB71-423127D01D06@cgl.ucsf.edu> References: <5B9D0DA8-DA32-48E9-AB71-423127D01D06@cgl.ucsf.edu> Message-ID: <79E98A16-8FF7-4542-8982-101F7A81B87A@me.com> Hi Elaine, Thank you for the suggestion. I was not aware of the label opt / selattr options. The charge of the octenoic acid was - 0.999, not +. My mistake and apologies for this. Best wishes George On Apr 18, 2014, at 2:05 PM, Elaine Meng wrote: > Hi George, > The calculation of charges for nonstandard residues is done by the Antechamber package included with Chimera, rather than Chimera directly. I'm guessing that small (e.g. 0.001) deviations from integer total charges are fairly common and are caused by rounding of the per-atom values. > > > I don't know of any way to prevent that (maybe the amber list people would have comments?), but once you see the total you can manually edit the charges, either in the output file (as you did) or directly in Chimera with the "setattr" command. You would still have to decide which charges to adjust and how much to adjust them yourself, however, so I'm not sure if you would consider changing them in Chimera to be more intelligent. It might be easier just to edit the output file. > > Nevertheless, an example with neutral octenoic acid fetched from Pub3D. Commands: > > open pubchem:543977 > addcharge > > ... this reports net charge 0.001. So I show the charge values as labels and can change one or more, for example: > > labelopt info charge > label > setattr a charge -.488 @o1 > label > > But now I wonder why your octenoic acid charge was close to 1. Shouldn't it be close to -1, or 0 if you are using the protonated form? > > Sorry I don't have a better answer about enforcing integral charge. Wishing you a good weekend too, > 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 Apr 18, 2014, at 4:28 AM, George Tzotzos wrote: > >> In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same. >> >> Apologies for bothering you with this question. >> >> A good weekend to you all >> >> George >> >> On Apr 18, 2014, at 8:03 AM, George Tzotzos wrote: >> >>> Hi everybody, >>> >>> I?m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. >>> Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. >>> >>> Is there a way to force the charge on the ligand to be +1.000? >>> >>> Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). >>> >>> Regards >>> George > From ashok9869 at gmail.com Sun Apr 20 12:10:28 2014 From: ashok9869 at gmail.com (ashok rout) Date: Sun, 20 Apr 2014 12:10:28 -0700 Subject: [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix) Message-ID: Hi, I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer. Regards, Ashok -- thanks & regards, Ashok -------------- next part -------------- An HTML attachment was scrubbed... URL: From Anshul.Bhardwaj at jefferson.edu Sun Apr 20 20:43:23 2014 From: Anshul.Bhardwaj at jefferson.edu (Anshul Bhardwaj) Date: Mon, 21 Apr 2014 03:43:23 +0000 Subject: [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix) In-Reply-To: References: Message-ID: <4fa4e6e0d0cf4d4fb7ffb5b46591bdcd@BY2PR05MB693.namprd05.prod.outlook.com> Hi Ashok, Chimera experts may be able to explain you how to calculate coiled-coil radius in the Chimera, nonetheless, for our purposes we have recently used the program TWISTER (Strelkov, S. V. & Burkhard, P. (2002). J. Struct. Biol. 137, 54?64.) that analyzes various coiled-coil parameters including coiled-coil radius from the pdb coordinate file. You may want to give it a try, it is very easy to use. We summarized our results in the form of table that you can find in the published article Bhardwaj, A., Casjens, SR., Cingolani, G. Exploring the atomic structure and conformational flexibility of a 320?? long engineered viral fiber using X-ray crystallography (2014) Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):342-53. You can request the program TWISTER from Sergei V. Strelkov, sergei.strelkov at pharm.kuleuven.be From TWISTER documentation; Program TWISTER (2006 version) AUTHOR Sergei V. Strelkov e-mail: sergei.strelkov at pharm.kuleuven.be PURPOSE The program TWISTER is designed to analyse the local geometry of coiled-coil (cc) structures. With the three-dimensional coordinates on input, TWISTER first traces the alpha-helical axes and then the cc axis. Thereafter the local cc parameters are determined as a function of residue number. In addition, heptad positions are assigned based on structural criteria. The current version of the program is designed to analyse parallel coiled coils with residue numbering in different chains being in register; however, see a note on antiparallel / out-of-register coiled coils below. REFERENCE Strelkov, S.V., and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137, 54-64. Please consult this publication for full description of program function and definitions. DISTRIBUTION The program executables can be obtained from the author on request. The program is written in standard C programming language. SUPPORTED PLATFORMS 1. Linux: Use the executable tw2006_linux_exe. 2. Windows: You must install the free unix emulator cygwin (www.cygwin.com) first. Make sure that you have installed the tcsh shell (available in cygwin but not installed by default). Then use the tw2006_cygwin_exe. 3. OSX: The current executable tw2006_osx_exe is outdated and will only run under older versions of OSX. 4. SGI IRIX: Use tw2006_sgi_exe. USAGE Please use a short shell script (see twister_example.sh) to run the program, as running the program directly from command line may not work on all platforms. A sample output from this script with the GCN4 zipper trimer is provided in subdirectory /example. Please edit this example script according to your needs. Input is a standard PDB format coordinate file. It is sufficient to input the C-alpha coordinates only. Within the shell script, the user has to specify which part of the structure to analyse (e.g. residues 101 to 151 of chains A, B and C if these form a triple-stranded coiled coil). There are two output files. The first one is a log file that contains a table of geometrical parameters versus residue number. In addition, average values of each parameter over all residues and their standard deviations are output. The log file can be piped into the program XLOGGRAPH which is part of the CCP4 package to produce plots from the tables. Alternatively, any other graphing software can be used. The second output file includes the coordinates of all alpha-helix axes and of the cc axis. The axes appear as polypeptide chains containing C-alpha atoms only and can be visualised with any biomolecular graphics software such as RASMOL or PyMol. DESCRIPTION OF THE LOG FILE 1. Sequence and heptad assignment TWISTER assigns the heptad positions on the basis of the structure. First the a and d positions are assigned based on their proximity to the cc axis. The residues for which the heptad position could not be assigned are labelled 'z'. 2. Coiled-coil parameters These are tabulated for every residue with the exception of the N- and C-terminal residues. CC_PHASE: cc phase in degrees relative to zero phase at the first residue. CC_RAD: local cc radius in A. CC_RISE: cc rise per residue (measured along the cc axis). CC_PIT: local cc pitch calculated as 2Pi*CC_RIS/CC_DANG. If the local cc geometry is right-handed, the pitch value is followed by a letter 'R'. CC_DANG: increment of the cc phase per residue. This is negative for a left-handed geometry and positive for a right-handed one. POS: heptad position. CR_ANG: the angle (first introduced by F. Crick) which defines the phase of the Calpha atom relative to the cc axis. A_RAD: alpha-helical radius. A_RIS: alpha-helical rise. RES/TUR: number of residues per one alpha-helical turn. A_DANG: increment of the alpha-helical phase per residue. AXIS_CUR: curvature of the alpha-helical axis in 1/A. 3. Crick angles for residues in a and d positions. 4. A table for XLOGGRAPH. A NOTE ON ANTIPARALLEL AND OUT-OF-REGISTER COILED COILS The current version of the program is designed to work on parallel coiled coils with residue numbering in all chains being in register. However, both these limitations can be overcome by renumbering the side chains manually so that to bring them into register. In an antiparallel structure, this would require inverting some chain(s). Here is an example. Suppose you want to analyse a two- stranded antiparallel coiled coil consisting of residues A1 to A20 (downward chain) and B51 to B70(upward chain), with residues A1 and B70 being in register. Then you have to renumber chain B so that residue B70 becomes B1, B69 becomes B2 etc. (renumbering Calphas suffices). Thereafter run TWISTER as follows: ~/myprogs/twister/twister << eof > $log $title $infile $outfile 1 20 A B eof The sequence will be read from the first chain listed, in this case chain A. BUGS AND FURTHER DEVELOPMENT Please report bugs and send your comments and suggestions to sergei.strelkov at pharm.kuleuven.be Hope this helps! Best, Anshul Bhardwaj Anshul Bhardwaj, Ph.D. Faculty, Department of Biochemistry and Molecular Biology Manager, Kimmel Cancer Center X-ray Crystallography and Molecular Interactions Thomas Jefferson University 233 South 10th Street, BLSB suite 822 Philadelphia, PA 19107 Tel: (215) 503-4587 Anshul.Bhardwaj at Jefferson.edu http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm ________________________________ From: chimera-users-bounces at cgl.ucsf.edu on behalf of ashok rout Sent: Sunday, April 20, 2014 3:10 PM To: chimera-users at cgl.ucsf.edu Mailing List Subject: [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix) Hi, I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer. Regards, Ashok -- thanks & regards, Ashok The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Apr 21 09:03:50 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 21 Apr 2014 09:03:50 -0700 Subject: [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix) In-Reply-To: References: Message-ID: <74A06841-7F45-4706-AEA5-D804C6E39E08@cgl.ucsf.edu> Hi Ashok, It depends on how "core diameter" is defined. I searched for "coiled-coil" together with "core diameter" and found it once in a 2004 paper, but no specific definition was given. It was probably meant as a general description rather than a specific measurement, i.e. several different measurements would show the general property of an expanded core: you would just need to apply the same measurement to different trimer structures in order to compare them. In Chimera, possibilities are to (a) measure any atom-atom distance, for example between an alpha-carbon in one helix and the closest alpha-carbon in another helix. For example, Ctrl-click to select one atom, Shift-Ctrl-doubleclick to select the second atom and choose "show distance" from the resulting context menu. (b) use Axes/Planes/Centroids (in menu under Tools? Structure Analysis) to calculate a separate axis for each helix based on its backbone atoms and then measure pairwise axis-axis distance. Each axis is shown as a cylinder. (c ) use Axes/Planes/Centroids to calculate one axis for all three helices together based on all their backbone atoms, with the option to set axis radius based on average axis-atom distance (diameter = 2x radius). For example: command: open 1coi command: sym Menu: Presets? interactive 2 (all atoms) command: select protein & @n,ca,c,o Menu: Tools? Structure Analysis? Axes/Planes/Centroids ? then choose to define axes. In the Define Axes dialog, choose the "selected atoms/centroids" option with "Replace existing axes" and "Radius: average axis-atom distance", Apply. Then see what radius is reported in the Structure Measurements table (in this case 6.9 Angstroms, so diameter measured in this way would be 13.8 angstroms). The third one sounds closest to what I think of as a diameter, but these are just guesses as how to to measure it. If you have some specific definition, use that instead. 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 Apr 20, 2014, at 12:10 PM, ashok rout wrote: > Hi, > I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer. > Regards, > Ashok From jiserte at unq.edu.ar Mon Apr 21 09:59:20 2014 From: jiserte at unq.edu.ar (jiserte at unq.edu.ar) Date: Mon, 21 Apr 2014 13:59:20 -0300 Subject: [Chimera-users] Problem with charges when writing mol2 file with a python script. Message-ID: <20140421135920.Horde.4KT8L9iM8SRJ1i1yZCh_eQ6@correo.unq.edu.ar> I'm trying to write a simple python script to open a mol2 file with a ligand, add hydrogens, add charges and write it into another mol2. The script is this: ----------------------------------------- import chimera???????????????????????????????????? #1 from chimera import runCommand???????????????????? #2 runCommand('open ligands/lig_in.mol2')?????? ? ? ? #3 runCommand('addh')???????????????????????????????? #4 runCommand('addcharge')??????????????????????????? #5 runCommand('write format mol2 #0 lig_out.mol2')??? #6 ------------------------------------------ The result mol2 file does no contain any charges. However, if a run another script that is exactly like this but does not contain the last line (#6),? and then execute the command 'write format mol2 #0 lig_out.mol2' manually, the mol2 file contains charges. I don't understand why there is a difference with both methods. best regards. javier -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Apr 21 13:46:05 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 21 Apr 2014 13:46:05 -0700 Subject: [Chimera-users] Problem with charges when writing mol2 file with a python script. In-Reply-To: <20140421135920.Horde.4KT8L9iM8SRJ1i1yZCh_eQ6@correo.unq.edu.ar> References: <20140421135920.Horde.4KT8L9iM8SRJ1i1yZCh_eQ6@correo.unq.edu.ar> Message-ID: Hi Javier, If you are running this script with the Chimera graphical interface showing (i.e. not by running Chimera from a shell command line with the '--nogui' flag), then what's happening is that you are getting the "formal charge confirmation" dialog but since it's not a modal dialog the rest of Chimera keeps running, including your script. So your log_out.mol2 file has already been written (with 0.0 charges for the ligand atoms) before you can even click the OK button on the dialog. So, to get the result you want you either have to run your script in nogui mode, or you have to call the Python addcharge code directly. Here's code that would do that: from AddCharge import initiateAddCharges initiateAddCharges(method='am1-bcc', nogui=True) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 21, 2014, at 9:59 AM, jiserte at unq.edu.ar wrote: > I'm trying to write a simple python script to open a mol2 file with a ligand, add hydrogens, add charges and write it into another mol2. > The script is this: > ----------------------------------------- > import chimera #1 > from chimera import runCommand #2 > runCommand('open ligands/lig_in.mol2') #3 > runCommand('addh') #4 > runCommand('addcharge') #5 > runCommand('write format mol2 #0 lig_out.mol2') #6 > ------------------------------------------ > The result mol2 file does no contain any charges. > However, if a run another script that is exactly like this but does not contain the last line (#6), and then > execute the command 'write format mol2 #0 lig_out.mol2' manually, the mol2 file contains charges. > I don't understand why there is a difference with both methods. > best regards. > javier > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Apr 21 14:55:57 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 21 Apr 2014 14:55:57 -0700 Subject: [Chimera-users] Structure editing: add charge In-Reply-To: <5B9D0DA8-DA32-48E9-AB71-423127D01D06@cgl.ucsf.edu> References: <5B9D0DA8-DA32-48E9-AB71-423127D01D06@cgl.ucsf.edu> Message-ID: <28F10905-4586-4BE1-83C3-A642FB1DCC56@cgl.ucsf.edu> On Apr 18, 2014, at 10:05 AM, Elaine Meng wrote: > The calculation of charges for nonstandard residues is done by the Antechamber package included with Chimera, rather than Chimera directly. I'm guessing that small (e.g. 0.001) deviations from integer total charges are fairly common and are caused by rounding of the per-atom values. Exactly. Chimera uses Antechamber by sending it a Mol2 file as input and reading its output, which is also a Mol2 file. The charges for the atoms in the Mol2 file are three decimal places and therefore due to roundoff their sum may be non-integral, differing in the third decimal place. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.sariya_work at ymail.com Mon Apr 21 20:38:48 2014 From: s.sariya_work at ymail.com (Sanjeev Sariya) Date: Mon, 21 Apr 2014 20:38:48 -0700 (PDT) Subject: [Chimera-users] read file by python script and color pdb file with script Message-ID: <1398137928.31475.YahooMailNeo@web163803.mail.gq1.yahoo.com> Hello Chimera team, I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. ??? rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. PS: I had sent the same mail to chimera-dev at cgl.ucsf.edu ; Sorry, I didn't find this mailing list before. -- Regards Sariya -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.sariya_work at ymail.com Mon Apr 21 20:41:21 2014 From: s.sariya_work at ymail.com (Sanjeev Sariya) Date: Mon, 21 Apr 2014 20:41:21 -0700 (PDT) Subject: [Chimera-users] read file by python script and color pdb file with script In-Reply-To: <1398137928.31475.YahooMailNeo@web163803.mail.gq1.yahoo.com> References: <1398137928.31475.YahooMailNeo@web163803.mail.gq1.yahoo.com> Message-ID: <1398138081.71431.YahooMailNeo@web163804.mail.gq1.yahoo.com> Attached files. -- Regards Sariya On Monday, April 21, 2014 11:38 PM, Sanjeev Sariya wrote: Hello Chimera team, I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. ??? rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. PS: I had sent the same mail to chimera-dev at cgl.ucsf.edu ; Sorry, I didn't find this mailing list before. -- Regards Sariya -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: check Type: application/octet-stream Size: 6 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Q6UXT6.pdb Type: application/octet-stream Size: 266255 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: y.py Type: application/octet-stream Size: 455 bytes Desc: not available URL: From pett at cgl.ucsf.edu Tue Apr 22 11:04:17 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 22 Apr 2014 11:04:17 -0700 Subject: [Chimera-users] [chimera-dev] read file by python script and color pdb file with script In-Reply-To: <1398137638.55774.YahooMailNeo@web163802.mail.gq1.yahoo.com> References: <1398137638.55774.YahooMailNeo@web163802.mail.gq1.yahoo.com> Message-ID: Hi Sariya, Your "check" file contains this (one) line: 67 23 which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya wrote: > > I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. > I have chimera in my ~/bin/ > System specs: ubuntu 64 bit, 13.10, 4gb ram > > Below is the command I have used for script-chimera communication > > $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb > > > I am storing values in listu and want to use them for coloring my file loaded. > > rc("color blue :"+listu[0]+"-"+listu[1]) > > This works well, if hard coded > rc ("color red :55-86") > > I do not get any error. The particular protein length is not colored. > > attached 3 files. > Kindly suggest, how do I proceed. > > > -- > Regards > Sariya > > _______________________________________________ > 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: From egbutac at upstate.edu Tue Apr 22 17:27:07 2014 From: egbutac at upstate.edu (Chinaza Egbuta) Date: Tue, 22 Apr 2014 20:27:07 -0400 Subject: [Chimera-users] Transparency of selected atoms Message-ID: Hi, Is there a way to change the transparency of selected atoms in a model? I am trying to visualize what is behind the plane of my model without using the surface capping function. Thanks! CE Chinaza Egbuta Ph.D. Candidate Department of Pharmacology & SUNY Upstate Cancer Research Institute SUNY Upstate Medical University Syracuse, NY 13210 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 23 10:14:53 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Apr 2014 10:14:53 -0700 Subject: [Chimera-users] Transparency of selected atoms In-Reply-To: References: Message-ID: Hi CE, Sure, you can do it with the "transparency" command (in Chimera 1.7 and newer), for example: transparency 65,a sel ... to make the selected atoms 65% transparent. For details and options, see: The "sel" means the selected atoms, but alternatively, you can specify the atoms directly instead of having to select them first: 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 Apr 22, 2014, at 5:27 PM, Chinaza Egbuta wrote: > Hi, > Is there a way to change the transparency of selected atoms in a model? I am trying to visualize what is behind the plane of my model without using the surface capping function. > Thanks! > CE > > Chinaza Egbuta > Ph.D. Candidate > Department of Pharmacology & > SUNY Upstate Cancer Research Institute > SUNY Upstate Medical University > Syracuse, NY 13210 From jiserte at unq.edu.ar Wed Apr 23 12:48:02 2014 From: jiserte at unq.edu.ar (jiserte at unq.edu.ar) Date: Wed, 23 Apr 2014 16:48:02 -0300 Subject: [Chimera-users] Export Pov-Ray file with a python script. Message-ID: <20140423164802.Horde.XwxsaNCfQetMv6TgnLitAQ1@correo.unq.edu.ar> I'm writing a small python script to generate Pov-Ray with chimera. The script loads a pdb file containing a protein and a ligand, modifies the protein view to ribbon and the ligand to surface. Then exports the .pov file. However the image created by Pov-Ray shows only the surface of ligand. The image is shown correctly in the chimera GUI. If I run the commands one by one in the chimera command line, the .pov file generated is ok. The script is: ----------------------------------------- import chimera from chimera import runCommand runCommand('windowsize 800 600') runCommand('open ../../kinase.domain.2/A.4K9Y.pdb') runCommand('ribbon #0') runCommand('surf ligand') runCommand('export test.pov') ------------------------------------------ After running the script the ReplyLog contains: ----------------------------------------- A.4K9Y.pdb opened /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on hamal Copyright M.F. Sanner (March 2000) Compilation flags Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 436.845 Total solvent accessible surface area = 772.871 ----------------------------------------- Javier Iserte From meng at cgl.ucsf.edu Wed Apr 23 13:02:18 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Apr 2014 13:02:18 -0700 Subject: [Chimera-users] Export Pov-Ray file with a python script. In-Reply-To: <20140423164802.Horde.XwxsaNCfQetMv6TgnLitAQ1@correo.unq.edu.ar> References: <20140423164802.Horde.XwxsaNCfQetMv6TgnLitAQ1@correo.unq.edu.ar> Message-ID: <69CDA6F2-8806-4B00-AFBB-DD7CACEA8695@cgl.ucsf.edu> Hi Javier, I don't have an answer for your specific issue, but while others look at that, a few thoughts... You might also want to hide any atoms/bonds that are displayed (e.g. command: ~disp #0 ). Personally, I have better success making nice images directly in Chimera than via its export to raytracing option. If the main reason you're doing it is to get shadows and/or smoother-looking objects, you might try commands something like: set shadows setattr s density 8 set subdivision 10 However, I understand you may have other reasons for wanting povray files. 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 Apr 23, 2014, at 12:48 PM, jiserte at unq.edu.ar wrote: > I'm writing a small python script to generate Pov-Ray with chimera. The script loads a pdb file containing a protein and a ligand, modifies the protein view to ribbon and the ligand to surface. Then exports the .pov file. However the image created by Pov-Ray shows only the surface of ligand. > > The image is shown correctly in the chimera GUI. If I run the commands one by one in the chimera command line, the .pov file generated is ok. > > The script is: > ----------------------------------------- > import chimera > from chimera import runCommand > runCommand('windowsize 800 600') > runCommand('open ../../kinase.domain.2/A.4K9Y.pdb') > runCommand('ribbon #0') > runCommand('surf ligand') > runCommand('export test.pov') > ------------------------------------------ > > After running the script the ReplyLog contains: > > ----------------------------------------- > A.4K9Y.pdb opened > /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1 > MSMSLIB 1.3 started on hamal > Copyright M.F. Sanner (March 2000) > Compilation flags > > Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2 > 1 connected surface components > Total solvent excluded surface area = 436.845 > Total solvent accessible surface area = 772.871 > ----------------------------------------- > > Javier Iserte From gregc at cgl.ucsf.edu Wed Apr 23 13:27:49 2014 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 23 Apr 2014 13:27:49 -0700 Subject: [Chimera-users] Export Pov-Ray file with a python script. In-Reply-To: <20140423164802.Horde.XwxsaNCfQetMv6TgnLitAQ1@correo.unq.edu.ar> References: <20140423164802.Horde.XwxsaNCfQetMv6TgnLitAQ1@correo.unq.edu.ar> Message-ID: <53582245.9050101@cgl.ucsf.edu> So the trick is to do insert: runCommand('wait 1') before doing the export. That causes chimera to display the image before doing the export. And that is needed because the ribbon is not generated until it is displayed. HTH, Greg P.S. The POV-Ray output in the 1.9 candidate release (and the daily builds) has been modified to work with the new parallel POV-Ray 3.7. So if you are using POV-Ray, I would recommend installing the 3.7 version and then change the POV-Ray executable in the POV-Ray Options preference to use your installed POV-Ray instead of Chimera's built-in version. On 04/23/2014 12:48 PM, jiserte at unq.edu.ar wrote: > I'm writing a small python script to generate Pov-Ray with chimera. > The script loads a pdb file containing a protein and a ligand, > modifies the protein view to ribbon and the ligand to surface. Then > exports the .pov file. However the image created by Pov-Ray shows only > the surface of ligand. > > The image is shown correctly in the chimera GUI. If I run the commands > one by one in the chimera command line, the .pov file generated is ok. > > The script is: > ----------------------------------------- > import chimera > from chimera import runCommand > runCommand('windowsize 800 600') > runCommand('open ../../kinase.domain.2/A.4K9Y.pdb') > runCommand('ribbon #0') > runCommand('surf ligand') > runCommand('export test.pov') > ------------------------------------------ > > After running the script the ReplyLog contains: > > ----------------------------------------- > A.4K9Y.pdb opened > /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1 > MSMSLIB 1.3 started on hamal > Copyright M.F. Sanner (March 2000) > Compilation flags > > Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2 > 1 connected surface components > Total solvent excluded surface area = 436.845 > Total solvent accessible surface area = 772.871 > ----------------------------------------- > > Javier Iserte > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Thu Apr 24 12:01:55 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 24 Apr 2014 12:01:55 -0700 Subject: [Chimera-users] 1.9 release candidate Message-ID: <611647B6-9CBB-423C-A3F3-074F3266155A@cgl.ucsf.edu> Hi everybody, There is a release candidate of Chimera 1.9 on the download page. If you can, please try it out and let us know if you have any problems or questions. The differences between 1.9 and 1.8 are covered in the release notes. Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From hernando.sosa at einstein.yu.edu Thu Apr 24 14:22:53 2014 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Thu, 24 Apr 2014 21:22:53 +0000 Subject: [Chimera-users] Multiscale models color Message-ID: Hi, How do you control the color of the surfaces generated by the multi-scale models command "Make models" so that the user can specify the color associated with each chain? I tried to follow the documentation on how to do this but still I don't get it right as I didn't manage to change the colors assigned by default. Thanks Hernando -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Apr 24 14:56:05 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 24 Apr 2014 14:56:05 -0700 Subject: [Chimera-users] Multiscale models color In-Reply-To: References: Message-ID: <485C51D3-07FC-40D9-9689-BD60E6D28CB0@cgl.ucsf.edu> Hi Hernando, I don't know of a way to specify colors before making the models. You would make the Multiscale Models surfaces and then: (1) select the chains, Ctrl-click and Shift-Ctrl-click with the mouse, and/or using the top section of the Multiscale Models dialog (the buttons next to "Select chains" and "Extend") (2) when the desired set of chains is selected, either use the main Chimera menu "Actions? Color", or in the middle section of the Multiscale Models dialog ("Act on selected chains") click the square color well and use the Color Editor to change the color 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 Apr 24, 2014, at 2:22 PM, Hernando J Sosa wrote: > Hi, > How do you control the color of the surfaces generated by the multi-scale models command "Make models" so that the user can specify the color associated with each chain? > I tried to follow the documentation on how to do this but still I don't get it right as I didn't manage to change the colors assigned by default. > Thanks > Hernando From m.maletta at nki.nl Fri Apr 25 05:13:17 2014 From: m.maletta at nki.nl (m.maletta at nki.nl) Date: Fri, 25 Apr 2014 14:13:17 +0200 Subject: [Chimera-users] Print selected Message-ID: <2E815C4B1C03DC4C8EDB7DE167ECC8566C41268166@mstr-2.nki.nl> Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B Is there a way to get the list? Best and thank you in advance Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta at nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029 From tanja.schulz-gasch at roche.com Fri Apr 25 06:14:27 2014 From: tanja.schulz-gasch at roche.com (Schulz-Gasch, Tanja) Date: Fri, 25 Apr 2014 15:14:27 +0200 Subject: [Chimera-users] script Message-ID: Hi there, I hope you could help me with a little script. I am pretty sure, that something must exists already;-) I need to rotate around the y-axis in 2 degree steps for a total of 44 degree and at each step export a high res graphic. Rotation of the camera/view (keeping the look-at point) would be preferable compared to rotation of the object. Anything out there like this??? Thanks for your help, Tanja -- *Dr. Tanja Schulz-Gasch *Head of Communications & Operations, pRED Basel Bldg 69, 308 Grenzacherstrasse 124 4070 Basel Switzerland Mobile: +41 (0) 79 578 4672 Work: +41 (0) 61 688 8309 Email: tanja.schulz-gasch @roche.com Web: www.roche.com *Confidentiality note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Apr 25 13:52:52 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 25 Apr 2014 13:52:52 -0700 Subject: [Chimera-users] Print selected In-Reply-To: <2E815C4B1C03DC4C8EDB7DE167ECC8566C41268166@mstr-2.nki.nl> References: <2E815C4B1C03DC4C8EDB7DE167ECC8566C41268166@mstr-2.nki.nl> Message-ID: <362EC468-0300-479E-A780-68AA600260C6@cgl.ucsf.edu> Dear Max, The best way is to use the Find Clashes/Contacts tool (in menu under Tools... Structure Analysis) or its command version "findclash". Either way you can define two sets of atoms, chain A and chain B in your case, and a cutoff distance, and then get a list of the distances saved to a file or to the Reply Log. The cutoff you specify is not center-to-center distance, but "overlap" = the overlap between the surfaces of the VDW spheres, where 0 is exactly touching, positive is intersecting, negative is the separation of the VDW surfaces. Nevertheless the list of pairwise atom-atom results will include both the overlap values and the center-to-center distances, and if you really prefer the strict center-to-center distance cutoff, you can (manually) filter the results by that criterion. For example, commands including option to write results to the Reply Log: open 1zik preset apply int 2 findclash :.a&protein test :.b&protein overlap -0.5 hbond 0.0 log true The command has several options including "saveFile" as an alternative to "log", selecting the atoms, and drawing lines. The center-to-center distances are the last column in the results. To get larger distances you would use a larger negative overlap cutoff. The graphical interface (Find Clashes/Contacts tool) can do the same things. It is fairly self-explanatory, but to define two sets of atoms you'd first select one set, then "Designate", then select the second set and "Designate... as second set": 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 Apr 25, 2014, at 5:13 AM, wrote: > Dear all, > I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. > I manage to do the first part with this command, but I do not manage to have a list of all the distances found. > select #0:.A za<3.5 & #0:.B > > Is there a way to get the list? > Best and thank you in advance > Max From meng at cgl.ucsf.edu Fri Apr 25 14:16:50 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 25 Apr 2014 14:16:50 -0700 Subject: [Chimera-users] script In-Reply-To: References: Message-ID: Hi Tanja, In Chimera, I believe the commands move the objects, not the camera, but otherwise it can be done using the commands "perframe" (to do some things at every frame), "turn" (to rotate around Y axis) and "copy" (to save the image file). For example, the following saves PNG files named 001.png, 002.png, ... 022.png as a structure is rotated in 2? increments about the Y axis: perframe "turn y 2; copy png file ~/Desktop/$1.png" frames 22 zero 3 See manual for explanation of command options and more examples: 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 Apr 25, 2014, at 6:14 AM, Schulz-Gasch, Tanja wrote: > Hi there, > I hope you could help me with a little script. I am pretty sure, that something must exists already;-) > I need to rotate around the y-axis in 2 degree steps for a total of 44 degree and at each step export a high res graphic. Rotation of the camera/view (keeping the look-at point) would be preferable compared to rotation of the object. Anything out there like this??? > Thanks for your help, Tanja From hernando.sosa at einstein.yu.edu Sat Apr 26 06:39:40 2014 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Sat, 26 Apr 2014 13:39:40 +0000 Subject: [Chimera-users] Multiscale models color In-Reply-To: <485C51D3-07FC-40D9-9689-BD60E6D28CB0@cgl.ucsf.edu> References: , <485C51D3-07FC-40D9-9689-BD60E6D28CB0@cgl.ucsf.edu> Message-ID: Thanks Elaine, The extend command is what I was missing. The following command sequence did do it. Tools->Multiscale Models-> Make Models Select -> chain (from the main menu) Tools->Multiscale Models->Extend Copies Action->Color ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Thursday, April 24, 2014 5:56 PM To: Hernando J Sosa Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Multiscale models color Hi Hernando, I don't know of a way to specify colors before making the models. You would make the Multiscale Models surfaces and then: (1) select the chains, Ctrl-click and Shift-Ctrl-click with the mouse, and/or using the top section of the Multiscale Models dialog (the buttons next to "Select chains" and "Extend") (2) when the desired set of chains is selected, either use the main Chimera menu "Actions? Color", or in the middle section of the Multiscale Models dialog ("Act on selected chains") click the square color well and use the Color Editor to change the color 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 Apr 24, 2014, at 2:22 PM, Hernando J Sosa wrote: > Hi, > How do you control the color of the surfaces generated by the multi-scale models command "Make models" so that the user can specify the color associated with each chain? > I tried to follow the documentation on how to do this but still I don't get it right as I didn't manage to change the colors assigned by default. > Thanks > Hernando From m.maletta at nki.nl Mon Apr 28 05:23:23 2014 From: m.maletta at nki.nl (m.maletta at nki.nl) Date: Mon, 28 Apr 2014 14:23:23 +0200 Subject: [Chimera-users] Print selected In-Reply-To: <362EC468-0300-479E-A780-68AA600260C6@cgl.ucsf.edu> References: <2E815C4B1C03DC4C8EDB7DE167ECC8566C41268166@mstr-2.nki.nl>, <362EC468-0300-479E-A780-68AA600260C6@cgl.ucsf.edu> Message-ID: <2E815C4B1C03DC4C8EDB7DE167ECC8566C41268170@mstr-2.nki.nl> Dear Elaine, Thank you a lot for your help. It really worked perfectly. I changed the radius of all the atoms with vdwdefine so that only the distance from the center matter. Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta at nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Friday, 25 April 2014 10:52 PM To: Massimiliano Maletta Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Print selected Dear Max, The best way is to use the Find Clashes/Contacts tool (in menu under Tools... Structure Analysis) or its command version "findclash". Either way you can define two sets of atoms, chain A and chain B in your case, and a cutoff distance, and then get a list of the distances saved to a file or to the Reply Log. The cutoff you specify is not center-to-center distance, but "overlap" = the overlap between the surfaces of the VDW spheres, where 0 is exactly touching, positive is intersecting, negative is the separation of the VDW surfaces. Nevertheless the list of pairwise atom-atom results will include both the overlap values and the center-to-center distances, and if you really prefer the strict center-to-center distance cutoff, you can (manually) filter the results by that criterion. For example, commands including option to write results to the Reply Log: open 1zik preset apply int 2 findclash :.a&protein test :.b&protein overlap -0.5 hbond 0.0 log true The command has several options including "saveFile" as an alternative to "log", selecting the atoms, and drawing lines. The center-to-center distances are the last column in the results. To get larger distances you would use a larger negative overlap cutoff. The graphical interface (Find Clashes/Contacts tool) can do the same things. It is fairly self-explanatory, but to define two sets of atoms you'd first select one set, then "Designate", then select the second set and "Designate... as second set": 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 Apr 25, 2014, at 5:13 AM, wrote: > Dear all, > I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. > I manage to do the first part with this command, but I do not manage to have a list of all the distances found. > select #0:.A za<3.5 & #0:.B > > Is there a way to get the list? > Best and thank you in advance > Max From jdougherty2718 at gmail.com Sat Apr 26 13:13:48 2014 From: jdougherty2718 at gmail.com (John Dougherty) Date: Sat, 26 Apr 2014 16:13:48 -0400 Subject: [Chimera-users] Question About Using Chimera In Python Scripts with Other Features Message-ID: Hello, I am not very computer savvy and very new to programming. I am using Windows 7, Python 2.7.3 32 bit I would like to know if it is possible to use features from Chimera in a python script. For example: from chimera import * from otherprogram import * otherprogram stuff runCommand('blah blah blah') Chimera does some things the other program does not and vice versa. My life would be made much easier if I could just integrate them into one script. I do not understand the instructions about this matter which are posted on the FAQs on the website. Sincerely, -- John J. Dougherty III Biomathematics Major Rutgers, New Brunswick (P) 856 981 9491 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tanja.schulz-gasch at roche.com Sun Apr 27 01:58:14 2014 From: tanja.schulz-gasch at roche.com (Schulz-Gasch, Tanja) Date: Sun, 27 Apr 2014 10:58:14 +0200 Subject: [Chimera-users] script In-Reply-To: References: Message-ID: <7420648988675035847@unknownmsgid> thanks, this really was what i was looking for! btw, i saw that chimera is able to export a set of lenticular images. do you have any experience with that? some contact who can produce then such a 3d image??? have a nice we, tanja Sent from my iPhone > On 26.04.2014, at 00:01, Elaine Meng wrote: > > Hi Tanja, > In Chimera, I believe the commands move the objects, not the camera, but otherwise it can be done using the commands "perframe" (to do some things at every frame), "turn" (to rotate around Y axis) and "copy" (to save the image file). > > For example, the following saves PNG files named 001.png, 002.png, ... 022.png as a structure is rotated in 2? increments about the Y axis: > perframe "turn y 2; copy png file ~/Desktop/$1.png" frames 22 zero 3 > > See manual for explanation of command options and more examples: > > > > > 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 Apr 25, 2014, at 6:14 AM, Schulz-Gasch, Tanja wrote: >> >> Hi there, >> I hope you could help me with a little script. I am pretty sure, that something must exists already;-) >> I need to rotate around the y-axis in 2 degree steps for a total of 44 degree and at each step export a high res graphic. Rotation of the camera/view (keeping the look-at point) would be preferable compared to rotation of the object. Anything out there like this??? >> Thanks for your help, Tanja > From jb3401 at c2b2.columbia.edu Sun Apr 27 15:24:15 2014 From: jb3401 at c2b2.columbia.edu (Joshua Broyde) Date: Sun, 27 Apr 2014 18:24:15 -0400 (EDT) Subject: [Chimera-users] (no subject) Message-ID: <574e8ba8-30de-49bb-a5f3-99127dbd4546@mail.c2b2.columbia.edu> Hi, > I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? > I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. > > Sincerely, > Joshua Broyde From meng at cgl.ucsf.edu Mon Apr 28 09:45:22 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Apr 2014 09:45:22 -0700 Subject: [Chimera-users] lenticular images from Chimera In-Reply-To: <7420648988675035847@unknownmsgid> References: <7420648988675035847@unknownmsgid> Message-ID: <0A5322DC-556A-40F8-8098-A2F166B8632B@cgl.ucsf.edu> Hi Tanja, I haven't made lenticular images personally, but others in our lab have done so. If you didn't see it already, here is documentation (prerequisites and instructions): As detailed in that page, you would need additional software (besides Chimera) to interlace the images, a high-res printer, the lensing material itself, and a cold laminator. 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 Apr 27, 2014, at 1:58 AM, "Schulz-Gasch, Tanja" wrote: > thanks, this really was what i was looking for! > btw, i saw that chimera is able to export a set of lenticular images. > do you have any experience with that? some contact who can produce > then such a 3d image??? > > have a nice we, tanja From pett at cgl.ucsf.edu Mon Apr 28 11:06:04 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 28 Apr 2014 11:06:04 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <574e8ba8-30de-49bb-a5f3-99127dbd4546@mail.c2b2.columbia.edu> References: <574e8ba8-30de-49bb-a5f3-99127dbd4546@mail.c2b2.columbia.edu> Message-ID: <0E92469A-5878-4FF6-B916-72128017577D@cgl.ucsf.edu> Hi Joshua, The first thing you should do is make sure you have the latest driver installed for your graphics card. Based on the info you provided, I believe the latest release for your card was 4/24/14 -- only 4 days ago! Go to the AMD drivers site here: Download Drivers and input the values for your system to get to the latest drivers. If that doesn't help, my best guess as to the issue is that the card/driver can't show dashed lines beyond a certain thickness and that the supersampling done while saving the image requires lines thicker than the card supports (each "tile" of the supersampled image is essentially a zoomed-in depiction of that part of the image and is later sampled down to its final size -- which reduces aliasing artifacts). Therefore the two things to try are to reduce the amount of supersampling as you save the image, or reduce the thickness of the dashed lines before you save the image. There is a "Supersample" control on the Save-Image dialog, and there is a "supersample" keyword to the "copy" command, if that's what you're using. You can reduce the line width of the hydrogen bonds by bringing up the PseudoBond Panel (in the General Controls tool category) and double clicking on the "hydrogen bonds" group (assuming you've made some hydrogen bonds). The "line width" control is in the lower part of the inspector that comes up. I hope one of these things work! :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 27, 2014, at 3:24 PM, Joshua Broyde wrote: > Hi, >> I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? >> I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. >> >> Sincerely, >> Joshua Broyde > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Apr 28 15:55:05 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Apr 2014 15:55:05 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <1690299D-90AC-44A6-A437-4F717B4CD872@cgl.ucsf.edu> References: <1690299D-90AC-44A6-A437-4F717B4CD872@cgl.ucsf.edu> Message-ID: Hi Joshua, The linewidth issue is mentioned in the supersampling documentation, but you wouldn't be expected to know that your problem was related to supersampling in the first place! Most people report encounter it as the lines being too thin rather than being completely invisible. If you use the Image Save dialog, it reports near the bottom of the dialog the "effective maximum linewidth" given the specified level of supersampling and image pixel dimensions. Elaine On Apr 28, 2014, at 3:43 PM, Eric Pettersen wrote: > Hi Joshua, > I'm glad to hear it worked! And of course you're welcome. Don't hesitate to send other problems or concerns to the list, and I'm sure you're right that others will benefit from having the info Googlable from the list archive. > > --Eric > > On Apr 28, 2014, at 3:39 PM, Joshua Broyde wrote: > >> Dear Eric, >> Thank you so much. The first thing I did is change the supersampling from 3x3 to 1x1 and it worked! Thanks so much! >> >> Sincerel, >> Joshua Broyde >> p.s. feel free to share this email with others who have this problem. When I googled "dashed lines not saving chimera".Thanks again! >> >> ----- Original Message ----- >> From: "Eric Pettersen" >> To: "Joshua Broyde" >> Cc: chimera-users at cgl.ucsf.edu >> Sent: Monday, April 28, 2014 2:06:04 PM >> Subject: Re: [Chimera-users] (no subject) >> >> Hi Joshua, >> The first thing you should do is make sure you have the latest driver installed for your graphics card. Based on the info you provided, I believe the latest release for your card was 4/24/14 -- only 4 days ago! Go to the AMD drivers site here: >> >> >> Download Drivers >> >> >> and input the values for your system to get to the latest drivers. >> If that doesn't help, my best guess as to the issue is that the card/driver can't show dashed lines beyond a certain thickness and that the supersampling done while saving the image requires lines thicker than the card supports (each "tile" of the supersampled image is essentially a zoomed-in depiction of that part of the image and is later sampled down to its final size -- which reduces aliasing artifacts). Therefore the two things to try are to reduce the amount of supersampling as you save the image, or reduce the thickness of the dashed lines before you save the image. >> There is a "Supersample" control on the Save-Image dialog, and there is a "supersample" keyword to the "copy" command, if that's what you're using. >> You can reduce the line width of the hydrogen bonds by bringing up the PseudoBond Panel (in the General Controls tool category) and double clicking on the "hydrogen bonds" group (assuming you've made some hydrogen bonds). The "line width" control is in the lower part of the inspector that comes up. >> I hope one of these things work! :-) >> >> >> --Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> >> On Apr 27, 2014, at 3:24 PM, Joshua Broyde < jb3401 at c2b2.columbia.edu > wrote: >> >> >> Hi, >> >> >> I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? >> I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > From gregc at cgl.ucsf.edu Mon Apr 28 16:01:00 2014 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 28 Apr 2014 16:01:00 -0700 Subject: [Chimera-users] Question About Using Chimera In Python Scripts with Other Features In-Reply-To: References: Message-ID: <535EDDAC.2030006@cgl.ucsf.edu> So the answer is that in theory it is possible. It is easier on Linux and Mac OS X, but not impossible on Windows. In all cases, it is easier to put other Python modules into Chimera than the other way around. Then run the Python script using Chimera with the open command or the File / Open menu item. The first thing to try is to set the CHIMERAPATH environment variable (like PYTHONPATH, but just for Chimera), to point to the directory (or directories) with the modules from the other program. There is a high chance of conflicts with Chimera modules, but if it works, you're done. To set environment variables on Windows, go to the Control Panel / System / Advanced system settings / Environment Variables and create the CHIMERAPATH environment variable. The next option is to use CHIMERAPATH pointing to a new directory where you copy just what you need. This might be needed anyway if there are file permission problems with the first approach. Lastly, specially for Windows, my heavy handed approach that I occasionally use for testing: As the administrator: (1) change the ownership of the Chimera installation to be yourself, then (2) copy the modules you need from the other program to CHIMERA\bin\Lib\site-packages\. In this case, you can edit the Chimera Python files if needed to get things to work. HTH, Greg On 04/26/2014 01:13 PM, John Dougherty wrote: > Hello, > I am not very computer savvy and very new to programming. I am using > Windows 7, Python 2.7.3 32 bit > I would like to know if it is possible to use features from Chimera in > a python script. For example: > > from chimera import * > from otherprogram import * > > otherprogram stuff > runCommand('blah blah blah') > > > Chimera does some things the other program does not and vice versa. My > life would be made much easier if I could just integrate them into one > script. > > I do not understand the instructions about this matter which are > posted on the FAQs on the website. > > Sincerely, > > > -- > John J. Dougherty III > Biomathematics Major > Rutgers, New Brunswick > (P) 856 981 9491 From sdrakulic at cib.csic.es Tue Apr 29 03:49:28 2014 From: sdrakulic at cib.csic.es (SRDA.DRAKULIC.599589) Date: Tue, 29 Apr 2014 12:49:28 +0200 Subject: [Chimera-users] related with Fit in map option Message-ID: <20140429124928.Horde.iKg6gWZ9J19HWUR8sfE5-A1@webmail.csic.es> Hi, I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values: cross correlation: 0.8447; average map value 9.526; and number of atoms outside the contour: 1709/7621 (or 22.42%) For the open state: cross correlation: 0.8385; average map value 9.085; and number of atoms outside the contour: 2064/8124 (or 25.42%) Are those differences big enough to say with certainty that my protein is at conformation similar to the clenched one or due to the EM map resolution this can not be said. Sincerely, Srdja Drakulic From miguel.ortiz-lombardia at afmb.univ-mrs.fr Tue Apr 29 08:49:32 2014 From: miguel.ortiz-lombardia at afmb.univ-mrs.fr (=?UTF-8?B?TWlndWVsIE9ydGl6IExvbWJhcmTDrWE=?=) Date: Tue, 29 Apr 2014 17:49:32 +0200 Subject: [Chimera-users] A question on tunnelling chimera through ssh between a linux server and OSX client Message-ID: <535FCA0C.4040401@afmb.univ-mrs.fr> Hi all, I understand that this is not a typical use of chimera, so I don't expect much support, but I would appreciate if someone can give me a clue to solve the issue... We have a GNU/Linux server (Debian wheezy) with some EM software installed on it. One of these programs calls at some point chimera to show something on which the user has to act upon (or just check, not sure, I'm not the user as you've guessed) This machine is accessed from client OSX machines via ssh. All permissions are set so X11 is seamlessly tunnelled between them (checked with many graphical programs) Now, for a OSX client running on 10.6.8 (snow leopard) and using Apple's X11 the whole process works without problems. But for a OSX on 10.7.5 (lion) with a parallel installation of Apple's X11 and Xquartz 2.7.5 the first small window opens and then the chimera process hangs (it can be killed via Ctrl-C, which returns the control to the program that launched chimera and things can proceed, though without the information provided by chimera) If I connect to the Linux server from the lion machine and directly execute chimera I make a different observation: the first small window opens but then chimera crashes leaving this error in the terminal: Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1360 Current serial number in output stream: 1360 Now, I would appreciate any clues on the meaning and possible solution of this error or at least any directions on how to properly remove both Apple's X11 and Xquartz (they are supposed to be able to work side-by-side but I presume that a possible source of problems could arise from some conflict between them) AND re-install them to test them in a fresh install. Downgrading the lion machine to snow leopard does not seem to be an option... Thank you! Cheers, -- Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR7257) CNRS, Aix-Marseille Universit? Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia From jmsstarlight at gmail.com Tue Apr 29 03:45:49 2014 From: jmsstarlight at gmail.com (James Starlight) Date: Tue, 29 Apr 2014 14:45:49 +0400 Subject: [Chimera-users] Preparation of the protein-ligand system for the amber simulation Message-ID: Dear Chimera Users, I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example Thanks for help, James -------------- next part -------------- An HTML attachment was scrubbed... URL: From maja_divjak at yahoo.com.au Tue Apr 29 06:31:56 2014 From: maja_divjak at yahoo.com.au (Maja Divjak) Date: Tue, 29 Apr 2014 06:31:56 -0700 (PDT) Subject: [Chimera-users] Saving ribbons as PDBs? Message-ID: <1398778316.28591.YahooMailMobile@web162601.mail.bf1.yahoo.com> Hello Chimera Gurus, Is there a way to save ribbon structures as PDBs for import into Maya? I've found only the surface structures are saved in the PDB, even though I am working with the ribbon structure in chimera initially. If there is a way to do this, I would be mightily pleased! I used to export chimera domains as vrml files and then convert them to maya files and both the ribbon and surface structures would be included. You can reply to my work email at divjak.m at wehi.edu.au if you prefer. Thank you so much and best wishes, Maja Divjak, PhD Biomedical Animator Walter and Eliza Hall Institute of Medical Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.garton at utoronto.ca Tue Apr 29 07:34:33 2014 From: michael.garton at utoronto.ca (Michael Garton) Date: Tue, 29 Apr 2014 14:34:33 +0000 Subject: [Chimera-users] select zone & rename script Message-ID: Hi all, Can anyone show me a good way to select all residues that are <2? from zinc atoms, then rename any selected CYS and HIS, to CYM and HIN respectively ... I'm trying to write a script to do this on ~300 files. Thanks!! Mike Here's what I have so far import os from chimera import runCommand as rc from chimera import replyobj # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) rc("select :ZNB zr<2") rc("writesel "reslist + fn") rc("close all") rc("stop now") -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickmwalter at gmail.com Tue Apr 29 13:36:23 2014 From: nickmwalter at gmail.com (Nick Walter) Date: Tue, 29 Apr 2014 15:36:23 -0500 Subject: [Chimera-users] multi-channel solid rendering Message-ID: Hello, I've been attempting to create a movie in Chimera using multiple data files in solid style volume rendering, and I have been running into an issue where Chimera consistently shows the last channel to be loaded on top, regardless of the spacial position of the data with respect to the other solid channels. I found this message ( http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006329.html) which explains that multi-channel solid rendering was removed in 2008. I was wondering, if there are any plans to reinstate this feature, or if you were aware of any work-arounds that would work well for creating movies. Thank you for your time, Nick Walter -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 29 14:43:51 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 29 Apr 2014 14:43:51 -0700 Subject: [Chimera-users] Preparation of the protein-ligand system for the amber simulation In-Reply-To: References: Message-ID: Hi James, I believe not - one of the main limitations is that there is very little ability to use anything other than the parameters you get from the force field choices listed in the dialog for standard residues and the Antechamber process automatically used for nonstandard residues (i.e. small molecules). You can only substitute in different partial charges for nonstandard residues, and even that is rather labor-intensive: 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 Apr 29, 2014, at 3:45 AM, James Starlight wrote: > Dear Chimera Users, > I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example > Thanks for help, > James From pett at cgl.ucsf.edu Tue Apr 29 14:44:23 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 29 Apr 2014 14:44:23 -0700 Subject: [Chimera-users] select zone & rename script In-Reply-To: References: Message-ID: <6B8E0E7B-2326-492E-BFC2-6728BA5FCF3A@cgl.ucsf.edu> Hi Mike, The tricks you need to know are that: 1) You can use the '&' operator in an atom spec to get the intersection of two atom specs. Therefore ":CYS & sel" will get all CYS residues in the current selection and only those residues, and: 2) You can use the 'setattr' command to change a residue's type. Therefore, once you've used your zone command to select what you want, this command will rename selected CYS residues to CYM: setattr r type CYM :CYS & sel Similarly for HIS/HIN change: setattr r type HIN :HIS & sel Therefore you can insert these commands in your script to get the result you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 29, 2014, at 7:34 AM, Michael Garton wrote: > Hi all, > > Can anyone show me a good way to select all residues that are <2? from zinc atoms, then rename any selected CYS and HIS, to CYM and HIN respectively ... I'm trying to write a script to do this on ~300 files. > > Thanks!! > Mike > > Here's what I have so far > > import os > from chimera import runCommand as rc > from chimera import replyobj > > # gather the names of .pdb files in the folder > file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] > > # loop through the files, opening, processing, and closing each in turn > for fn in file_names: > replyobj.status("Processing " + fn) # show what file we're working on > > rc("open " + fn) > > rc("select :ZNB zr<2") > rc("writesel "reslist + fn") > > rc("close all") > > rc("stop now") > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 29 14:55:58 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 29 Apr 2014 14:55:58 -0700 Subject: [Chimera-users] Saving ribbons as PDBs? In-Reply-To: <1398778316.28591.YahooMailMobile@web162601.mail.bf1.yahoo.com> References: <1398778316.28591.YahooMailMobile@web162601.mail.bf1.yahoo.com> Message-ID: <32E5FD68-787B-4446-9303-6E9B1B0B4CF5@cgl.ucsf.edu> Hi Maja, I guess you don't really mean PDB files: those just contain the atomic coordinates rather than the representations. I haven't done it myself, but from searching online I found a page that suggests you may be able to convert from VRML exported from Chimera into another format for Maya. Chimera can export OBJ but surfaces only, whereas VRML export includes ribbons. The page above doesn't mention ribbons, however. Chimera export can be done from the File menu or using the export 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 Apr 29, 2014, at 6:31 AM, Maja Divjak wrote: > Hello Chimera Gurus, > > Is there a way to save ribbon structures as PDBs for import into Maya? I've found only the surface structures are saved in the PDB, even though I am working with the ribbon structure in chimera initially. If there is a way to do this, I would be mightily pleased! I used to export chimera domains as vrml files and then convert them to maya files and both the ribbon and surface structures would be included. You can reply to my work email at divjak.m at wehi.edu.au if you prefer. > > Thank you so much and best wishes, > > Maja Divjak, PhD > Biomedical Animator > Walter and Eliza Hall Institute of Medical Research From gregc at cgl.ucsf.edu Tue Apr 29 15:35:46 2014 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 29 Apr 2014 15:35:46 -0700 Subject: [Chimera-users] A question on tunnelling chimera through ssh between a linux server and OSX client In-Reply-To: <535FCA0C.4040401@afmb.univ-mrs.fr> References: <535FCA0C.4040401@afmb.univ-mrs.fr> Message-ID: <53602942.2040901@cgl.ucsf.edu> Unfortunately, while the remote display of OpenGL applications should work, it is poorly supported since the demise of SGI and DEC workstations. When it does work, it is usually because the same OpenGL driver is installed on both the server and client computers. Normally, your best option for the Mac would be to use the XQuartz from http://xquartz.macosforge.org/ and since that didn't work, your next best option is to use remote desktop application like vnc. I don't know if you can have multiple separate desktops with vnc for each user, so that might be limited to one user at a time. You could also try updating the Mesa packages on the server (especially the mesa-glx packages). Newer versions of Mesa are much better at supporting remote OpenGL (via the GLX protocol). It appears that wheezy has Mesa 8, and debian-testing only has Mesa 9, instead of the lastest Mesa 10, so if you go this route, I'd recommend compiling Mesa 10 yourself if possible. HTH, Greg On 04/29/2014 08:49 AM, Miguel Ortiz Lombard?a wrote: > Hi all, > > I understand that this is not a typical use of chimera, so I don't > expect much support, but I would appreciate if someone can give me a > clue to solve the issue... > > We have a GNU/Linux server (Debian wheezy) with some EM software > installed on it. One of these programs calls at some point chimera to > show something on which the user has to act upon (or just check, not > sure, I'm not the user as you've guessed) This machine is accessed from > client OSX machines via ssh. All permissions are set so X11 is > seamlessly tunnelled between them (checked with many graphical programs) > Now, for a OSX client running on 10.6.8 (snow leopard) and using Apple's > X11 the whole process works without problems. But for a OSX on 10.7.5 > (lion) with a parallel installation of Apple's X11 and Xquartz 2.7.5 the > first small window opens and then the chimera process hangs (it can be > killed via Ctrl-C, which returns the control to the program that > launched chimera and things can proceed, though without the information > provided by chimera) > > If I connect to the Linux server from the lion machine and directly > execute chimera I make a different observation: the first small window > opens but then chimera crashes leaving this error in the terminal: > > Error of failed request: GLXBadCurrentWindow > Major opcode of failed request: 149 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 1360 > Current serial number in output stream: 1360 > > Now, I would appreciate any clues on the meaning and possible solution > of this error or at least any directions on how to properly remove both > Apple's X11 and Xquartz (they are supposed to be able to work > side-by-side but I presume that a possible source of problems could > arise from some conflict between them) AND re-install them to test them > in a fresh install. > > Downgrading the lion machine to snow leopard does not seem to be an > option... > > Thank you! > Cheers, > From meng at cgl.ucsf.edu Tue Apr 29 15:42:44 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 29 Apr 2014 15:42:44 -0700 Subject: [Chimera-users] related with Fit in map option In-Reply-To: <20140429124928.Horde.iKg6gWZ9J19HWUR8sfE5-A1@webmail.csic.es> References: <20140429124928.Horde.iKg6gWZ9J19HWUR8sfE5-A1@webmail.csic.es> Message-ID: Hi Srdja, I am no EM expert, but my best guess is that this is a scientific judgement call. In other words, there is no specific correlation number or statistic (or difference when comparing two possibilities) that allows you to state definitively that a map matches a certain conformation. For example, the map might represent some other conformation that isn't exactly like either of the atomic structures.The fitting statistics are additional pieces of evidence that could be combined with other knowledge to reach a conclusion of what is most probable. Perhaps others who actually work with EM data will have an opinion, however. 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 Apr 29, 2014, at 3:49 AM, "SRDA.DRAKULIC.599589" wrote: > Hi, > I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values: > cross correlation: 0.8447; > average map value 9.526; > and number of atoms outside the contour: 1709/7621 (or 22.42%) > For the open state: > cross correlation: 0.8385; > average map value 9.085; > and number of atoms outside the contour: 2064/8124 (or 25.42%) > Are those differences big enough to say with certainty that my protein is at conformation similar to the clenched one or due to the EM map resolution this can not be said. > Sincerely, > Srdja Drakulic From goddard at sonic.net Tue Apr 29 17:06:36 2014 From: goddard at sonic.net (Tom Goddard) Date: Tue, 29 Apr 2014 17:06:36 -0700 Subject: [Chimera-users] related with Fit in map option In-Reply-To: References: <20140429124928.Horde.iKg6gWZ9J19HWUR8sfE5-A1@webmail.csic.es> Message-ID: <22CB9749-42C8-4449-8063-7918B2FF7CFD@sonic.net> Hi Srdja, I agree with Elaine that these small differences in correlation are not strong evidence. You should look at where the molecular models fail to match to the EM map to get a better understanding. You can make a simulated map from each molecular model and do a local correlation coloring to see where the differences are. http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#localcorr Or maybe better for seeing the differences you could morph between the experimental map and simulated molecule maps. http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#morphmap You?ll need to resample the simulated map (made with molmap) on the grid of the experimental map, so both maps have the same grid to do this (e.g. "vop resample #1 ongrid #0? where #1 is the simulated map and #0 the experimental map). Tom On Apr 29, 2014, at 3:42 PM, Elaine Meng wrote: > Hi Srdja, > I am no EM expert, but my best guess is that this is a scientific judgement call. In other words, there is no specific correlation number or statistic (or difference when comparing two possibilities) that allows you to state definitively that a map matches a certain conformation. For example, the map might represent some other conformation that isn't exactly like either of the atomic structures.The fitting statistics are additional pieces of evidence that could be combined with other knowledge to reach a conclusion of what is most probable. > > Perhaps others who actually work with EM data will have an opinion, however. > 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 Apr 29, 2014, at 3:49 AM, "SRDA.DRAKULIC.599589" wrote: > >> Hi, >> I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values: >> cross correlation: 0.8447; >> average map value 9.526; >> and number of atoms outside the contour: 1709/7621 (or 22.42%) >> For the open state: >> cross correlation: 0.8385; >> average map value 9.085; >> and number of atoms outside the contour: 2064/8124 (or 25.42%) >> Are those differences big enough to say with certainty that my protein is at conformation similar to the clenched one or due to the EM map resolution this can not be said. >> Sincerely, >> Srdja Drakulic > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Tue Apr 29 22:35:13 2014 From: goddard at sonic.net (Tom Goddard) Date: Tue, 29 Apr 2014 22:35:13 -0700 Subject: [Chimera-users] multi-channel solid rendering In-Reply-To: References: Message-ID: Hi Nick, Yes, Chimera does not correctly blend two overlayed transparent models, so blending ?solid? style (ie volumetric) density map display of 2 or more maps does not blend the colors. Usually one map simply covers the other one. I?ve put a script blend.py on the Chimera Python scripts web page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts that blends 2 or more maps (actually simply adds the red,green,blue,opacity values pointwise). For example runscript /Users/goddard/blend.py #1-3 #4 will add the solid-style colors currently shown for maps #1, 2 and 3 creating a model #4. Then I?d want to hide #1-3 to show only #4: ~modeldisp #1-3 The created model #4 is not a density map, it is a volumetric model, so it will not appear in the volume viewer dialog, only in Model Panel. It will not automatically update if you change the map colorings. After you update the map colorings, or map region displayed, you would have to show those maps (so the new colors actually get computed), then rerun the blend.py script. You can use the same model #4 when you rerun the script and it will reuse that model. I?m not sure this script will help you, it is a cumbersome process to show the blended colors. I tested it in Chimera 1.9 (release candidate). Maybe blending of solid style map colors will be put back into Chimera 2. It certainly would if we decide to support optical microscopy where imaging multiple fluorescent labels is common. Currently our Chimera 1 target audience is electron microscopy where multi-channel imaging is almost never done. Such new developments are probably at least a year away. Tom On Apr 29, 2014, at 1:36 PM, Nick Walter wrote: > Hello, > > I've been attempting to create a movie in Chimera using multiple data files in solid style volume rendering, and I have been running into an issue where Chimera consistently shows the last channel to be loaded on top, regardless of the spacial position of the data with respect to the other solid channels. I found this message (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006329.html) which explains that multi-channel solid rendering was removed in 2008. I was wondering, if there are any plans to reinstate this feature, or if you were aware of any work-arounds that would work well for creating movies. > > Thank you for your time, > Nick Walter > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmsstarlight at gmail.com Wed Apr 30 03:21:05 2014 From: jmsstarlight at gmail.com (James Starlight) Date: Wed, 30 Apr 2014 14:21:05 +0400 Subject: [Chimera-users] Preparation of the protein-ligand system for the amber simulation In-Reply-To: References: Message-ID: Hi Elaine, thanks for suggestions. Could you tell me if it's possible to use some scripts to make system preparations using amber parameters without Chimera's GUI? James 2014-04-30 1:43 GMT+04:00 Elaine Meng : > Hi James, > I believe not - one of the main limitations is that there is very little > ability to use anything other than the parameters you get from the force > field choices listed in the dialog for standard residues and the > Antechamber process automatically used for nonstandard residues (i.e. small > molecules). You can only substitute in different partial charges for > nonstandard residues, and even that is rather labor-intensive: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations > > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified > > > > 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 Apr 29, 2014, at 3:45 AM, James Starlight > wrote: > > > Dear Chimera Users, > > I wounder to know if it's possible to use combination of the amber ff > with the cgenff for the both parametrization of the small ligands in > complex with the proteins using amber tools built in Chimera's? Does it > possible to use some scripts instead of GUI for such tasks ? I'll be > thankfull for some tutorial or example > > Thanks for help, > > James > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Apr 30 11:54:40 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 30 Apr 2014 11:54:40 -0700 Subject: [Chimera-users] Preparation of the protein-ligand system for the amber simulation In-Reply-To: References: Message-ID: <818D137F-42A8-4C75-A3C3-2C0FE8FBEF4E@cgl.ucsf.edu> Hi James, It depends a little on what "system preparations" means to you, but if you mean "clean up for MD/docking" by eliminating alt locs, adding missing side chains, assigning charges, etc. then yes you can. The following two-line script will take the currently open model and run a "zero step" minimization on it (thereby only preparing it for minimization) and then write out a mol2 file named "prepped.mol2: in your home directory: minimize nsteps 0 cgsteps 0 write format mol2 0 ~/prepped.mol2 You may want to look at the documentation for the 'minimize' and 'write' commands to see if there are any other options you'd also want to use. If the above lines were in a file named "prep.cmd" the you could prepare 3FX2 with: chimera --nogui pdb:3fx2 prep.cmd Obviously you must want to do this on a lot of files, so you should look at the page in the programmer's guide that discusses looping through data files and performing commands such as the above on them: Very Basic Chimera Programming Primer I think it's pretty clear how you would adapt the example given in the primer to use the commands you need. If you need further help though just ask. If your original question means something else though, like writing out a prmtop file, that's possible but quite a bit more complicated -- so I'm not going to go into that here unless you say something. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 30, 2014, at 3:21 AM, James Starlight wrote: > Hi Elaine, > > thanks for suggestions. Could you tell me if it's possible to use some scripts to make system preparations using amber parameters without Chimera's GUI? > > > James > > > 2014-04-30 1:43 GMT+04:00 Elaine Meng : > Hi James, > I believe not - one of the main limitations is that there is very little ability to use anything other than the parameters you get from the force field choices listed in the dialog for standard residues and the Antechamber process automatically used for nonstandard residues (i.e. small molecules). You can only substitute in different partial charges for nonstandard residues, and even that is rather labor-intensive: > > > > > 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 Apr 29, 2014, at 3:45 AM, James Starlight wrote: > > > Dear Chimera Users, > > I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example > > Thanks for help, > > James > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguel.ortiz-lombardia at afmb.univ-mrs.fr Wed Apr 30 23:17:33 2014 From: miguel.ortiz-lombardia at afmb.univ-mrs.fr (Miguel Ortiz Lombardia) Date: Thu, 01 May 2014 08:17:33 +0200 Subject: [Chimera-users] A question on tunnelling chimera through ssh between a linux server and OSX client In-Reply-To: <53602942.2040901@cgl.ucsf.edu> References: <535FCA0C.4040401@afmb.univ-mrs.fr> <53602942.2040901@cgl.ucsf.edu> Message-ID: <5361E6FD.8030005@afmb.univ-mrs.fr> Hi Greg, Thank you very much for your help! I tried VNC, but GL is not conveyed by VNC, or not easily. I tried first with tightvnc, but got an error on the GL transport, even in the machine where X11 was enough to remotely open Chimera. I also tried something called VirtualGL combined with TurboVNC but got the same error. I presume I did not properly understand this set up... Anyway, I have yet to try your second suggestion, concerning the Mesa libraries. Perhaps that will work. Thanks again! Cheers, Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR7257) CNRS, Aix-Marseille Universit? Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia El 30/04/14 00:35, Greg Couch escribi?: > Unfortunately, while the remote display of OpenGL applications should > work, it is poorly supported since the demise of SGI and DEC > workstations. When it does work, it is usually because the same OpenGL > driver is installed on both the server and client computers. > > Normally, your best option for the Mac would be to use the XQuartz from > http://xquartz.macosforge.org/ and since that didn't work, your next > best option is to use remote desktop application like vnc. I don't know > if you can have multiple separate desktops with vnc for each user, so > that might be limited to one user at a time. You could also try > updating the Mesa packages on the server (especially the mesa-glx > packages). Newer versions of Mesa are much better at supporting remote > OpenGL (via the GLX protocol). It appears that wheezy has Mesa 8, and > debian-testing only has Mesa 9, instead of the lastest Mesa 10, so if > you go this route, I'd recommend compiling Mesa 10 yourself if possible. > > HTH, > > Greg > > On 04/29/2014 08:49 AM, Miguel Ortiz Lombard?a wrote: >> Hi all, >> >> I understand that this is not a typical use of chimera, so I don't >> expect much support, but I would appreciate if someone can give me a >> clue to solve the issue... >> >> We have a GNU/Linux server (Debian wheezy) with some EM software >> installed on it. One of these programs calls at some point chimera to >> show something on which the user has to act upon (or just check, not >> sure, I'm not the user as you've guessed) This machine is accessed from >> client OSX machines via ssh. All permissions are set so X11 is >> seamlessly tunnelled between them (checked with many graphical programs) >> Now, for a OSX client running on 10.6.8 (snow leopard) and using Apple's >> X11 the whole process works without problems. But for a OSX on 10.7.5 >> (lion) with a parallel installation of Apple's X11 and Xquartz 2.7.5 the >> first small window opens and then the chimera process hangs (it can be >> killed via Ctrl-C, which returns the control to the program that >> launched chimera and things can proceed, though without the information >> provided by chimera) >> >> If I connect to the Linux server from the lion machine and directly >> execute chimera I make a different observation: the first small window >> opens but then chimera crashes leaving this error in the terminal: >> >> Error of failed request: GLXBadCurrentWindow >> Major opcode of failed request: 149 (GLX) >> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >> Serial number of failed request: 1360 >> Current serial number in output stream: 1360 >> >> Now, I would appreciate any clues on the meaning and possible solution >> of this error or at least any directions on how to properly remove both >> Apple's X11 and Xquartz (they are supposed to be able to work >> side-by-side but I presume that a possible source of problems could >> arise from some conflict between them) AND re-install them to test them >> in a fresh install. >> >> Downgrading the lion machine to snow leopard does not seem to be an >> option... >> >> Thank you! >> Cheers, >> > >