From lp212 at cam.ac.uk Tue Feb 3 01:25:45 2015 From: lp212 at cam.ac.uk (Luca Pellegrini) Date: Tue, 3 Feb 2015 09:25:45 +0000 Subject: [Chimera-users] Command line problem Message-ID: <6E2B6B1C-562F-483C-B089-009CA67F7245@cam.ac.uk> Hi, I am having the following problem when I try to use the command line. When I select ?Command line? from the ?Favorites? menu, the command line window appears, but I can?t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can?t see what I type. Any idea of what?s going on? I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. Thanks for any advice. Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212 at cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59 From angshu at klyuniv.ac.in Tue Feb 3 02:17:41 2015 From: angshu at klyuniv.ac.in (angshu at klyuniv.ac.in) Date: Tue, 03 Feb 2015 04:17:41 -0600 Subject: [Chimera-users] Help Needed Message-ID: <8aa9531a11884263ced67fa7a85e591a@klyuniv.ac.in> Hi, I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein. For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A. Please let me know. Thanks. Angshuman From meng at cgl.ucsf.edu Tue Feb 3 10:06:13 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Feb 2015 10:06:13 -0800 Subject: [Chimera-users] finding residues in distance zone In-Reply-To: <8aa9531a11884263ced67fa7a85e591a@klyuniv.ac.in> References: <8aa9531a11884263ced67fa7a85e591a@klyuniv.ac.in> Message-ID: <9132F628-730D-4CF1-8DE4-C4E2B0FBAD02@cgl.ucsf.edu> Hi Angshuman, Sure, it just requires knowing how to do a more complicated command. Could be something like: select :.B-C & :78.A z<5 ~select ~ protein The first command would select residues in chains B,C that are also within 5 angstroms of residue 78 in chain A. The second one would un-select any residues that are not protein (because B and C might also include water, ions, etc.). See the documentation for how to specify atoms in the command line, including distance zones and combinations. Also you wouldn't have to use selection (command "select" in the examples above). You could do something else like show residue labels ("rlabel") or color the residues (e.g. "color red"). Or instead of an atomic center to atomic center distance cutoff, you could use the Find Clashes/Contacts tool (in menu under Tools? Structure Analysis, or the "findclash" command) to find all the contacts based on distances between the VDW surfaces of atoms. That tool can draw lines to show the contacts. There is a similar tool and command specifically for finding H-bonds: This tutorial has examples of using both FindHBond and Find Clashes/Contacts: 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 Feb 3, 2015, at 2:17 AM, angshu at klyuniv.ac.in wrote: > Hi, > I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein. > For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A. > Please let me know. > Thanks. > Angshuman From goddard at sonic.net Tue Feb 3 13:46:33 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 3 Feb 2015 13:46:33 -0800 Subject: [Chimera-users] Command line problem In-Reply-To: <6E2B6B1C-562F-483C-B089-009CA67F7245@cam.ac.uk> References: <6E2B6B1C-562F-483C-B089-009CA67F7245@cam.ac.uk> Message-ID: <1A4995C8-CA84-4CE5-8AB2-96D63AA39089@sonic.net> Hi Luca, I just tried Chimera 1.10.1 with Mac OS 10.10.2 and had no trouble with the command-line. I notice though that your Chimera build 40415 is not the Chimera 1.10.1 production version which has build number 40427. I think it is unlikely that your Chimrea 1.10.1 release candidate is different in a way that effects this bug but you should try the actual 1.10.1 release. My only guess is that your Chimera preferences file is somehow messing things up. You might try renaming the preferences file so Chimera starts with a new one to see if that fixes it. Your preferences file is ~/.chimera/preferences so a terminal command to rename it is mv ~/.chimera/preferences ~/.chimera/preferences.keep then start Chimera to see if that solves the problem. To report bugs such as this use Chimera menu Help / Report a Bug? so we get more info about your system and Chimera version. Tom > On Feb 3, 2015, at 1:25 AM, Luca Pellegrini wrote: > > Hi, > > I am having the following problem when I try to use the command line. When I select ?Command line? from the ?Favorites? menu, the command line window appears, but I can?t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can?t see what I type. Any idea of what?s going on? > > I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. > > Thanks for any advice. > > Kind regards, > Luca > > Luca Pellegrini > Department of Biochemistry > University of Cambridge > 80 Tennis Court Road > Cambridge CB2 1GA > UK > From letizia.meregalli at tum.de Tue Feb 3 09:48:08 2015 From: letizia.meregalli at tum.de (Letizia Meregalli) Date: Tue, 3 Feb 2015 18:48:08 +0100 Subject: [Chimera-users] Error: UnboundLocalError: local variable 'i' referenced before assignment Message-ID: Hi, I have a tRNA molecule and I would like to measure the angles between two nitrogenous bases. I created two planes, each for each base. When I select both planes, in order to measure the angles between them (Structure Measurements Axes/Planes/Centroids) I get following message: Exception in Tk callback Function: > (type: ) Args: ('1',) Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/CGLtk/Table.py", line 1043, in _browseCmd self.userBrowseCmd(self.selected()) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 268, in _tableCB self.feedback(sels) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) : local variable 'i' referenced before assignment UnboundLocalError: local variable 'i' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) See reply log for Python traceback. I really don?t know how can I solve this problem.. I?d be really grateful if you could help me or give me some hints! thank you a lot Letizia -------------- next part -------------- An HTML attachment was scrubbed... URL: From yarovoy at ucdavis.edu Tue Feb 3 14:28:57 2015 From: yarovoy at ucdavis.edu (Vladimir Yarov-Yarovoy) Date: Tue, 03 Feb 2015 14:28:57 -0800 Subject: [Chimera-users] multiple Chimera sessions on Mac Message-ID: <54D14BA9.4070403@ucdavis.edu> Hello, Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. Thank you, Vladimir From meng at cgl.ucsf.edu Tue Feb 3 15:18:04 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Feb 2015 15:18:04 -0800 Subject: [Chimera-users] multiple Chimera sessions on Mac In-Reply-To: <54D14BA9.4070403@ucdavis.edu> References: <54D14BA9.4070403@ucdavis.edu> Message-ID: <3518CE56-AC02-4961-87FF-4BCD433F5243@cgl.ucsf.edu> Hi Vladimir, We just ran a test on Yosemite and didn't have any problem doing this. Chimera was installed in Applications, so we opened two Terminal windows, and in each one, entered: /Applications/Chimera.app/Contents/MacOS/chimera ? resulting in two running instances of Chimera. The main thing is to substitute in the correct path and app name depending on where you installed Chimera and whether you changed its name. I'm not sure what you didn't mean by "doesn't work," however. There are general instructions for starting from the command line here: Creating aliases as described in that earlier chimera-users post is only for convenience as a typing shortcut, but it's not necessary. 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 Feb 3, 2015, at 2:28 PM, Vladimir Yarov-Yarovoy wrote: > Hello, > Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. > Thank you, > Vladimir From meng at cgl.ucsf.edu Tue Feb 3 15:18:04 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Feb 2015 15:18:04 -0800 Subject: [Chimera-users] multiple Chimera sessions on Mac In-Reply-To: <54D14BA9.4070403@ucdavis.edu> References: <54D14BA9.4070403@ucdavis.edu> Message-ID: Hi Vladimir, We just ran a test on Yosemite and didn't have any problem doing this. Chimera was installed in Applications, so we opened two Terminal windows, and in each one, entered: /Applications/Chimera.app/Contents/MacOS/chimera ? resulting in two running instances of Chimera. The main thing is to substitute in the correct path and app name depending on where you installed Chimera and whether you changed its name. I'm not sure what you didn't mean by "doesn't work," however. There are general instructions for starting from the command line here: Creating aliases as described in that earlier chimera-users post is only for convenience as a typing shortcut, but it's not necessary. 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 Feb 3, 2015, at 2:28 PM, Vladimir Yarov-Yarovoy wrote: > Hello, > Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. > Thank you, > Vladimir From pett at cgl.ucsf.edu Tue Feb 3 15:19:40 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Feb 2015 15:19:40 -0800 Subject: [Chimera-users] Error: UnboundLocalError: local variable 'i' referenced before assignment In-Reply-To: References: Message-ID: Hi Letizia, Thanks for reporting the problem, though next time you might want to use the Report a Bug menu item (in the help menu). Anyway, I will get a fix in but there's a pretty easy workaround until then: don't blank out the "plane name" when you create the plane. Give it some actual name (or use the default). Just don't blank it! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 3, 2015, at 9:48 AM, Letizia Meregalli wrote: > Hi, > I have a tRNA molecule and I would like to measure the angles between two nitrogenous bases. I created two planes, each for each base. When I select both planes, in order to measure the angles between them (Structure Measurements Axes/Planes/Centroids) I get following message: > > > Exception in Tk callback > Function: > (type: ) > Args: ('1',) > Traceback (innermost last): > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ > return apply(self.func, args) > File "/Applications/Chimera.app/Contents/Resources/share/CGLtk/Table.py", line 1043, in _browseCmd > self.userBrowseCmd(self.selected()) > File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 268, in _tableCB > self.feedback(sels) > File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback > diff = " ".join(words2[i:]) > : local variable 'i' referenced before assignment > > UnboundLocalError: local variable 'i' referenced before assignment > > File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback > diff = " ".join(words2[i:]) > > See reply log for Python traceback. > > > > I really don?t know how can I solve this problem.. I?d be really grateful if you could help me or give me some hints! > thank you a lot > > Letizia > _______________________________________________ > 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 lp212 at cam.ac.uk Tue Feb 3 15:35:51 2015 From: lp212 at cam.ac.uk (Luca Pellegrini) Date: Tue, 3 Feb 2015 23:35:51 +0000 Subject: [Chimera-users] Command line problem In-Reply-To: <1A4995C8-CA84-4CE5-8AB2-96D63AA39089@sonic.net> References: <6E2B6B1C-562F-483C-B089-009CA67F7245@cam.ac.uk> <1A4995C8-CA84-4CE5-8AB2-96D63AA39089@sonic.net> Message-ID: <060EEECB-6F26-433C-A984-BA88F3A117A1@cam.ac.uk> Hi Tom, I started Chimera with a new pref file as you suggested and the problem disappeared. Thanks for the prompt help. Best wishes, Luca Sent from my iPhone On 3 Feb 2015, at 21:46, Tom Goddard wrote: > Hi Luca, > > I just tried Chimera 1.10.1 with Mac OS 10.10.2 and had no trouble with the command-line. I notice though that your Chimera build 40415 is not the Chimera 1.10.1 production version which has build number 40427. I think it is unlikely that your Chimrea 1.10.1 release candidate is different in a way that effects this bug but you should try the actual 1.10.1 release. > > My only guess is that your Chimera preferences file is somehow messing things up. You might try renaming the preferences file so Chimera starts with a new one to see if that fixes it. Your preferences file is > > ~/.chimera/preferences > > so a terminal command to rename it is > > mv ~/.chimera/preferences ~/.chimera/preferences.keep > > then start Chimera to see if that solves the problem. > > To report bugs such as this use Chimera menu Help / Report a Bug? so we get more info about your system and Chimera version. > > Tom > > >> On Feb 3, 2015, at 1:25 AM, Luca Pellegrini wrote: >> >> Hi, >> >> I am having the following problem when I try to use the command line. When I select ?Command line? from the ?Favorites? menu, the command line window appears, but I can?t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can?t see what I type. Any idea of what?s going on? >> >> I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. >> >> Thanks for any advice. >> >> Kind regards, >> Luca >> >> Luca Pellegrini >> Department of Biochemistry >> University of Cambridge >> 80 Tennis Court Road >> Cambridge CB2 1GA >> UK > From yarovoy at ucdavis.edu Tue Feb 3 16:56:23 2015 From: yarovoy at ucdavis.edu (Vladimir Yarov-Yarovoy) Date: Tue, 03 Feb 2015 16:56:23 -0800 Subject: [Chimera-users] multiple Chimera sessions on Mac In-Reply-To: <3518CE56-AC02-4961-87FF-4BCD433F5243@cgl.ucsf.edu> References: <54D14BA9.4070403@ucdavis.edu> <3518CE56-AC02-4961-87FF-4BCD433F5243@cgl.ucsf.edu> Message-ID: <54D16E37.2090103@ucdavis.edu> Hi Elaine, Thank you! - it worked. The alias that I have on my Mac by default is not working with multiple terminal windows: alias chimera='open -a '\''/Applications/Chimera.app'\''' I created new alias that works fine: alias chim='/Applications/Chimera.app/Contents/MacOS/chimera' Vladimir On 2/3/15 3:18 PM, Elaine Meng wrote: > Hi Vladimir, > We just ran a test on Yosemite and didn't have any problem doing this. Chimera was installed in Applications, so we opened two Terminal windows, and in each one, entered: > > /Applications/Chimera.app/Contents/MacOS/chimera > > ? resulting in two running instances of Chimera. The main thing is to substitute in the correct path and app name depending on where you installed Chimera and whether you changed its name. > > I'm not sure what you didn't mean by "doesn't work," however. > > There are general instructions for starting from the command line here: > > > Creating aliases as described in that earlier chimera-users post is only for convenience as a typing shortcut, but it's not necessary. > 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 Feb 3, 2015, at 2:28 PM, Vladimir Yarov-Yarovoy wrote: > >> Hello, >> Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. >> Thank you, >> Vladimir From aka895 at gmail.com Thu Feb 5 03:41:14 2015 From: aka895 at gmail.com (Ankit Agrawal) Date: Thu, 5 Feb 2015 17:11:14 +0530 Subject: [Chimera-users] Help in executing python script in per-frame analysis Message-ID: Hi I am analysing a protein molecule (MD simulations). I wrote a python script to calculate inertia for the protein and ran it over 40000 frames. I got a data in log file but it is creating a ellipsoid around the molecule. I want 3 axes of the ellipsoid to be shown in that protein molecule not the ellipsoid as it covers the whole protein molecule. So that I can easily visualize the movement of all 3 axes of ellipsoid over the 40000 frames (means how the axes are changing during trajectory run). Thanks Ankit Department of Chemical Science IISER-Mohali, India -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Feb 5 11:30:50 2015 From: goddard at sonic.net (Tom Goddard) Date: Thu, 5 Feb 2015 11:30:50 -0800 Subject: [Chimera-users] Help in executing python script in per-frame analysis In-Reply-To: References: Message-ID: Hi Ankit, Chimera does not have a display style to show the inertia of a molecule as 3 axes. But here is a quick way to hack that in. You can change a little bit of Python code in your Chimera 1.10 distribution so that it shows three narrow ellipsoids that represent the axes. Use a text editor to edit chimera/share/measure/inertia.py or on Mac Chimera.app/Contents/Resources/share/measure/inertia.py and replace the ellipsoid surface function def ellipsoid_surface(axes, lengths, center, color, surface): xf = surface.openState.xform.inverse() sa, sc = transform_ellipsoid(axes, center, xf) varray, tarray = ellipsoid_geometry(sc, sa, lengths) p = surface.addPiece(varray, tarray, color) p.save_in_session = True return p with def ellipsoid_surface(axes, lengths, center, color, surface): xf = surface.openState.xform.inverse() sa, sc = transform_ellipsoid(axes, center, xf) for sx,sy,sz in [(1,.05,.05), (.05,1,.05), (.05,.05,1)]: lx,ly,lz = lengths varray, tarray = ellipsoid_geometry(sc, sa, (lx*sx,ly*sy,lz*sz)) p = surface.addPiece(varray, tarray, color) p.save_in_session = True return p then save the file, restart Chimera and now ?measure inertia #0 color yellow? will show the 3 axes. Make sure to keep the indentation of the code since that is important in the Python computer language. This change is scaling down 2 of the 3 ellipsoid axes by a factor of 0.05. You can change the 0.05 value to say 0.01 if you want thinner axis ellipsoids. Tom > On Feb 5, 2015, at 3:41 AM, Ankit Agrawal wrote: > > Hi > I am analysing a protein molecule (MD simulations). I wrote a python script to calculate inertia for the protein and ran it over 40000 frames. I got a data in log file but it is creating a ellipsoid around the molecule. > > I want 3 axes of the ellipsoid to be shown in that protein molecule not the ellipsoid as it covers the whole protein molecule. So that I can easily visualize the movement of all 3 axes of ellipsoid over the 40000 frames (means how the axes are changing during trajectory run). > > Thanks > Ankit > Department of Chemical Science > IISER-Mohali, India > _______________________________________________ > 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: inertiaaxes.jpg Type: image/jpeg Size: 43469 bytes Desc: not available URL: From aka895 at gmail.com Thu Feb 5 20:53:18 2015 From: aka895 at gmail.com (Ankit Agrawal) Date: Fri, 6 Feb 2015 10:23:18 +0530 Subject: [Chimera-users] Help in writing python code Message-ID: Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame. Here is the python code in per-frame analysis. from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green") Thanks. Ankit -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Feb 6 08:17:06 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 6 Feb 2015 08:17:06 -0800 Subject: [Chimera-users] Help in writing python code In-Reply-To: References: Message-ID: <32F9E715-7364-4BB4-B886-E43DE7792295@cgl.ucsf.edu> Hi Ankit, You would just use the ?close? Chimera command to close the new axes model each time, e.g. ?close #2? if the axes model is #2. You can see which one it is in the Model Panel (under Favorites in the menu). I would expect it to be the next unused number. Before actually running a script for a whole trajectory you should generally work out the necessary commands ?by hand? (interactively) for one or two frames 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 Feb 5, 2015, at 8:53 PM, Ankit Agrawal wrote: > Hi > I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame. > > Here is the python code in per-frame analysis. > > from chimera import runCommand > frame = mdInfo['frame'] > runCommand("measure inertia #1:0-120 color yellow") > runCommand("measure inertia #1:120-237 color green") > > Thanks. > Ankit From aka895 at gmail.com Fri Feb 6 09:34:22 2015 From: aka895 at gmail.com (Ankit Agrawal) Date: Fri, 6 Feb 2015 23:04:22 +0530 Subject: [Chimera-users] Help in writing python code In-Reply-To: <32F9E715-7364-4BB4-B886-E43DE7792295@cgl.ucsf.edu> References: <32F9E715-7364-4BB4-B886-E43DE7792295@cgl.ucsf.edu> Message-ID: Thanks. I got it. On 06-Feb-2015 9:47 pm, "Elaine Meng" wrote: > Hi Ankit, > You would just use the ?close? Chimera command to close the new axes model > each time, e.g. ?close #2? if the axes model is #2. You can see which one > it is in the Model Panel (under Favorites in the menu). I would expect it > to be the next unused number. > > Before actually running a script for a whole trajectory you should > generally work out the necessary commands ?by hand? (interactively) for one > or two frames 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 Feb 5, 2015, at 8:53 PM, Ankit Agrawal wrote: > > > Hi > > I am doing trajectory analysis which has 40000 frames. So for all frames > I wanted to calculate the all three inertia axes. That I did. But problem > is that when I run the python code it starts making all the three axes for > each frames that becomes messy. So I want a little change in my code so > that during trajectory analysis it should create axes but should delete or > hide the previous axes also. So during run I will see only the axes which > are related to that frame. > > > > Here is the python code in per-frame analysis. > > > > from chimera import runCommand > > frame = mdInfo['frame'] > > runCommand("measure inertia #1:0-120 color yellow") > > runCommand("measure inertia #1:120-237 color green") > > > > Thanks. > > Ankit > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadia_raboana at hotmail.fr Sat Feb 7 04:49:34 2015 From: nadia_raboana at hotmail.fr (Nadia Raboana) Date: Sat, 7 Feb 2015 20:49:34 +0800 Subject: [Chimera-users] Ramachandran plot statistics Message-ID: Hello,I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions.Thank you for answering me.Best regards, Nadia RaboanatahirySchool of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan, CHINA -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Feb 7 08:52:15 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 7 Feb 2015 08:52:15 -0800 Subject: [Chimera-users] Ramachandran plot statistics In-Reply-To: References: Message-ID: <242C736F-661C-4877-B104-A84FA703A45F@cgl.ucsf.edu> Hi Nadia, You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed. First assign the probabilities to the residues: in the Ramachandran Plot dialog, click the button at the bottom to ?Assign Residue Probabilities? (or use the ramachandran command option ?assign?): Then in Select by Attribute (Chimera menu: Select? By Attribute Value) choose attributes of ?residues? with Attribute: ramaProb ? that will show a histogram of the probability values. Then you can move the green bars to enclose the range of probabilities you want to select. After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector. Then you would divide by the total number of amino acid residues to get the percentage. You could count the total number of amino acid residues, for example, by using command ?select protein? and then clicking the green magnifying glass. 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 Feb 7, 2015, at 4:49 AM, Nadia Raboana wrote: > Hello, > I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions. > Thank you for answering me. > Best regards, > Nadia Raboanatahiry From mborgnia at nih.gov Sat Feb 7 13:34:30 2015 From: mborgnia at nih.gov (Mario J. Borgnia) Date: Sat, 07 Feb 2015 16:34:30 -0500 Subject: [Chimera-users] Change selection mode programatically Message-ID: <54D684E6.3020406@nih.gov> Hi, I am trying to find a way to split a complex selection pattern among a number of lines in a script. I was expecting that this would be an option to the select command, but apparently it is not. I know that I can combine "select" commands by changing the selection mode to "append" in the GUI, but I am struggling to find the way of doing this from command line or from a script. Is there a way to change the selection mode to "append" without using the GUI? Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia at nih.gov | +---------------------------------+ From meng at cgl.ucsf.edu Sat Feb 7 13:51:21 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 7 Feb 2015 13:51:21 -0800 Subject: [Chimera-users] Change selection mode programatically In-Reply-To: <54D684E6.3020406@nih.gov> References: <54D684E6.3020406@nih.gov> Message-ID: <5BB3D897-4D62-4DC3-A027-4F251377778C@cgl.ucsf.edu> Hi Mario, In command-line specifications there are operator symbols that often (but not always) allow you to specify what you want: the vertical bar ?|? is for union, the ampersand ?&? is for intersection, and tilde ?~? is for negation. Unfortunately there are no parentheses, which can be limiting. Sometimes it also requires a bit of experimentation to verify which operations are taking priority. See ?combinations? in the atom-spec docs, and also examples in the Quick Ref PDF. If you are actually working with selection as opposed to simply specification, you can subtract from a selection created in an earlier command with a subsequent ?~select? command. For example, commands: select protein & ligand z<5 ~select :trp ? would first select protein residues (amino acids) within 5 angstroms of residues classified as ligand, then deselect any tryptophans. Further, you can add to an existing selection using the union operator, for example: select sel | solvent ? would add all residues classified as solvent to the existing selection. 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 Feb 7, 2015, at 1:34 PM, Mario J. Borgnia wrote: > Hi, > I am trying to find a way to split a complex selection pattern among a > number of lines in a script. I was expecting that this would be an > option to the select command, but apparently it is not. I know that I > can combine "select" commands by changing the selection mode to "append" > in the GUI, but I am struggling to find the way of doing this from > command line or from a script. > > Is there a way to change the selection mode to "append" without using > the GUI? > Thanks > Mario From mborgnia at nih.gov Sat Feb 7 14:12:51 2015 From: mborgnia at nih.gov (Mario J. Borgnia) Date: Sat, 07 Feb 2015 17:12:51 -0500 Subject: [Chimera-users] Change selection mode programatically In-Reply-To: <5BB3D897-4D62-4DC3-A027-4F251377778C@cgl.ucsf.edu> References: <54D684E6.3020406@nih.gov> <5BB3D897-4D62-4DC3-A027-4F251377778C@cgl.ucsf.edu> Message-ID: <54D68DE3.6060101@nih.gov> Elaine, You are great! It does help. Thanks for answering in real time. The solution that worked in my case is extending the selection by combination. I was missing the "selected" attribute in the combination, instead I was looking for some option like "append" to the select command. select #1:lys select selected|#1:arg select selected|#1:305.A and so on... Thanks again! Mario. PS: The shortcuts in commands, although helpful, can be confusing. Take "sel" in "sel sel|aromatic", it first stands for select and then for selected... On 02/07/2015 04:51 PM, Elaine Meng wrote: > Hi Mario, > In command-line specifications there are operator symbols that often (but not always) allow you to specify what you want: the vertical bar ?|? is for union, the ampersand ?&? is for intersection, and tilde ?~? is for negation. Unfortunately there are no parentheses, which can be limiting. Sometimes it also requires a bit of experimentation to verify which operations are taking priority. See ?combinations? in the atom-spec docs, and also examples in the Quick Ref PDF. > > > > > If you are actually working with selection as opposed to simply specification, you can subtract from a selection created in an earlier command with a subsequent ?~select? command. > > > For example, commands: > > select protein & ligand z<5 > ~select :trp > > ? would first select protein residues (amino acids) within 5 angstroms of residues classified as ligand, then deselect any tryptophans. > > Further, you can add to an existing selection using the union operator, for example: > > select sel | solvent > > ? would add all residues classified as solvent to the existing selection. > > 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 Feb 7, 2015, at 1:34 PM, Mario J. Borgnia wrote: > >> Hi, >> I am trying to find a way to split a complex selection pattern among a >> number of lines in a script. I was expecting that this would be an >> option to the select command, but apparently it is not. I know that I >> can combine "select" commands by changing the selection mode to "append" >> in the GUI, but I am struggling to find the way of doing this from >> command line or from a script. >> >> Is there a way to change the selection mode to "append" without using >> the GUI? >> Thanks >> Mario From nadia_raboana at hotmail.fr Sun Feb 8 17:51:54 2015 From: nadia_raboana at hotmail.fr (Nadia Raboana) Date: Mon, 9 Feb 2015 01:51:54 +0000 Subject: [Chimera-users] =?utf-8?q?Ramachandran_plot_statistics?= Message-ID: Hi, It works perfectly, thank you for helping me. Best regards, Nadia Sent from Windows Mail From: Elaine Meng Sent: ?February? ?8?, ?2015 ?12?:?52? ?AM To: Nadia Raboana CC: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Ramachandran plot statistics Hi Nadia, You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed. First assign the probabilities to the residues: in the Ramachandran Plot dialog, click the button at the bottom to ?Assign Residue Probabilities? (or use the ramachandran command option ?assign?): Then in Select by Attribute (Chimera menu: Select? By Attribute Value) choose attributes of ?residues? with Attribute: ramaProb ? that will show a histogram of the probability values. Then you can move the green bars to enclose the range of probabilities you want to select. After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector. Then you would divide by the total number of amino acid residues to get the percentage. You could count the total number of amino acid residues, for example, by using command ?select protein? and then clicking the green magnifying glass. 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 Feb 7, 2015, at 4:49 AM, Nadia Raboana wrote: > Hello, > I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions. > Thank you for answering me. > Best regards, > Nadia Raboanatahiry -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Mon Feb 9 00:15:18 2015 From: chiendarret at gmail.com (Francesco Pietra) Date: Mon, 9 Feb 2015 09:15:18 +0100 Subject: [Chimera-users] CHIMERA movie with parm7/dcd Message-ID: Hello: In the recent past, issues in running movie with parm7 files were solved. Now, with ambertools14 problems come out again, unless I dropped into a silly mistake. That is, parm7/dcd was refused because no top file was found. Renaming the prm7 extension prmtop led to File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" Thanks for your kind attention francesco pietra -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter.blaas at meduniwien.ac.at Mon Feb 9 03:49:58 2015 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Mon, 09 Feb 2015 12:49:58 +0100 Subject: [Chimera-users] command line Message-ID: <54D89EE6.6060703@meduniwien.ac.at> Hi, sorry for asking again an old question but I lost the solution: how do I show single solid planes of several volumes? I tried: 'vol all style solid plane one axis z' and many combinations thereof but it always tells me: 'volume invalid planes argument "one": Value must be one of x,y,z, got "one" when I try ' vol all style solid plane z' it tells me: 'volume invalid planes argument "z"' and so on.... Thanks a lot for your patience, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ From meng at cgl.ucsf.edu Mon Feb 9 08:32:25 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Feb 2015 08:32:25 -0800 Subject: [Chimera-users] command line In-Reply-To: <54D89EE6.6060703@meduniwien.ac.at> References: <54D89EE6.6060703@meduniwien.ac.at> Message-ID: <195BC531-351E-40DD-9534-4888EE1BE991@cgl.ucsf.edu> Hi Dieter, No worries, it can be hard to find the information sometimes! There is another mandatory argument following the axis, the index of the plane to show. Usage of the option is given here: planes axis,start[,end[,increment[,depth]]] ? where "start" is the index of the plane to show, could be an integer or real number. The brackets indicate optional arguments, but start isn't optional. Thus, your command could be something like: volume all planes z,10 (no space after the comma) If you want to show planes of different indices for the different volumes, you would need to use a separate command for each with the actual model number instead of "all". 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 Feb 9, 2015, at 3:49 AM, Dieter Blaas wrote: > Hi, > sorry for asking again an old question but I lost the solution: > > how do I show single solid planes of several volumes? > I tried: 'vol all style solid plane one axis z' and many combinations thereof but it always tells me: > 'volume invalid planes argument "one": Value must be one of x,y,z, got "one" > when I try ' vol all style solid plane z' it tells me: > 'volume invalid planes argument "z"' and so on.... > Thanks a lot for your patience, best, Dieter > From dieter.blaas at meduniwien.ac.at Mon Feb 9 09:47:15 2015 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Mon, 09 Feb 2015 18:47:15 +0100 Subject: [Chimera-users] command line In-Reply-To: <195BC531-351E-40DD-9534-4888EE1BE991@cgl.ucsf.edu> References: <54D89EE6.6060703@meduniwien.ac.at> <195BC531-351E-40DD-9534-4888EE1BE991@cgl.ucsf.edu> Message-ID: <54D8F2A3.8060203@meduniwien.ac.at> Hi Elaine, thanks a lot! I believe that it was the final value that confused me as the GUI sets it automatically to the middle of the volume! In the command line it must be given explicitly. Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ Am 09.02.2015 um 17:32 schrieb Elaine Meng: > Hi Dieter, > No worries, it can be hard to find the information sometimes! There is another mandatory argument following the axis, the index of the plane to show. > > Usage of the option is given here: > > > planes axis,start[,end[,increment[,depth]]] > > ? where "start" is the index of the plane to show, could be an integer or real number. The brackets indicate optional arguments, but start isn't optional. Thus, your command could be something like: > > volume all planes z,10 > > (no space after the comma) If you want to show planes of different indices for the different volumes, you would need to use a separate command for each with the actual model number instead of "all". 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 Feb 9, 2015, at 3:49 AM, Dieter Blaas wrote: > >> Hi, >> sorry for asking again an old question but I lost the solution: >> >> how do I show single solid planes of several volumes? >> I tried: 'vol all style solid plane one axis z' and many combinations thereof but it always tells me: >> 'volume invalid planes argument "one": Value must be one of x,y,z, got "one" >> when I try ' vol all style solid plane z' it tells me: >> 'volume invalid planes argument "z"' and so on.... >> Thanks a lot for your patience, best, Dieter >> From jug25 at psu.edu Mon Feb 9 09:55:20 2015 From: jug25 at psu.edu (Jian Guan) Date: Mon, 9 Feb 2015 12:55:20 -0500 Subject: [Chimera-users] radial density map Message-ID: <00aa01d04491$9279d8f0$b76d8ad0$@psu.edu> Hi all, I have a mrc map of virus, T=7 icosahedron. Does anyone know how to make radial density map (averaged radial density VS radius of virion)? I tried chimera method of shortcut rd. It took long time but return one result. For the rd result, is it make along x, y or z axis? Or along assigned axis, like 5 fold symmetric axis? I have asymmetric extra density around 5-fold axis. What will happen in my case if use rd? Are there any other ways to make the plot besides of rd? Thank you so much. Sincerely yours, Jian -------------- next part -------------- An HTML attachment was scrubbed... URL: From moldham at mail.rockefeller.edu Sun Feb 8 13:40:37 2015 From: moldham at mail.rockefeller.edu (Michael Oldham) Date: Sun, 8 Feb 2015 16:40:37 -0500 Subject: [Chimera-users] adding morphs to scene animation in Chimera Message-ID: <00920CE3-E815-4B41-AACF-9860409C5508@rockefeller.edu> Chimera users, I want to use a combination of various scene selections and morphs in a Chimera animation. Can someone tell me how morphs and scenes be combined to make one movie. Thanks Mike Oldham Rockefeller University From j.eiros-zamora14 at imperial.ac.uk Mon Feb 9 06:39:03 2015 From: j.eiros-zamora14 at imperial.ac.uk (Juan Eiros Zamora) Date: Mon, 09 Feb 2015 14:39:03 +0000 Subject: [Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera Message-ID: <54D8C687.90501@imperial.ac.uk> Hi all, I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the structureViz2 plugin. I use structureviz to open chimera through cytoscape and load an MD trajectory of a protein to create a RIN through Analysis --> Residue interaction network... What I am trying to do is colour the nodes in cytoscape based on which chain they belong to. My protein has three chains, and in chimera I color each differently. In cytoscape, I go to apps --> structureviz--> synchronize residue colors. Here I am given two options. The first one is ?Apply colors from current network view to associated Chimera models?: This one works fine, but it is not what I want. What I want to do is the second option: ?Apply colors from associated Chimera models to current network view?, but when I clik on OK it does nothing. Anybody having the same problem or some suggestions on how I might solve this? Much appreciated, Juan Eiros -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Feb 9 10:54:20 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Feb 2015 10:54:20 -0800 Subject: [Chimera-users] adding morphs to scene animation in Chimera In-Reply-To: <00920CE3-E815-4B41-AACF-9860409C5508@rockefeller.edu> References: <00920CE3-E815-4B41-AACF-9860409C5508@rockefeller.edu> Message-ID: <0614A9AB-F2CD-4E88-B516-AD18FE6C8F1D@cgl.ucsf.edu> Hi Mike, You would first create all the morph trajectories of interest, then for each morph, create a scene showing the first frame of the range you want to play and another scene showing the last frame of the range you want to play. These scenes should also have the desired display styles, colors, etc. Then you add those two scenes as keyframes to the Timeline in the Animation GUI. The transition between the two will proceed through the intervening trajectory frames as described under keyframe Duration in the Animation docs: The other way to include morphing in an animation is to use a command script with "coordset" to play back the trajectories, with various other commands (instead of scenes) to change colors, styles, and orientations. There are a couple of examples with command scripts in the Chimera Animation Gallery: Kinase morph: Ball-and-socket motion: Those only include one morph trajectory each, but generalization to multiple morph trajectories is merely a matter of having additional already-created morph trajectories (usually saved in a session), hiding one trajectory and showing another, and having additional "coordset" commands to play back the subsequent trajectory models. 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 Feb 8, 2015, at 1:40 PM, Michael Oldham wrote: > Chimera users, > > I want to use a combination of various scene selections and morphs in a Chimera animation. Can someone tell me how morphs and scenes be combined to make one movie. > > Thanks > > Mike Oldham > Rockefeller University From pett at cgl.ucsf.edu Mon Feb 9 11:09:07 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 9 Feb 2015 11:09:07 -0800 Subject: [Chimera-users] CHIMERA movie with parm7/dcd In-Reply-To: References: Message-ID: <0712AEC3-613C-40AE-BD8F-6B30AFD10012@cgl.ucsf.edu> Hi Francesco, I think you've dome this before. If you are using a prmtop/DCD combo you need to choose the "NAMD (prmtop/DCD)" format, not the "Amber" format. Maybe you should note this down somewhere. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 9, 2015, at 12:15 AM, Francesco Pietra wrote: > Hello: > In the recent past, issues in running movie with parm7 files were solved. Now, with ambertools14 problems come out again, unless I dropped into a silly mistake. > > That is, parm7/dcd was refused because no top file was found. Renaming the prm7 extension prmtop led to > > > File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame > raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" > > Thanks for your kind attention > > francesco pietra > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Mon Feb 9 13:17:51 2015 From: goddard at sonic.net (Tom Goddard) Date: Mon, 9 Feb 2015 13:17:51 -0800 Subject: [Chimera-users] radial density map In-Reply-To: <00aa01d04491$9279d8f0$b76d8ad0$@psu.edu> References: <00aa01d04491$9279d8f0$b76d8ad0$@psu.edu> Message-ID: <302054D2-D9C1-41E9-BA11-AE5D66090CE7@sonic.net> Hi Jian, Chimera does not make radial density plots. I guess you found the RadialDensity.zip extension which creates the ?rd? shortcut on the Chimera scripts web page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts There is an old mailing list message I wrote about that extension http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008697.html which says that it prints to the Chimera reply log the average radial density as a function of distance from the center. Make sure your map origin is at the center of the virus (volume dialog menu Features / Coordinates, Origin Index value). You can plot that data in any graphing program. Each value is the average over a thin spherical shell so it does not depend on any axis. This won?t help you if you just want the density on a 1-dimensional line coincident with a symmetry axis. Tom > On Feb 9, 2015, at 9:55 AM, Jian Guan wrote: > > Hi all, > I have a mrc map of virus, T=7 icosahedron. Does anyone know how to make radial density map (averaged radial density VS radius of virion)? > I tried chimera method of shortcut rd. It took long time but return one result. For the rd result, is it make along x, y or z axis? Or along assigned axis, like 5 fold symmetric axis? I have asymmetric extra density around 5-fold axis. What will happen in my case if use rd? > Are there any other ways to make the plot besides of rd? > Thank you so much. > Sincerely yours, > Jian > _______________________________________________ > 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 vamseedharr at gmail.com Mon Feb 9 15:25:39 2015 From: vamseedharr at gmail.com (vamsee) Date: Mon, 9 Feb 2015 18:25:39 -0500 Subject: [Chimera-users] Manipulate individual hexagons/pentagons in cage builder Message-ID: Hello Elaine, I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. Thank you yet again, Vamsee -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Feb 9 16:27:43 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 9 Feb 2015 16:27:43 -0800 Subject: [Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera In-Reply-To: <54D8C687.90501@imperial.ac.uk> References: <54D8C687.90501@imperial.ac.uk> Message-ID: <682BBDAA-2F49-4706-8859-0FDC16FD4EC1@cgl.ucsf.edu> Hi Juan, It certainly does behave as you describe. Our Cytoscape expert (Scooter Morris) is out sick right now and I would need his assistance to determine how to fix the network information/nodes so that the Chimera->Cytoscape coloring works. So unfortunately it will probably be a few days before we can offer any kind of usable fix for this. I'll post something when it's available. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora wrote: > Hi all, > > I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the structureViz2 plugin. > > I use structureviz to open chimera through cytoscape and load an MD trajectory of a protein to create a RIN through Analysis --> Residue interaction network... > What I am trying to do is colour the nodes in cytoscape based on which chain they belong to. My protein has three chains, and in chimera I color each differently. In cytoscape, I go to apps --> structureviz--> synchronize residue colors. Here I am given two options. The first one is ?Apply colors from current network view to associated Chimera models?: This one works fine, but it is not what I want. What I want to do is the second option: ?Apply colors from associated Chimera models to current network view?, but when I clik on OK it does nothing. > Anybody having the same problem or some suggestions on how I might solve this? > Much appreciated, > Juan Eiros > > _______________________________________________ > 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 kosinski at embl.de Tue Feb 10 07:19:33 2015 From: kosinski at embl.de (Jan Kosinski) Date: Tue, 10 Feb 2015 16:19:33 +0100 Subject: [Chimera-users] pymol get_view and set_view in Chimera? Message-ID: <54DA2185.2030504@embl.de> Is there an equivalent of pymol get_view and set_view in Chimera? I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View). Thanks in advance, Jan From meng at cgl.ucsf.edu Tue Feb 10 08:21:59 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Feb 2015 08:21:59 -0800 Subject: [Chimera-users] pymol get_view and set_view in Chimera? In-Reply-To: <54DA2185.2030504@embl.de> References: <54DA2185.2030504@embl.de> Message-ID: Dear Jan, I believe "savepos" and "reset" are the Chimera equivalents, e.g. savepos name1 [...move stuff around...] savepos name2 reset name1 reset name2 80 What savepos saves sounds like the same stuff as in the pymol setview description, not sure why you rejected it as the equivalent: Chimera also allows saving/restoring scenes, which besides the position information also include display styles, colors, etc. See the "scene" command: Because scenes contain more information than positions, they can make Chimera session files rather large. 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 Feb 10, 2015, at 7:19 AM, Jan Kosinski wrote: > Is there an equivalent of pymol get_view and set_view in Chimera? > > I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View). > > Thanks in advance, > Jan > From meng at cgl.ucsf.edu Tue Feb 10 08:36:55 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Feb 2015 08:36:55 -0800 Subject: [Chimera-users] Manipulate individual hexagons/pentagons in cage builder In-Reply-To: References: Message-ID: <7EA4B07F-7555-4EE9-B308-2280317CD9F9@cgl.ucsf.edu> Hi Vamsee, Seems like an under-determined or under-defined problem, as one might expect an infinite number of ways to misassemble a set of subunits. If there were any experimental information on the nature of the misassembly, that might help, but even so, I don't have elegant ideas of how to generate it in Chimera. The cage is a created as a bunch of markers (fake atoms, where each is a separate residue) with links (fake bonds) between them. If you can select just the markers in an individual polygon with the mouse, then you can move them manually (leaving the others unmoved) with the Movement Mouse Mode tool. It's in the menu under Tools? Movement, and you would use the mode to "Move selection". Doing this several times might be tedious, and the resulting model might be a figment of your imagination, however! 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 Feb 9, 2015, at 3:25 PM, vamsee wrote: > Hello Elaine, > I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. > Thank you yet again, > Vamsee From kosinski at embl.de Tue Feb 10 08:53:04 2015 From: kosinski at embl.de (Jan Kosinski) Date: Tue, 10 Feb 2015 17:53:04 +0100 Subject: [Chimera-users] pymol get_view and set_view in Chimera? In-Reply-To: References: <54DA2185.2030504@embl.de> Message-ID: <54DA3770.80105@embl.de> Dear Elaine, I would like to be able to copy the position info to a chimera script rather than a session. With set_view/get_view it is possible. The one can write a script that sets window size, set view, load structures, change appearance, and render a figure. If one needs to change a file from which model is loaded, with script it involves quick edit of a text file. I seek for that just for convenience of having everything in one editable script rather than keeping a session with saved positions. Best, Jan On 02/10/2015 05:21 PM, Elaine Meng wrote: > Dear Jan, > I believe "savepos" and "reset" are the Chimera equivalents, e.g. > > savepos name1 > [...move stuff around...] > savepos name2 > reset name1 > reset name2 80 > > What savepos saves sounds like the same stuff as in the pymol setview description, not sure why you rejected it as the equivalent: > > > Chimera also allows saving/restoring scenes, which besides the position information also include display styles, colors, etc. See the "scene" command: > > > Because scenes contain more information than positions, they can make Chimera session files rather large. > 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 Feb 10, 2015, at 7:19 AM, Jan Kosinski wrote: > >> Is there an equivalent of pymol get_view and set_view in Chimera? >> >> I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View). >> >> Thanks in advance, >> Jan >> -- Jan Kosinski, PhD Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg Germany From meng at cgl.ucsf.edu Tue Feb 10 09:00:34 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Feb 2015 09:00:34 -0800 Subject: [Chimera-users] pymol get_view and set_view in Chimera? In-Reply-To: <54DA3770.80105@embl.de> References: <54DA2185.2030504@embl.de> <54DA3770.80105@embl.de> Message-ID: <2A669162-FC7D-42FB-8F4D-2BF03E9793CE@cgl.ucsf.edu> Ah, I see. I normally create a script but also save the session to be used along with the script. In that case, there is no equivalent. Although there are Chimera commands to set scale, clipping plane positions, etc. they are all for relative changes rather than to some absolute value. Sorry about that, Elaine On Feb 10, 2015, at 8:53 AM, Jan Kosinski wrote: > Dear Elaine, > > I would like to be able to copy the position info to a chimera script rather than a session. With set_view/get_view it is possible. The one can write a script that sets window size, set view, load structures, change appearance, and render a figure. If one needs to change a file from which model is loaded, with script it involves quick edit of a text file. > > I seek for that just for convenience of having everything in one editable script rather than keeping a session with saved positions. > > Best, > Jan > > On 02/10/2015 05:21 PM, Elaine Meng wrote: >> Dear Jan, >> I believe "savepos" and "reset" are the Chimera equivalents, e.g. >> >> savepos name1 >> [...move stuff around...] >> savepos name2 >> reset name1 >> reset name2 80 >> >> What savepos saves sounds like the same stuff as in the pymol setview description, not sure why you rejected it as the equivalent: >> >> >> Chimera also allows saving/restoring scenes, which besides the position information also include display styles, colors, etc. See the "scene" command: >> >> >> Because scenes contain more information than positions, they can make Chimera session files rather large. >> 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 Feb 10, 2015, at 7:19 AM, Jan Kosinski wrote: >> >>> Is there an equivalent of pymol get_view and set_view in Chimera? >>> >>> I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View). >>> >>> Thanks in advance, >>> Jan >>> > > > -- > Jan Kosinski, PhD > Structural and Computational Biology Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1 > 69117 Heidelberg > Germany > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From kosinski at embl.de Tue Feb 10 09:05:03 2015 From: kosinski at embl.de (Jan Kosinski) Date: Tue, 10 Feb 2015 18:05:03 +0100 Subject: [Chimera-users] pymol get_view and set_view in Chimera? In-Reply-To: <2A669162-FC7D-42FB-8F4D-2BF03E9793CE@cgl.ucsf.edu> References: <54DA2185.2030504@embl.de> <54DA3770.80105@embl.de> <2A669162-FC7D-42FB-8F4D-2BF03E9793CE@cgl.ucsf.edu> Message-ID: <54DA3A3F.1020506@embl.de> OK, I stay with using scripts in combination with sessions then! Thanks for your always super fast response :-) Jan On 02/10/2015 06:00 PM, Elaine Meng wrote: > Ah, I see. I normally create a script but also save the session to be used along with the script. > > In that case, there is no equivalent. Although there are Chimera commands to set scale, clipping plane positions, etc. they are all for relative changes rather than to some absolute value. Sorry about that, > Elaine > > On Feb 10, 2015, at 8:53 AM, Jan Kosinski wrote: > >> Dear Elaine, >> >> I would like to be able to copy the position info to a chimera script rather than a session. With set_view/get_view it is possible. The one can write a script that sets window size, set view, load structures, change appearance, and render a figure. If one needs to change a file from which model is loaded, with script it involves quick edit of a text file. >> >> I seek for that just for convenience of having everything in one editable script rather than keeping a session with saved positions. >> >> Best, >> Jan >> >> On 02/10/2015 05:21 PM, Elaine Meng wrote: >>> Dear Jan, >>> I believe "savepos" and "reset" are the Chimera equivalents, e.g. >>> >>> savepos name1 >>> [...move stuff around...] >>> savepos name2 >>> reset name1 >>> reset name2 80 >>> >>> What savepos saves sounds like the same stuff as in the pymol setview description, not sure why you rejected it as the equivalent: >>> >>> >>> Chimera also allows saving/restoring scenes, which besides the position information also include display styles, colors, etc. See the "scene" command: >>> >>> >>> Because scenes contain more information than positions, they can make Chimera session files rather large. >>> 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 Feb 10, 2015, at 7:19 AM, Jan Kosinski wrote: >>> >>>> Is there an equivalent of pymol get_view and set_view in Chimera? >>>> >>>> I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View). >>>> >>>> Thanks in advance, >>>> Jan >>>> >> >> -- >> Jan Kosinski, PhD >> Structural and Computational Biology Unit >> European Molecular Biology Laboratory (EMBL) >> Meyerhofstrasse 1 >> 69117 Heidelberg >> Germany >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -- Jan Kosinski, PhD Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg Germany From moldham at mail.rockefeller.edu Tue Feb 10 03:30:58 2015 From: moldham at mail.rockefeller.edu (Michael Oldham) Date: Tue, 10 Feb 2015 06:30:58 -0500 Subject: [Chimera-users] adding morphs to scene animation in Chimera In-Reply-To: <0614A9AB-F2CD-4E88-B516-AD18FE6C8F1D@cgl.ucsf.edu> References: <00920CE3-E815-4B41-AACF-9860409C5508@rockefeller.edu> <0614A9AB-F2CD-4E88-B516-AD18FE6C8F1D@cgl.ucsf.edu> Message-ID: <3BD30A75-1E0C-4A16-BF02-C232D70B119A@rockefeller.edu> Thanks Elaine. Michael Oldham Sent from my iPhone > On Feb 9, 2015, at 1:54 PM, Elaine Meng wrote: > > Hi Mike, > You would first create all the morph trajectories of interest, then for each morph, create a scene showing the first frame of the range you want to play and another scene showing the last frame of the range you want to play. These scenes should also have the desired display styles, colors, etc. Then you add those two scenes as keyframes to the Timeline in the Animation GUI. The transition between the two will proceed through the intervening trajectory frames as described under keyframe Duration in the Animation docs: > > > The other way to include morphing in an animation is to use a command script with "coordset" to play back the trajectories, with various other commands (instead of scenes) to change colors, styles, and orientations. There are a couple of examples with command scripts in the Chimera Animation Gallery: > > Kinase morph: > > > Ball-and-socket motion: > > > Those only include one morph trajectory each, but generalization to multiple morph trajectories is merely a matter of having additional already-created morph trajectories (usually saved in a session), hiding one trajectory and showing another, and having additional "coordset" commands to play back the subsequent trajectory models. > 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 Feb 8, 2015, at 1:40 PM, Michael Oldham wrote: >> >> Chimera users, >> >> I want to use a combination of various scene selections and morphs in a Chimera animation. Can someone tell me how morphs and scenes be combined to make one movie. >> >> Thanks >> >> Mike Oldham >> Rockefeller University > From goddard at sonic.net Tue Feb 10 11:48:06 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 10 Feb 2015 11:48:06 -0800 Subject: [Chimera-users] Manipulate individual hexagons/pentagons in cage builder In-Reply-To: References: Message-ID: <68ED8690-F127-4C49-94FD-0F02CA907361@sonic.net> I?m not sure what you mean by ?incorrectly attached pentagons and hexagons?. Do you mean the edge of a pentagon does not align with the edge of a neighboring hexagon? Or do you mean the cage has large holes because the topology (pattern of connections) does not make it close? The former can be done by hand with ?move selection? mouse mode as Elaine mentioned and the latter can be done just as a normal use of the cage builder tool. Tom > On Feb 9, 2015, at 3:25 PM, vamsee wrote: > > Hello Elaine, > > > I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. > > > Thank you yet again, > > > Vamsee > _______________________________________________ > 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 alejandro.virrueta at yale.edu Wed Feb 11 08:50:18 2015 From: alejandro.virrueta at yale.edu (Alejandro Virrueta) Date: Wed, 11 Feb 2015 11:50:18 -0500 Subject: [Chimera-users] UnitCell.molecule_center(): Attribute does not exist Message-ID: Hello all, I'm trying to execute the script to fill out the crystal unit cell found here: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] Where did the attribute go? Is there some other module I could use? Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. Any help is greatly appreciated! Thanks! Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From scooter at cgl.ucsf.edu Wed Feb 11 10:17:26 2015 From: scooter at cgl.ucsf.edu (Scooter Morris) Date: Wed, 11 Feb 2015 10:17:26 -0800 Subject: [Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera Message-ID: <54DB9CB6.2050709@cgl.ucsf.edu> Hi Juan, I've uploaded a new version of structureViz (1.0.1) that should fix your problem. Don't hesitate to let us know if there are other issues/enhancements you would like to see. -- scooter On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora > wrote: > Hi all, > > I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the > structureViz2 plugin. > > I use structureviz to open chimera through cytoscape and load an MD > trajectory of a protein to create a RIN through Analysis --> Residue > interaction network... > > What I am trying to do is colour the nodes in cytoscape based on which > chain they belong to. My protein has three chains, and in chimera I > color each differently. In cytoscape, I go to apps --> structureviz--> > synchronize residue colors. Here I am given two options. The first one > is ?Apply colors from current network view to associated Chimera > models?: This one works fine, but it is not what I want. What I want > to do is the second option: ?Apply colors from associated Chimera > models to current network view?, but when I clik on OK it does nothing. > > Anybody having the same problem or some suggestions on how I might > solve this? > > Much appreciated, > > Juan Eiros > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Feb 11 10:20:36 2015 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 Feb 2015 10:20:36 -0800 Subject: [Chimera-users] UnitCell.molecule_center(): Attribute does not exist In-Reply-To: References: Message-ID: <0A831E43-B01E-43EF-981E-9ECF6BACC915@sonic.net> Hi Alex, There were in fact two problems in the unit cell example code caused by changes in Chimera Python APIs over the years. I?ve updated the example ? the web site will be updated over night. The fixed code is attached. Thanks for reporting the problem. Tom > On Feb 11, 2015, at 8:50 AM, Alejandro Virrueta wrote: > > Hello all, > > I'm trying to execute the script to fill out the crystal unit cell found here: > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 > > However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: > > ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] > > Where did the attribute go? > Is there some other module I could use? > Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. > > Any help is greatly appreciated! Thanks! > Alex > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ucell.py Type: text/x-python-script Size: 1102 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrozell at rci.rutgers.edu Thu Feb 12 16:27:51 2015 From: sbrozell at rci.rutgers.edu (Scott Brozell) Date: Thu, 12 Feb 2015 19:27:51 -0500 Subject: [Chimera-users] Announcement: Release of DOCK 6.7 Message-ID: <20150213002751.GC14401@casegroup.rutgers.edu> We are pleased to announce the release of DOCK 6.7. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. In version 6.7 the default values for several input parameters were updated based mainly on a performance assessment using large data sets and employing multiple metrics including pose reproduction, cross-docking, and database enrichment For full information on what is new in DOCK 6.7, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.7.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu From deligkaris at gmail.com Mon Feb 16 20:30:22 2015 From: deligkaris at gmail.com (Christos Deligkaris) Date: Mon, 16 Feb 2015 22:30:22 -0600 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: References: Message-ID: Dear all, I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: ************** #!/usr/bin/env python import re,os,sys,math, decimal, subprocess from copy import deepcopy from openeye.oechem import * from decimal import * script_file=open("chimera_script_for_" + "ligand" +".com", 'w') script_file.write("open "+ "127D" +"\n") script_file.write("open " + "127D" +"\n") script_file.write("open "+ "ligand.pdb" +"\n") script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") script_file.write("stop") script_file.close print script_file.name chimera=subprocess.call(["chimera", " --nogui ", " chimera_script_for_ligand.com"]) print chimera #delete the script, leaving just the flipped ligand #os.remove(script_file.name) ******************* When I run the script, it successfully generates the .com chimera script. However, I get the following error message: ******************* [christos at biophysics Desktop]$ ./script.py chimera_script_for_ligand.com Traceback (most recent call last): File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in value = chimeraInit.init(sys.argv) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init splash.create() File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create sync=chimera.debug) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable 1 ********************** The python script successfully creates the .com script: ****************************** [christos at biophysics Desktop]$ more chimera_script_for_ligand.com open 127D open 127D open ligand.pdb match #0:6 #1:18 write format pdb 2 flipped_ligand stop *************************** and if I manually execute this chimera script, everything works out well: ************************** [christos at biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com Fetching 127D from web site www.rcsb.org 0 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Fetching 127D from web site www.rcsb.org 88 Kbytes received 80 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Opening ligand.pdb... ligand.pdb opened Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues Executing match ['#0:6', '#1:18'], no iteration RMSD between 21 atom pairs is 0.630 angstroms Wrote flipped_ligand into /home/christos/Desktop ***************************** Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Feb 16 21:02:01 2015 From: goddard at sonic.net (Tom Goddard) Date: Mon, 16 Feb 2015 21:02:01 -0800 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: References: Message-ID: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> Hi Christos, I think your error is because the ??nogui? option in your subprocess.call() has spaces before and after inside the quote marks. Take those spaces out and I bet it will work. The error seems to be trying to create the Chimera splash screen which would not happen in nogui mode. Tom > On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote: > > Dear all, > > I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: > > ************** > > #!/usr/bin/env python > import re,os,sys,math, decimal, subprocess > from copy import deepcopy > from openeye.oechem import * > from decimal import * > > script_file=open("chimera_script_for_" + "ligand" +".com", 'w') > script_file.write("open "+ "127D" +"\n") > script_file.write("open " + "127D" +"\n") > script_file.write("open "+ "ligand.pdb" +"\n") > script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") > script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") > script_file.write("stop") > script_file.close > print script_file.name > chimera=subprocess.call(["chimera", " --nogui ", "chimera_script_for_ligand.com "]) > print chimera > #delete the script, leaving just the flipped ligand > #os.remove(script_file.name ) > > ******************* > > When I run the script, it successfully generates the .com chimera script. However, I get the following error message: > > ******************* > > [christos at biophysics Desktop]$ ./script.py > chimera_script_for_ligand.com > Traceback (most recent call last): > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in > value = chimeraInit.init(sys.argv) > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init > splash.create() > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create > sync=chimera.debug) > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ > self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) > _tkinter.TclError: no display name and no $DISPLAY environment variable > 1 > > ********************** > > The python script successfully creates the .com script: > > ****************************** > > [christos at biophysics Desktop]$ more chimera_script_for_ligand.com > open 127D > open 127D > open ligand.pdb > match #0:6 #1:18 > write format pdb 2 flipped_ligand > stop > > *************************** > > and if I manually execute this chimera script, everything works out well: > > ************************** > > [christos at biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com > Fetching 127D from web site www.rcsb.org > 0 Kbytes received > Fetch 127D: finished > Done fetching 127D; verifying... > Opening 127D... > #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > Opening VRML model in 127D - Nucleotides... > 127D opened > Opened VRML model in 127D - Nucleotides > Opened 127D containing 1 model, 639 atoms, and 146 residues > Fetching 127D from web site www.rcsb.org > 88 Kbytes received > 80 Kbytes received > Fetch 127D: finished > Done fetching 127D; verifying... > Opening 127D... > #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > Opening VRML model in 127D - Nucleotides... > 127D opened > Opened VRML model in 127D - Nucleotides > Opened 127D containing 1 model, 639 atoms, and 146 residues > Opening ligand.pdb... > ligand.pdb opened > Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues > Executing match ['#0:6', '#1:18'], no iteration > > RMSD between 21 atom pairs is 0.630 angstroms > Wrote flipped_ligand into /home/christos/Desktop > > ***************************** > > Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, > > Christos Deligkaris, PhD > Assistant Professor of Physics, Drury University > 900 N Benton Ave, Springfield MO, 65802 > Office Phone: (417) 873-7234 > www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris > > > > _______________________________________________ > 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 deligkaris at gmail.com Tue Feb 17 06:44:24 2015 From: deligkaris at gmail.com (Christos Deligkaris) Date: Tue, 17 Feb 2015 08:44:24 -0600 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> References: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> Message-ID: Thank you Tom. If I take out the spaces, those error messages disappear. It seems that that was a chimera issue. However, the chimera .com script is still not being executed with the subprocess.call command. I am not sure now whether this is a chimera issue or a python issue.... Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris On Mon, Feb 16, 2015 at 11:02 PM, Tom Goddard wrote: > Hi Christos, > > I think your error is because the ??nogui? option in your > subprocess.call() has spaces before and after inside the quote marks. Take > those spaces out and I bet it will work. The error seems to be trying to > create the Chimera splash screen which would not happen in nogui mode. > > Tom > > > On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote: > > Dear all, > > I have a python script that creates a .com command script for chimera and > then attempts to run the chimera script. Here is the python script: > > ************** > > #!/usr/bin/env python > import re,os,sys,math, decimal, subprocess > from copy import deepcopy > from openeye.oechem import * > from decimal import * > > script_file=open("chimera_script_for_" + "ligand" +".com", 'w') > script_file.write("open "+ "127D" +"\n") > script_file.write("open " + "127D" +"\n") > script_file.write("open "+ "ligand.pdb" +"\n") > script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") > script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") > script_file.write("stop") > script_file.close > print script_file.name > chimera=subprocess.call(["chimera", " --nogui ", " > chimera_script_for_ligand.com"]) > print chimera > #delete the script, leaving just the flipped ligand > #os.remove(script_file.name) > > ******************* > > When I run the script, it successfully generates the .com chimera script. > However, I get the following error message: > > ******************* > > [christos at biophysics Desktop]$ ./script.py > chimera_script_for_ligand.com > Traceback (most recent call last): > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line > 69, in > value = chimeraInit.init(sys.argv) > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", > line 638, in init > splash.create() > File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", > line 25, in create > sync=chimera.debug) > File > "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", > line 1747, in __init__ > self.tk = _tkinter.create(screenName, baseName, className, > interactive, wantobjects, useTk, sync, use) > _tkinter.TclError: no display name and no $DISPLAY environment variable > 1 > > ********************** > > The python script successfully creates the .com script: > > ****************************** > > [christos at biophysics Desktop]$ more chimera_script_for_ligand.com > open 127D > open 127D > open ligand.pdb > match #0:6 #1:18 > write format pdb 2 flipped_ligand > stop > > *************************** > > and if I manually execute this chimera script, everything works out well: > > ************************** > > [christos at biophysics Desktop]$ chimera --nogui > chimera_script_for_ligand.com > Fetching 127D from web site www.rcsb.org > 0 Kbytes received > Fetch 127D: finished > Done fetching 127D; verifying... > Opening 127D... > #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > Opening VRML model in 127D - Nucleotides... > 127D opened > Opened VRML model in 127D - Nucleotides > Opened 127D containing 1 model, 639 atoms, and 146 residues > Fetching 127D from web site www.rcsb.org > 88 Kbytes received > 80 Kbytes received > Fetch 127D: finished > Done fetching 127D; verifying... > Opening 127D... > #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') > > Opening VRML model in 127D - Nucleotides... > 127D opened > Opened VRML model in 127D - Nucleotides > Opened 127D containing 1 model, 639 atoms, and 146 residues > Opening ligand.pdb... > ligand.pdb opened > Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues > Executing match ['#0:6', '#1:18'], no iteration > > RMSD between 21 atom pairs is 0.630 angstroms > Wrote flipped_ligand into /home/christos/Desktop > > ***************************** > > Why do I get the error message when I attempt to run chimera through > script.py? Is this a python issue or a chimera issue? I appreciate any > thoughts on solving this problem....thank you, > > Christos Deligkaris, PhD > Assistant Professor of Physics, Drury University > 900 N Benton Ave, Springfield MO, 65802 > Office Phone: (417) 873-7234 > www2.drury.edu/christos > @DeligkarisGroup +ChristosDeligkaris > > > > > _______________________________________________ > 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 Tue Feb 17 08:28:04 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 17 Feb 2015 08:28:04 -0800 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: References: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> Message-ID: <16134CA3-326A-4B12-88BB-973300056532@sonic.net> Hi Christos, Now I think your problem is the line script_file.close You need script_file.close() with parentheses since close is a function. Without that the command file you wrote is not closed before running chimera, and probably the file will not be written until closed because of buffering. The spaces in the --nogui option is not a Chimera bug. When you use subprocess.call() the arguments > On Feb 17, 2015, at 6:44 AM, Christos Deligkaris wrote: > > Thank you Tom. If I take out the spaces, those error messages disappear. It seems that that was a chimera issue. > > However, the chimera .com script is still not being executed with the subprocess.call command. I am not sure now whether this is a chimera issue or a python issue.... > > Christos Deligkaris, PhD > Assistant Professor of Physics, Drury University > 900 N Benton Ave, Springfield MO, 65802 > Office Phone: (417) 873-7234 > www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris > > > >> On Mon, Feb 16, 2015 at 11:02 PM, Tom Goddard wrote: >> Hi Christos, >> >> I think your error is because the ??nogui? option in your subprocess.call() has spaces before and after inside the quote marks. Take those spaces out and I bet it will work. The error seems to be trying to create the Chimera splash screen which would not happen in nogui mode. >> >> Tom >> >> >>> On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote: >>> >>> Dear all, >>> >>> I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: >>> >>> ************** >>> >>> #!/usr/bin/env python >>> import re,os,sys,math, decimal, subprocess >>> from copy import deepcopy >>> from openeye.oechem import * >>> from decimal import * >>> >>> script_file=open("chimera_script_for_" + "ligand" +".com", 'w') >>> script_file.write("open "+ "127D" +"\n") >>> script_file.write("open " + "127D" +"\n") >>> script_file.write("open "+ "ligand.pdb" +"\n") >>> script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") >>> script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") >>> script_file.write("stop") >>> script_file.close >>> print script_file.name >>> chimera=subprocess.call(["chimera", " --nogui ", "chimera_script_for_ligand.com"]) >>> print chimera >>> #delete the script, leaving just the flipped ligand >>> #os.remove(script_file.name) >>> >>> ******************* >>> >>> When I run the script, it successfully generates the .com chimera script. However, I get the following error message: >>> >>> ******************* >>> >>> [christos at biophysics Desktop]$ ./script.py >>> chimera_script_for_ligand.com >>> Traceback (most recent call last): >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in >>> value = chimeraInit.init(sys.argv) >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init >>> splash.create() >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create >>> sync=chimera.debug) >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ >>> self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) >>> _tkinter.TclError: no display name and no $DISPLAY environment variable >>> 1 >>> >>> ********************** >>> >>> The python script successfully creates the .com script: >>> >>> ****************************** >>> >>> [christos at biophysics Desktop]$ more chimera_script_for_ligand.com >>> open 127D >>> open 127D >>> open ligand.pdb >>> match #0:6 #1:18 >>> write format pdb 2 flipped_ligand >>> stop >>> >>> *************************** >>> >>> and if I manually execute this chimera script, everything works out well: >>> >>> ************************** >>> >>> [christos at biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com >>> Fetching 127D from web site www.rcsb.org >>> 0 Kbytes received >>> Fetch 127D: finished >>> Done fetching 127D; verifying... >>> Opening 127D... >>> #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> Opening VRML model in 127D - Nucleotides... >>> 127D opened >>> Opened VRML model in 127D - Nucleotides >>> Opened 127D containing 1 model, 639 atoms, and 146 residues >>> Fetching 127D from web site www.rcsb.org >>> 88 Kbytes received >>> 80 Kbytes received >>> Fetch 127D: finished >>> Done fetching 127D; verifying... >>> Opening 127D... >>> #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> Opening VRML model in 127D - Nucleotides... >>> 127D opened >>> Opened VRML model in 127D - Nucleotides >>> Opened 127D containing 1 model, 639 atoms, and 146 residues >>> Opening ligand.pdb... >>> ligand.pdb opened >>> Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues >>> Executing match ['#0:6', '#1:18'], no iteration >>> >>> RMSD between 21 atom pairs is 0.630 angstroms >>> Wrote flipped_ligand into /home/christos/Desktop >>> >>> ***************************** >>> >>> Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, >>> >>> Christos Deligkaris, PhD >>> Assistant Professor of Physics, Drury University >>> 900 N Benton Ave, Springfield MO, 65802 >>> Office Phone: (417) 873-7234 >>> www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris >>> >>> >>> >>> _______________________________________________ >>> 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 deligkaris at gmail.com Tue Feb 17 08:30:11 2015 From: deligkaris at gmail.com (Christos Deligkaris) Date: Tue, 17 Feb 2015 10:30:11 -0600 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: <16134CA3-326A-4B12-88BB-973300056532@sonic.net> References: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> <16134CA3-326A-4B12-88BB-973300056532@sonic.net> Message-ID: That fixed it! The python script now runs chimera through the command script just fine! Thank you Tom, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris On Tue, Feb 17, 2015 at 10:28 AM, Tom Goddard wrote: > Hi Christos, > > Now I think your problem is the line > > script_file.close > > You need > > script_file.close() > > with parentheses since close is a function. Without that the command file > you wrote is not closed before running chimera, and probably the file will > not be written until closed because of buffering. > > The spaces in the --nogui option is not a Chimera bug. When you use > subprocess.call() the arguments > > On Feb 17, 2015, at 6:44 AM, Christos Deligkaris > wrote: > > Thank you Tom. If I take out the spaces, those error messages disappear. > It seems that that was a chimera issue. > > However, the chimera .com script is still not being executed with the > subprocess.call command. I am not sure now whether this is a chimera issue > or a python issue.... > > Christos Deligkaris, PhD > Assistant Professor of Physics, Drury University > 900 N Benton Ave, Springfield MO, 65802 > Office Phone: (417) 873-7234 > www2.drury.edu/christos > @DeligkarisGroup +ChristosDeligkaris > > > > > On Mon, Feb 16, 2015 at 11:02 PM, Tom Goddard wrote: > >> Hi Christos, >> >> I think your error is because the ??nogui? option in your >> subprocess.call() has spaces before and after inside the quote marks. Take >> those spaces out and I bet it will work. The error seems to be trying to >> create the Chimera splash screen which would not happen in nogui mode. >> >> Tom >> >> >> On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote: >> >> Dear all, >> >> I have a python script that creates a .com command script for chimera and >> then attempts to run the chimera script. Here is the python script: >> >> ************** >> >> #!/usr/bin/env python >> import re,os,sys,math, decimal, subprocess >> from copy import deepcopy >> from openeye.oechem import * >> from decimal import * >> >> script_file=open("chimera_script_for_" + "ligand" +".com", 'w') >> script_file.write("open "+ "127D" +"\n") >> script_file.write("open " + "127D" +"\n") >> script_file.write("open "+ "ligand.pdb" +"\n") >> script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") >> script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") >> script_file.write("stop") >> script_file.close >> print script_file.name >> chimera=subprocess.call(["chimera", " --nogui ", " >> chimera_script_for_ligand.com"]) >> print chimera >> #delete the script, leaving just the flipped ligand >> #os.remove(script_file.name) >> >> ******************* >> >> When I run the script, it successfully generates the .com chimera script. >> However, I get the following error message: >> >> ******************* >> >> [christos at biophysics Desktop]$ ./script.py >> chimera_script_for_ligand.com >> Traceback (most recent call last): >> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line >> 69, in >> value = chimeraInit.init(sys.argv) >> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", >> line 638, in init >> splash.create() >> File >> "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line >> 25, in create >> sync=chimera.debug) >> File >> "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", >> line 1747, in __init__ >> self.tk = _tkinter.create(screenName, baseName, className, >> interactive, wantobjects, useTk, sync, use) >> _tkinter.TclError: no display name and no $DISPLAY environment variable >> 1 >> >> ********************** >> >> The python script successfully creates the .com script: >> >> ****************************** >> >> [christos at biophysics Desktop]$ more chimera_script_for_ligand.com >> open 127D >> open 127D >> open ligand.pdb >> match #0:6 #1:18 >> write format pdb 2 flipped_ligand >> stop >> >> *************************** >> >> and if I manually execute this chimera script, everything works out well: >> >> ************************** >> >> [christos at biophysics Desktop]$ chimera --nogui >> chimera_script_for_ligand.com >> Fetching 127D from web site www.rcsb.org >> 0 Kbytes received >> Fetch 127D: finished >> Done fetching 127D; verifying... >> Opening 127D... >> #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >> >> #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >> >> Opening VRML model in 127D - Nucleotides... >> 127D opened >> Opened VRML model in 127D - Nucleotides >> Opened 127D containing 1 model, 639 atoms, and 146 residues >> Fetching 127D from web site www.rcsb.org >> 88 Kbytes received >> 80 Kbytes received >> Fetch 127D: finished >> Done fetching 127D; verifying... >> Opening 127D... >> #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >> >> #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >> >> Opening VRML model in 127D - Nucleotides... >> 127D opened >> Opened VRML model in 127D - Nucleotides >> Opened 127D containing 1 model, 639 atoms, and 146 residues >> Opening ligand.pdb... >> ligand.pdb opened >> Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues >> Executing match ['#0:6', '#1:18'], no iteration >> >> RMSD between 21 atom pairs is 0.630 angstroms >> Wrote flipped_ligand into /home/christos/Desktop >> >> ***************************** >> >> Why do I get the error message when I attempt to run chimera through >> script.py? Is this a python issue or a chimera issue? I appreciate any >> thoughts on solving this problem....thank you, >> >> Christos Deligkaris, PhD >> Assistant Professor of Physics, Drury University >> 900 N Benton Ave, Springfield MO, 65802 >> Office Phone: (417) 873-7234 >> www2.drury.edu/christos >> @DeligkarisGroup >> +ChristosDeligkaris >> >> >> >> _______________________________________________ >> 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 goddard at sonic.net Tue Feb 17 08:32:35 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 17 Feb 2015 08:32:35 -0800 Subject: [Chimera-users] Fwd: Problem running chimera through a command script In-Reply-To: References: <64DA9195-DA49-4474-8C9E-B717E94F5A89@sonic.net> Message-ID: <2C257D9F-0C00-4CB8-8069-880BBAE85672@sonic.net> Finishing the previous email.. the subprocess.call() arguments need to have leading and trailing whitespace removed or it is unlikely to work when calling any shell command. Only if the shell command argument is a general text string that permits leading whitespace would work. Tom > On Feb 17, 2015, at 6:44 AM, Christos Deligkaris wrote: > > Thank you Tom. If I take out the spaces, those error messages disappear. It seems that that was a chimera issue. > > However, the chimera .com script is still not being executed with the subprocess.call command. I am not sure now whether this is a chimera issue or a python issue.... > > Christos Deligkaris, PhD > Assistant Professor of Physics, Drury University > 900 N Benton Ave, Springfield MO, 65802 > Office Phone: (417) 873-7234 > www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris > > > >> On Mon, Feb 16, 2015 at 11:02 PM, Tom Goddard wrote: >> Hi Christos, >> >> I think your error is because the ??nogui? option in your subprocess.call() has spaces before and after inside the quote marks. Take those spaces out and I bet it will work. The error seems to be trying to create the Chimera splash screen which would not happen in nogui mode. >> >> Tom >> >> >>> On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote: >>> >>> Dear all, >>> >>> I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: >>> >>> ************** >>> >>> #!/usr/bin/env python >>> import re,os,sys,math, decimal, subprocess >>> from copy import deepcopy >>> from openeye.oechem import * >>> from decimal import * >>> >>> script_file=open("chimera_script_for_" + "ligand" +".com", 'w') >>> script_file.write("open "+ "127D" +"\n") >>> script_file.write("open " + "127D" +"\n") >>> script_file.write("open "+ "ligand.pdb" +"\n") >>> script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") >>> script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") >>> script_file.write("stop") >>> script_file.close >>> print script_file.name >>> chimera=subprocess.call(["chimera", " --nogui ", "chimera_script_for_ligand.com"]) >>> print chimera >>> #delete the script, leaving just the flipped ligand >>> #os.remove(script_file.name) >>> >>> ******************* >>> >>> When I run the script, it successfully generates the .com chimera script. However, I get the following error message: >>> >>> ******************* >>> >>> [christos at biophysics Desktop]$ ./script.py >>> chimera_script_for_ligand.com >>> Traceback (most recent call last): >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in >>> value = chimeraInit.init(sys.argv) >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init >>> splash.create() >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create >>> sync=chimera.debug) >>> File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ >>> self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) >>> _tkinter.TclError: no display name and no $DISPLAY environment variable >>> 1 >>> >>> ********************** >>> >>> The python script successfully creates the .com script: >>> >>> ****************************** >>> >>> [christos at biophysics Desktop]$ more chimera_script_for_ligand.com >>> open 127D >>> open 127D >>> open ligand.pdb >>> match #0:6 #1:18 >>> write format pdb 2 flipped_ligand >>> stop >>> >>> *************************** >>> >>> and if I manually execute this chimera script, everything works out well: >>> >>> ************************** >>> >>> [christos at biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com >>> Fetching 127D from web site www.rcsb.org >>> 0 Kbytes received >>> Fetch 127D: finished >>> Done fetching 127D; verifying... >>> Opening 127D... >>> #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> Opening VRML model in 127D - Nucleotides... >>> 127D opened >>> Opened VRML model in 127D - Nucleotides >>> Opened 127D containing 1 model, 639 atoms, and 146 residues >>> Fetching 127D from web site www.rcsb.org >>> 88 Kbytes received >>> 80 Kbytes received >>> Fetch 127D: finished >>> Done fetching 127D; verifying... >>> Opening 127D... >>> #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') >>> >>> Opening VRML model in 127D - Nucleotides... >>> 127D opened >>> Opened VRML model in 127D - Nucleotides >>> Opened 127D containing 1 model, 639 atoms, and 146 residues >>> Opening ligand.pdb... >>> ligand.pdb opened >>> Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues >>> Executing match ['#0:6', '#1:18'], no iteration >>> >>> RMSD between 21 atom pairs is 0.630 angstroms >>> Wrote flipped_ligand into /home/christos/Desktop >>> >>> ***************************** >>> >>> Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, >>> >>> Christos Deligkaris, PhD >>> Assistant Professor of Physics, Drury University >>> 900 N Benton Ave, Springfield MO, 65802 >>> Office Phone: (417) 873-7234 >>> www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris >>> >>> >>> >>> _______________________________________________ >>> 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 moldham at mail.rockefeller.edu Mon Feb 16 14:59:51 2015 From: moldham at mail.rockefeller.edu (Michael Oldham) Date: Mon, 16 Feb 2015 17:59:51 -0500 Subject: [Chimera-users] showing shapes in only selected Chimera animation scenes Message-ID: Chimera users, I am making an animation that needs to include either a box generated with an opened .bild file using a .box command or a rectangle generated by "shape rectangle? I wish the box or rectangle to appear in some scenes but not in others. My problem is, if I choose to show the box or rectangle in the first scene then it is shown in all subsequent scenes even if they were created in which the box or rectangle were not shown. Any suggestions on how to show the box or rectangle in only selected scenes of the animation. Thanks Mike Oldham Rockefeller University From goddard at sonic.net Tue Feb 17 12:08:27 2015 From: goddard at sonic.net (Tom Goddard) Date: Tue, 17 Feb 2015 12:08:27 -0800 Subject: [Chimera-users] showing shapes in only selected Chimera animation scenes In-Reply-To: References: Message-ID: <95C01DFC-0F82-45ED-B252-2DDBA7C694F0@sonic.net> Hi Mike, The Chimera animation dialog that works with scenes is only useful for making the simplest of movies because scenes don?t save complete state and few transitions are available. For movies that run into those limitations you should use Chimera command scripts to create movies. For hiding or showing a rectangle the ?modeldisp? command would be used in such a script. Here is a Chimera movie making tutorial based on command scripts http://www.cgl.ucsf.edu/chimera/data/nih-oct2012/movies.html and here are examples of commands useful for animations http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html Tom > On Feb 16, 2015, at 2:59 PM, Michael Oldham wrote: > > Chimera users, > > I am making an animation that needs to include either a box generated with an opened .bild file using a .box command or a rectangle generated by "shape rectangle? > > I wish the box or rectangle to appear in some scenes but not in others. My problem is, if I choose to show the box or rectangle in the first scene then it is shown in all subsequent scenes even if they were created in which the box or rectangle were not shown. > > Any suggestions on how to show the box or rectangle in only selected scenes of the animation. > > > > Thanks > > Mike Oldham > > Rockefeller University > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From aka895 at gmail.com Tue Feb 17 21:49:56 2015 From: aka895 at gmail.com (Ankit Agrawal) Date: Wed, 18 Feb 2015 11:19:56 +0530 Subject: [Chimera-users] MD movie export from per frame script Message-ID: Hi all I want to write a script which can create movie (.mp4) from per frame script. Because I want to show all models in movie. Please help Thanks Ankit Agrawal Department of Chemical Science IISER Mohali, India -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Wed Feb 18 07:39:07 2015 From: olibclarke at gmail.com (Oliver Clarke) Date: Wed, 18 Feb 2015 10:39:07 -0500 Subject: [Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment Message-ID: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don?t know about them!): 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. Cheers, Oliver Clarke. From meng at cgl.ucsf.edu Wed Feb 18 08:56:15 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Feb 2015 08:56:15 -0800 Subject: [Chimera-users] MD movie export from per frame script In-Reply-To: References: Message-ID: <1D3508E4-20E3-4E97-9317-D7C8E2DA1646@cgl.ucsf.edu> On Feb 17, 2015, at 9:49 PM, Ankit Agrawal wrote: > Hi all > I want to write a script which can create movie (.mp4) from per frame script. Because I want to show all models in movie. Please help > Thanks > Ankit Agrawal > Department of Chemical Science > IISER Mohali, India Hi Ankit, The per-frame scripting feature in the MD Movie dialog is not intended for making movies. If you want to make a movie that includes playback of the trajectory being shown with MD Movie, there are two main choices: (1) use MD Movie menu: File? Record movie. This will create a movie of all or part of your trajectory, as specified in the dialog, and there are several choices for image quality and output format (including .mp4). See MD Movie documentation, especially the section "Recording a Movie": (2) if you want your movie to include some other things, like showing other structures, rotating, zooming, 2D labels etc. in addition to just playing back your trajectory, you could instead write a Chimera command script to control the whole process. The command to play back part or all of your trajectory is "coordset", and the command that controls movie recording and saving is "movie." See the list of movie-making commands and some example scripts: In that examples list, especially see "ball-and-socket motion" because the script includes playing back a trajectory that was created with morphing. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From meng at cgl.ucsf.edu Wed Feb 18 09:11:32 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Feb 2015 09:11:32 -0800 Subject: [Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment In-Reply-To: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> References: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> Message-ID: <334ECEB5-CFC5-4B97-8C2D-BB5B1998C988@cgl.ucsf.edu> Hi Oliver, There are some capabilities that at least partially cover these requests, which I'll try to outline here? (1) Subset analysis. If you have a tree being shown with your alignment, you can click a node in the tree and choose to open that branch of the alignment in a separate window. Then you can analyze that subset of sequences using the separate Multalign Viewer window. We don't have anything to limit analysis to a subset of what's in a sequence window, though. Trees to go with alignments are available from several sources, such as PFAM. You open the alignment, then from the alignment window menu choose Tree? Load, then browse to the tree file. (2) Conservation calculation options. Use Multalign Viewer menu: Preferences? Headers, and set Conservation style to AL2CO. Then you have a number of sophisticated choices for calculating conservation: entropy measure, variability measure, and sum-of-pairs with many choices of which AA similarity matrix to use, with or without sequence weighting and smoothing over windows. I'm continually wishing more people would make use of these, and try to mention them in all of my tutorials! The AL2CO options come from the program of that name provided by the Grishin group. Theoretically you could even make your own matrix and put it in the proper place for discovery by the code, although that would be a lot of work. Probably one of the existing matrices would be suitable, there are several BLOSUM, some PAM, and some structure-derived (SDM, HSDM). I added the latter fairly recently. You can also calculate your own custom values externally from Chimera and then load them in from a "header file," to be displayed above the alignment just like the built-in Conservation. See tutorial: Mapping Sequence Conservation on Structures with 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 Feb 18, 2015, at 7:39 AM, Oliver Clarke wrote: > Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. > > I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don?t know about them!): > > 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. > > 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. > > Cheers, > Oliver Clarke. From olibclarke at gmail.com Wed Feb 18 09:43:36 2015 From: olibclarke at gmail.com (Oliver Clarke) Date: Wed, 18 Feb 2015 12:43:36 -0500 Subject: [Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment In-Reply-To: <334ECEB5-CFC5-4B97-8C2D-BB5B1998C988@cgl.ucsf.edu> References: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> <334ECEB5-CFC5-4B97-8C2D-BB5B1998C988@cgl.ucsf.edu> Message-ID: <529EF759-554D-4581-B9DE-5A174C96F598@gmail.com> Hi Elaine, Many thanks for the detailed explanation - it certainly looks like there are some useful features here that I didn?t know about, and I will definitely take advantage of them in future. With regards to the conservation similarity features, I will read further, but I don?t quite know how to interpret the mavConservation attribute when conservation is calculated using the AL2CO method - it doesn?t seem to be a simple "percentage of sequences that are identical at this position? like it is otherwise - it does not range between 0 and 1, for example. What I would like, in addition to the present options, is have the option to take into account similarity, not just identity, when calculating mavConservation (or perhaps have a separate attribute, mavSimilar) - so that rather than mavConservation being the percentage of sequences that are identical at a given position, instead it would be the percentage of residues that are similar at a given position. Cheers, Oliver. > On Feb 18, 2015, at 12:11 PM, Elaine Meng wrote: > > Hi Oliver, > There are some capabilities that at least partially cover these requests, which I'll try to outline here? > > (1) Subset analysis. If you have a tree being shown with your alignment, you can click a node in the tree and choose to open that branch of the alignment in a separate window. Then you can analyze that subset of sequences using the separate Multalign Viewer window. We don't have anything to limit analysis to a subset of what's in a sequence window, though. Trees to go with alignments are available from several sources, such as PFAM. You open the alignment, then from the alignment window menu choose Tree? Load, then browse to the tree file. > > > > > > (2) Conservation calculation options. Use Multalign Viewer menu: Preferences? Headers, and set Conservation style to AL2CO. Then you have a number of sophisticated choices for calculating conservation: entropy measure, variability measure, and sum-of-pairs with many choices of which AA similarity matrix to use, with or without sequence weighting and smoothing over windows. I'm continually wishing more people would make use of these, and try to mention them in all of my tutorials! The AL2CO options come from the program of that name provided by the Grishin group. > > > > Theoretically you could even make your own matrix and put it in the proper place for discovery by the code, although that would be a lot of work. Probably one of the existing matrices would be suitable, there are several BLOSUM, some PAM, and some structure-derived (SDM, HSDM). I added the latter fairly recently. > > You can also calculate your own custom values externally from Chimera and then load them in from a "header file," to be displayed above the alignment just like the built-in Conservation. > > See tutorial: Mapping Sequence Conservation on Structures with 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 Feb 18, 2015, at 7:39 AM, Oliver Clarke wrote: > >> Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. >> >> I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don?t know about them!): >> >> 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. >> >> 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. >> >> Cheers, >> Oliver Clarke. > From meng at cgl.ucsf.edu Wed Feb 18 09:52:14 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Feb 2015 09:52:14 -0800 Subject: [Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment In-Reply-To: <529EF759-554D-4581-B9DE-5A174C96F598@gmail.com> References: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> <334ECEB5-CFC5-4B97-8C2D-BB5B1998C988@cgl.ucsf.edu> <529EF759-554D-4581-B9DE-5A174C96F598@gmail.com> Message-ID: Hi Oliver, The sum-of-pairs option does represent amino acid similarity, using the values in an amino acid similarity matrix of your choice. It's literally a sum of the values for the various combinations of pairs in the column. All AL2CO conservation values are then normalized so that positive always means more conserved and the value is in standard deviations from the mean (Z-score), regardless of which option is used. There is a full explanation in the Chimera docs and in the AL2CO paper. AL2CO: calculation of positional conservation in a protein sequence alignment. Pei J, Grishin NV. Bioinformatics. 2001 Aug;17(8):700-12. 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 Feb 18, 2015, at 9:43 AM, Oliver Clarke wrote: > Hi Elaine, > > Many thanks for the detailed explanation - it certainly looks like there are some useful features here that I didn?t know about, and I will definitely take advantage of them in future. > > With regards to the conservation similarity features, I will read further, but I don?t quite know how to interpret the mavConservation attribute when conservation is calculated using the AL2CO method - it doesn?t seem to be a simple "percentage of sequences that are identical at this position? like it is otherwise - it does not range between 0 and 1, for example. > > What I would like, in addition to the present options, is have the option to take into account similarity, not just identity, when calculating mavConservation (or perhaps have a separate attribute, mavSimilar) - so that rather than mavConservation being the percentage of sequences that are identical at a given position, instead it would be the percentage of residues that are similar at a given position. > > Cheers, > Oliver. From aka895 at gmail.com Wed Feb 18 10:05:55 2015 From: aka895 at gmail.com (Ankit Agrawal) Date: Wed, 18 Feb 2015 23:35:55 +0530 Subject: [Chimera-users] MD movie export from per frame script In-Reply-To: <1D3508E4-20E3-4E97-9317-D7C8E2DA1646@cgl.ucsf.edu> References: <1D3508E4-20E3-4E97-9317-D7C8E2DA1646@cgl.ucsf.edu> Message-ID: Thanks Elaine. On 18-Feb-2015 10:26 pm, "Elaine Meng" wrote: > > On Feb 17, 2015, at 9:49 PM, Ankit Agrawal wrote: > > > Hi all > > I want to write a script which can create movie (.mp4) from per frame > script. Because I want to show all models in movie. Please help > > Thanks > > Ankit Agrawal > > Department of Chemical Science > > IISER Mohali, India > > Hi Ankit, > The per-frame scripting feature in the MD Movie dialog is not intended for > making movies. > > If you want to make a movie that includes playback of the trajectory being > shown with MD Movie, there are two main choices: > > (1) use MD Movie menu: File? Record movie. This will create a movie of > all or part of your trajectory, as specified in the dialog, and there are > several choices for image quality and output format (including .mp4). See > MD Movie documentation, especially the section "Recording a Movie": > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html > > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#recording > > > > (2) if you want your movie to include some other things, like showing > other structures, rotating, zooming, 2D labels etc. in addition to just > playing back your trajectory, you could instead write a Chimera command > script to control the whole process. The command to play back part or all > of your trajectory is "coordset", and the command that controls movie > recording and saving is "movie." See the list of movie-making commands and > some example scripts: > > > > In that examples list, especially see "ball-and-socket motion" because the > script includes playing back a trajectory that was created with morphing. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Feb 18 11:34:39 2015 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 18 Feb 2015 11:34:39 -0800 Subject: [Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment In-Reply-To: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> References: <97F8A6D7-3B2A-4D3C-AFA2-C4AE1E170714@gmail.com> Message-ID: <3CC6AC8D-8543-4C59-85C8-9E2796B6D896@cgl.ucsf.edu> On Feb 18, 2015, at 7:39 AM, Oliver Clarke wrote: > 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. Making it easier to add conservation/consensus lines that apply to only subsets of sequences would indeed be pretty useful. It's actually already on my "to do" list (#12388 (allow conservation to be shown for sequence subsets)), but many things on my to-do list haven't been getting the attention I'd like as we work hard to try to get "Chimera 2" at least minimally up and running. Sort of as a corollary, this will probably get implemented in Chimera 2 rather than Chimera 1, which as you can imagine means it will be awhile before it sees the light of day. So for now you are going to have to use the less nice workarounds you are currently using to get your work done. I'm sorry about that. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From parravicini.chiara at gmail.com Fri Feb 20 03:12:03 2015 From: parravicini.chiara at gmail.com (Chiara Parravicini) Date: Fri, 20 Feb 2015 12:12:03 +0100 Subject: [Chimera-users] problem installation on linux 64 bit Message-ID: Dear Chimera Users, After installing Chimera from the precompiled version chimera-1.10.1-linux_x86_64.bin (the installation completed without any error), I get the following error when I run the binary: libGL error: unable to load driver: nouveau_dri.so libGL error: driver pointer missing libGL error: failed to load driver: nouveau libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 156 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1455 Current serial number in output stream: 1455 I would appreciate any help or suggestion! Many Thanks in advance Chiara -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Feb 20 10:10:33 2015 From: goddard at sonic.net (Tom Goddard) Date: Fri, 20 Feb 2015 10:10:33 -0800 Subject: [Chimera-users] problem installation on linux 64 bit In-Reply-To: References: Message-ID: <47D7C8B2-8730-4EB7-96B8-EF89B48467EC@sonic.net> These errors mean your system OpenGL graphics driver is not functioning. The fix is to install an updated graphics driver. If you have an nvidia or amd graphics card you can get a driver from their web sites. Tom > On Feb 20, 2015, at 3:12 AM, Chiara Parravicini wrote: > > Dear Chimera Users, > > After installing Chimera from the precompiled version chimera-1.10.1-linux_x86_64.bin (the installation completed without any error), I get the following error when I run the binary: > > libGL error: unable to load driver: nouveau_dri.so > libGL error: driver pointer missing > libGL error: failed to load driver: nouveau > libGL error: unable to load driver: swrast_dri.so > libGL error: failed to load driver: swrast > X Error of failed request: GLXBadContextTag > Major opcode of failed request: 156 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 1455 > Current serial number in output stream: 1455 > > I would appreciate any help or suggestion! > > Many Thanks in advance > > Chiara > > _______________________________________________ > 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 gregc at cgl.ucsf.edu Fri Feb 20 13:52:57 2015 From: gregc at cgl.ucsf.edu (gregc at cgl.ucsf.edu) Date: Fri, 20 Feb 2015 21:52:57 +0000 Subject: [Chimera-users] problem installation on linux 64 bit In-Reply-To: <47D7C8B2-8730-4EB7-96B8-EF89B48467EC@sonic.net> References: <47D7C8B2-8730-4EB7-96B8-EF89B48467EC@sonic.net> Message-ID: <7afcc1cde391242ad63dc0980ddab532@mail.cgl.ucsf.edu> Thinkng about this some more, the errors might be because you need to install some additional packages on your system besides a graphics driver -- the proprietary graphics drivers from AMD and NVIDIA are much better, less buggy and faster, than the open source ones.? If are using Ubuntu, you should have at least the libgl1-mesa-dri and libgl1-mesa-glx packages installed.? I'd also recommend installing the mesa-utils package for the glxinfo program.? And also on Ubuntu, use the Additional Drivers application to install the proprietary driver.? We do not recommend running Chimera on a virtual machine, the graphics support in virtual machines is too buggy in general, and will be significantly slower when it does work. To debug your OpenGL support, run the xdpyinfo program and confirm that the GLX extension is present.? If not, then you need to install additional packages from your Linux distribution and restart the X server (reboot or logout & login).? Run 'lspci | grep VGA' to see what kind of graphics card you have.? Then run 'glxinfo | grep "OpenGL vendor"' to see if the graphics driver a vendor supplied one or not.? If not, install the proprietary driver. You may have noticed that I have not yet mention Intel graphics.? That is because, with Intel graphics, your only choice is to use the open source driver.? That driver has improved a lot recently, but it is still buggier than the AMD and NVIDIA ones, and it is very difficult to install a newer driver unless you update your Linux system. ??? HTH, ??? Greg February 20 2015 10:11 AM, "Tom Goddard" wrote: ? These errors mean your system OpenGL graphics driver is not functioning. ?The fix is to install an updated graphics driver. ?If you have an nvidia or amd graphics card you can get a driver from their web sites. ? Tom ? ? ? On Feb 20, 2015, at 3:12 AM, Chiara Parravicini ?wrote:? Dear Chimera Users, ?After installing Chimera from the precompiled version? chimera-1.10.1-linux_x86_64.bin (the installation completed without any error),? I get the following error when I run the binary: libGL error: unable to load driver: nouveau_dri.so libGL error: driver pointer missing libGL error: failed to load driver: nouveau libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request:? GLXBadContextTag ? Major opcode of failed request:? 156 (GLX) ? Minor opcode of failed request:? 5 (X_GLXMakeCurrent) ? Serial number of failed request:? 1455 ? Current serial number in output stream:? 1455 ? I would appreciate any help or suggestion! ? Many Thanks in advance ? Chiara ?_______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu (mailto:Chimera-users at cgl.ucsf.edu) http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users) ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From tc2595 at bu.edu Fri Feb 20 14:54:20 2015 From: tc2595 at bu.edu (Tat Cheung Cheng) Date: Fri, 20 Feb 2015 17:54:20 -0500 Subject: [Chimera-users] about model coordinates Message-ID: Hi, I recently got a ~4.4A EM map and built a improved model using MDFF. The map and model is well aligned when loaded in Chimera. But it is off when I hit "center" in the volume viewer, as the origin is shifted. As I try to improve the model in Coot, the map and model isn't aligned at all in Coot, seemingly by the same offset when "center" button was hit. And also the values in the original index in the volume viewer is different from the values in the header in the density map. So I wonder what determines the origin index? and is it possible to find the shift and transform the coordinates in the model so as to align the model with the map in coot? Thanks a lot. Tc -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Feb 20 16:48:31 2015 From: goddard at sonic.net (Tom Goddard) Date: Fri, 20 Feb 2015 16:48:31 -0800 Subject: [Chimera-users] about model coordinates In-Reply-To: References: Message-ID: <12DCB644-1A7F-477D-A99B-47D5812F3A02@sonic.net> Hi Tc, As you say Chimera aligns your map and model correctly. So the problem is with Coot and so the Chimera list may not have an answer for you. You didn?t say the format of your map file but I guess it is MRC. In an MRC EM file the origin is typically in header fields called xorigin, yorigin, zorigin which are specific to EM data (MRC 2000 format) and are not part of the nearly identical CCP4 format used for x-ray maps that Coot is expecting. Here is some documentation on the MRC format (with floating point origin at words 50-52) http://www2.mrc-lmb.cam.ac.uk/image2000.html and here is some CCP4 map format documentation http://www.ccp4.ac.uk/html/maplib.html For CCP4 format (used for x-ray maps) the only origin fields are called NCSTART, NRSTART, NSSTART and are integers. They are used if an x-ray map contains just a subgrid of the unit cell. The EM origin in MRC maps is floating point allowing the origin to lie between grid points. When Chimera writes an MRC map it always sets the x-ray origin to grid point 0,0,0 since Chimera map support is intended for EM maps where the xorigin,yorigin,zorigin fields are used. So I think the following recipe is what you need to write out a new PDB file that will align in Coot. First find out the nrstart, ncstart, nsstart header vaules by opening the map in Chimera 1.10 or later and using the command ?volume #0 dump true? to show the header values. If the values are -50,-50,-50 then set the origin index in Chimera to 50,50,50 (change the sign of header values): volume #0 originIndex 50,50,50 (or use the volume dialog Features / Coordinates). Now the map is positioned where Coot expects it. Now move the PDB by the same amount. Compute the difference between the new origin index and the old, say the old origin Chimera reported was 30,30,30. Then you shifted the origin by 20,20,20 grid points, in other words the map moved by -20,-20,-20 grid points. If the grid spacing is 1.2 Angstroms then you need to shift the PDB by -24,-24,-24 so use Chimera command ?move -24,-24,-24 model #1 coord #1?. The save the PDB relative to the map coordinates with File / Save PDB?. This is a big pain caused by using a file format MRC that Coot does not understand. It would be much easier if you changed the map origin to say 0,0,0 so both sets of origin header fields (CCP4/MRC) agree then use MDFF with this map that MDFF and Coot will position in the same way. Tom > On Feb 20, 2015, at 2:54 PM, Tat Cheung Cheng wrote: > > Hi, > > I recently got a ~4.4A EM map and built a improved model using MDFF. The map and model is well aligned when loaded in Chimera. But it is off when I hit "center" in the volume viewer, as the origin is shifted. As I try to improve the model in Coot, the map and model isn't aligned at all in Coot, seemingly by the same offset when "center" button was hit. > And also the values in the original index in the volume viewer is different from the values in the header in the density map. So I wonder what determines the origin index? and is it possible to find the shift and transform the coordinates in the model so as to align the model with the map in coot? > > Thanks a lot. > > Tc > _______________________________________________ > 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 kzhang at mrc-lmb.cam.ac.uk Wed Feb 25 09:44:18 2015 From: kzhang at mrc-lmb.cam.ac.uk (kzhang at mrc-lmb.cam.ac.uk) Date: Wed, 25 Feb 2015 17:44:18 -0000 Subject: [Chimera-users] Inverse volume-erasing Message-ID: <251bb3d8bedc9868cf98ac763239b814.squirrel@mail.mrc-lmb.cam.ac.uk> Dear Chimera users, Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if I want to keep the density within the eraser while getting rid of other parts? Many thanks Kai From kzhang at mrc-lmb.cam.ac.uk Wed Feb 25 10:15:08 2015 From: kzhang at mrc-lmb.cam.ac.uk (kzhang at mrc-lmb.cam.ac.uk) Date: Wed, 25 Feb 2015 18:15:08 -0000 Subject: [Chimera-users] Inverse volume-erasing Message-ID: Thanks! This is a good solution. But I wonder if there's an interactive way just like the eraser, but doing the opposite thing. It might help on difficult cases when you want a real time feedback what you are erasing and keeping just in Chimera without external command. Kai > difference ma p > ???2015???2???25????????????????????? >> Dear Chimera users, >> Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if >> I want to keep the density within the eraser while getting rid of other parts? >> Many thanks >> Kai >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Wed Feb 25 12:39:13 2015 From: goddard at sonic.net (Tom Goddard) Date: Wed, 25 Feb 2015 12:39:13 -0800 Subject: [Chimera-users] Inverse volume-erasing In-Reply-To: <251bb3d8bedc9868cf98ac763239b814.squirrel@mail.mrc-lmb.cam.ac.uk> References: <251bb3d8bedc9868cf98ac763239b814.squirrel@mail.mrc-lmb.cam.ac.uk> Message-ID: <9CCAEC03-642A-48A1-BE6F-C5877A842ABD@sonic.net> Hi Kai, The Chimera volume eraser can erase everything outside the sphere using keyboard shortcut ?eo? as described in the documentation ? if you press the Help button on the Volume Eraser dialog you will see this. You have to enable keyboard shortcuts with menu Tools / General Controls / Keyboard Shortcuts or Chimera command ?ac? also enables them. But this probably isn?t what you want. because it does not add what is shown each time you move the sphere and use ?eo? it just keeps erasing everything outside the sphere. So it isn?t clear how you would use the uneraser sphere since how would you be able to see what you are trying to unerase, especially when you start with everything erased. But here?s a tricky idea. Open two copies of your map and erase one copy which will show the other copy underneath. Keep erasing the one copy until you exposed all the parts of the underneath map. Then subtract the full map minus the erased map (Chimera command: vop subtract #4 #5) to get just the part you exposed by erasing. Here?s a screen capture of my test. A few important things to make this work: the volume erase dialog acts on the map that is highlighted in the volume viewer dialog (shown with its name in blue in the attached image) ? click on the map name you are erasing in the volume viewer dialog to choose the right copy. If two copies of a map have the same threshold they are exactly on top of each other and one or parts of both may appear. You might want to raise the contour level of one copy so it is hidden by the lower contour level copy. Tom > On Feb 25, 2015, at 9:44 AM, wrote: > > Dear Chimera users, > > > Dose anyone know how to do inverse volume-erasing? Normally we use the > eraser to erase density we don't want to keep. However, what shall I do if > I want to keep the density within the eraser while getting rid of other > parts? > > Many thanks > Kai > > > _______________________________________________ > 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: unerase.png Type: image/png Size: 317420 bytes Desc: not available URL: From kzhang at mrc-lmb.cam.ac.uk Wed Feb 25 16:53:51 2015 From: kzhang at mrc-lmb.cam.ac.uk (Kai Zhang) Date: Thu, 26 Feb 2015 00:53:51 +0000 Subject: [Chimera-users] Inverse volume-erasing In-Reply-To: <9CCAEC03-642A-48A1-BE6F-C5877A842ABD@sonic.net> References: <251bb3d8bedc9868cf98ac763239b814.squirrel@mail.mrc-lmb.cam.ac.uk> <9CCAEC03-642A-48A1-BE6F-C5877A842ABD@sonic.net> Message-ID: <1424912031.5157.7.camel@Genius> Hi Tom, Many thanks for your detailed explanation! This is really helpful. Best, Kai On Wed, 2015-02-25 at 12:39 -0800, Tom Goddard wrote: > Hi Kai, > > > > The Chimera volume eraser can erase everything outside the sphere > using keyboard shortcut ?eo? as described in the documentation ? if > you press the Help button on the Volume Eraser dialog you will see > this. You have to enable keyboard shortcuts with menu Tools / General > Controls / Keyboard Shortcuts or Chimera command ?ac? also enables > them. But this probably isn?t what you want. because it does not add > what is shown each time you move the sphere and use ?eo? it just keeps > erasing everything outside the sphere. > > > So it isn?t clear how you would use the uneraser sphere since how > would you be able to see what you are trying to unerase, especially > when you start with everything erased. But here?s a tricky idea. > Open two copies of your map and erase one copy which will show the > other copy underneath. Keep erasing the one copy until you exposed > all the parts of the underneath map. Then subtract the full map minus > the erased map (Chimera command: vop subtract #4 #5) to get just the > part you exposed by erasing. Here?s a screen capture of my test. > > > A few important things to make this work: the volume erase dialog > acts on the map that is highlighted in the volume viewer dialog (shown > with its name in blue in the attached image) ? click on the map name > you are erasing in the volume viewer dialog to choose the right copy. > If two copies of a map have the same threshold they are exactly on > top of each other and one or parts of both may appear. You might want > to raise the contour level of one copy so it is hidden by the lower > contour level copy. > > > Tom > > > > > > > > > On Feb 25, 2015, at 9:44 AM, wrote: > > > > > > > > Dear Chimera users, > > > > > > Dose anyone know how to do inverse volume-erasing? Normally we use > > the > > eraser to erase density we don't want to keep. However, what shall I > > do if > > I want to keep the density within the eraser while getting rid of > > other > > parts? > > > > Many thanks > > Kai > > > > > > _______________________________________________ > > 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: unerase.png Type: image/png Size: 317420 bytes Desc: not available URL: From bobby.barnett at gmail.com Thu Feb 26 09:32:46 2015 From: bobby.barnett at gmail.com (Bobby Barnett) Date: Thu, 26 Feb 2015 12:32:46 -0500 Subject: [Chimera-users] Tutorials Message-ID: I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students. Bobby Barnett Department of Chemistry University of Chemistry -------------- next part -------------- An HTML attachment was scrubbed... URL: From hl_random at yahoo.com Wed Feb 25 17:45:45 2015 From: hl_random at yahoo.com (hy liao) Date: Thu, 26 Feb 2015 01:45:45 +0000 (UTC) Subject: [Chimera-users] Embed chimera into my gui code Message-ID: <817355518.176294.1424915145362.JavaMail.yahoo@mail.yahoo.com> Hi, I am creating a GUI using tkinter, and I would like to embed chimera into it. Specifically, I would like to display a 3D molecule density map using chimera and inside my GUI. Chimera would be activated while the GUI is on. Is there documentation to accomplish this? Thanks! Stu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 26 10:09:24 2015 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 26 Feb 2015 10:09:24 -0800 Subject: [Chimera-users] Tutorials In-Reply-To: References: Message-ID: Hi Bobby, We have quite a few Chimera tutorials, but the main issue for you is probably whether they are suitable for undergraduates. Maybe other undergraduate educators will have better suggestions or materials that they can send you; the tutorials that we provide do presuppose some knowledge of protein structure and organic chemistry, but you can take a look and see what you think... The User's Guide (included with Chimera download but also shown on our website) includes several tutorials, including "getting started" for Chimera beginners. You can get to the copies included in your download from the Chimera Help menu. The copies at our website are here, but if you stick with the downloaded ones (menu: Help? Tutorials) they are version-synchronized with the software. While "getting started" may be simplest in terms of Chimera, some of the others in the User's Guide that are more basic in terms of the science are the Surface Properties image tutorial and the Structure Analysis and Comparison tutorial. I usually suggest the latter for graduate students learning Chimera because it includes several common protein analysis tasks. There are also a bunch of tutorials on the website only, listed here: The most basic of these Chimera-wise is the expanded "getting started" 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 Feb 26, 2015, at 9:32 AM, Bobby Barnett wrote: > I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students. > > Bobby Barnett > > Department of Chemistry > University of Chemistry From gregc at cgl.ucsf.edu Thu Feb 26 13:20:19 2015 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 26 Feb 2015 13:20:19 -0800 Subject: [Chimera-users] Embed chimera into my gui code In-Reply-To: <817355518.176294.1424915145362.JavaMail.yahoo@mail.yahoo.com> References: <817355518.176294.1424915145362.JavaMail.yahoo@mail.yahoo.com> Message-ID: <54EF8E13.1080705@cgl.ucsf.edu> The short answer is: no -- there is no documentation to embed Chimera in another application. Our recommended and supported solution is for you to write a Chimera extension. See the incomplete Programmer's Guide's examples, http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/, in particular the "Working with the Chimera Extension Manager" example. That said, in the Linux distribution, you can easily see everything Chimera does at startup, look at the chimera shell script and all of the environment variables it sets, then look at CHIMERA/share/__main__.py and CHIMERA/share/chimeraInit.py. Windows and Mac OS X have similar startup procedures, but use a program instead of a shell script. We do not support it, but there is a chance that if you setup all of the appropriate environment variables and call chimeraInit.init with the appropriate arguments, that it will work. You should also use the same C/C++ compiler if you have any non-Python code. Good luck, Greg On 02/25/2015 05:45 PM, hy liao wrote: > Hi, > > I am creating a GUI using tkinter, and I would like to embed chimera > into it. > > Specifically, I would like to display a 3D molecule density map using > chimera and inside my GUI. Chimera would be activated while the GUI is > on. Is there documentation to accomplish this? > > Thanks! > > Stu > > > _______________________________________________ > 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: