From g.m.carstairs at dundee.ac.uk Fri Feb 1 02:43:28 2019 From: g.m.carstairs at dundee.ac.uk (Mungo Carstairs (Staff)) Date: Fri, 1 Feb 2019 10:43:28 +0000 Subject: [Chimera-users] Help: 'broken pipe' error Message-ID: Hi there, I'm experimenting with Jalview as Javascript talking to Chimera over the latter's REST server. The first few 'list models' commands work fine, but when I send a command 'open cifID:4zhp' I (usually but not always) get an error '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces below as to the reason for this? Thanks. Chimera 1.12 (build 41481) on OSX Sierra 10.12.6. REST server on host 127.0.0.1 port 53135 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 163, in _run replyobj.error(str(v) + '\n') File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 637, in error _replyStack[-1].error(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) See reply log for Python traceback. ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53326) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 159, in _run chimera.runCommand(cmd) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2750, in runCommand makeCommand(*args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", line 20, in command self.module("cmdline").process(cmdName, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 12, in process doList(args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 543, in doList doExtensionFunc(func, otherArgs, **kwargs) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 192, in listr replyobj.info(info) File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 625, in info _replyStack[-1].info(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 202, in message self.writeLine(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) See reply log for Python traceback. ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53329) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - [University of Dundee shield logo] Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org www.compbio.dundee.ac.uk g.m.carstairs at dundee.ac.uk [University of Dundee Facebook] [University of Dundee Twitter] [University of Dundee LinkedIn] [University of Dundee YouTube] [University of Dundee Instagram] [University of Dundee Snapchat] We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 16068657 at brookes.ac.uk Fri Feb 1 05:08:42 2019 From: 16068657 at brookes.ac.uk (Sam Freeman-Fox) Date: Fri, 1 Feb 2019 13:08:42 +0000 Subject: [Chimera-users] Running vina locally Message-ID: Hi, I am looking at running docking simulations locally, and see that with the vina command line execution (*vina* *docking* *receptor* *recmodel* *ligand* *ligmodel* *options <#options>) *one of the available options is to change the backend from using the Opal web service to a local executable. Could you advise on where I would be able to download such a local executable in order to get this to run. Many Thanks, Sam Freeman -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Fri Feb 1 07:27:06 2019 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Fri, 1 Feb 2019 10:27:06 -0500 Subject: [Chimera-users] Combine atom-spec non-alphanumeric no-nunderscore character error In-Reply-To: <9129A0F2-3363-4625-A352-F19AED7A6BCD@cgl.ucsf.edu> References: <81A43D45-3E61-45FE-B2F1-74D5CC1759C3@cgl.ucsf.edu> <9129A0F2-3363-4625-A352-F19AED7A6BCD@cgl.ucsf.edu> Message-ID: Thanks Elaine, but after I combine using the syntax that you mentioned, I get the entire molecule and not the chains that I selected. I also tried selecting the that chains that I want to combine from different models, and used "combine sel", I got the same result. On Wed, Jan 30, 2019 at 6:21 PM Elaine Meng wrote: > Hi Ahmad, > Commas separate items at the main symbol level # (model) : (residue) @ > (atom). They cannot be used to separate items at the sub-levels with dots > after those symbols #. (submodel) :. (chain ID) @. (atom alternate > location). > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy > > > > I agree it can be confusing. In our next-gen program ChimeraX we only use > the dot for submodels, and chain has its own symbol. > Best, > Elaine > > > On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa > wrote: > > > > Thanks, I will try that, but quickly, I often use commas with selection > and it works fine, what's the difference between the commas and the colons? > > > > On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng wrote: > > Hi Ahmad, > > The specification is wrong for two reasons: > > (1) need colon instead of comma, for example #1:.k:.e > > (2) you would need to either remove the space between the two models or > put quotes around the whole thing like "#1:.k:.e #2:.k:.e" > > > > However, more important is that ?combine? will include all the atoms in > the whole models even if you only specify some chains. It says this in the > second paragraph: > > > > > > So what you really wanted to do is to delete all the other atoms before > you combine the two models, something like > > > > select #1:.k:.e #2:.k:.e > > delete ~sel > > combine #1,2 > > > > (also make sure you really have models #1 and #2, since the first model > is #0 and you might need to use #0 and #1 instead? check in the Model > Panel, opened from Favorites menu) > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa > wrote: > > > > > > I'm trying to combine a few chains from different models. I'm using: > combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure > why my selection isn't working! > > > > > > Regards. > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Feb 1 09:52:58 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 1 Feb 2019 09:52:58 -0800 Subject: [Chimera-users] Combine atom-spec non-alphanumeric no-nunderscore character error In-Reply-To: References: <81A43D45-3E61-45FE-B2F1-74D5CC1759C3@cgl.ucsf.edu> <9129A0F2-3363-4625-A352-F19AED7A6BCD@cgl.ucsf.edu> Message-ID: <509039DC-0F04-4A19-815C-690BADA0F569@cgl.ucsf.edu> Hi Ahmad, In my first reply (and in the manual page), I already told you that ?combine? would give the whole models. In the second part of that reply, I gave commands to select and DELETE the unselected parts before you use ?combine.? See previous reply below or at Best, Elaine > On Feb 1, 2019, at 7:27 AM, Ahmad Khalifa wrote: > > Thanks Elaine, but after I combine using the syntax that you mentioned, I get the entire molecule and not the chains that I selected. > > I also tried selecting the that chains that I want to combine from different models, and used "combine sel", I got the same result. > > On Wed, Jan 30, 2019 at 6:21 PM Elaine Meng wrote: > Hi Ahmad, > Commas separate items at the main symbol level # (model) : (residue) @ (atom). They cannot be used to separate items at the sub-levels with dots after those symbols #. (submodel) :. (chain ID) @. (atom alternate location). > > > > I agree it can be confusing. In our next-gen program ChimeraX we only use the dot for submodels, and chain has its own symbol. > Best, > Elaine > > > On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa wrote: > > > > Thanks, I will try that, but quickly, I often use commas with selection and it works fine, what's the difference between the commas and the colons? > > > > On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng wrote: > > Hi Ahmad, > > The specification is wrong for two reasons: > > (1) need colon instead of comma, for example #1:.k:.e > > (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e" > > > > However, more important is that ?combine? will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: > > > > > > So what you really wanted to do is to delete all the other atoms before you combine the two models, something like > > > > select #1:.k:.e #2:.k:.e > > delete ~sel > > combine #1,2 > > > > (also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead? check in the Model Panel, opened from Favorites menu) > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa wrote: > > > > > > I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working! > > > > > > Regards. > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Feb 1 10:08:58 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 1 Feb 2019 10:08:58 -0800 Subject: [Chimera-users] Running vina locally In-Reply-To: References: Message-ID: <562F349D-9DFD-4BE2-8BF6-84AE4E4091AB@cgl.ucsf.edu> Hi Sam, Autodock Vina is developed by the Trott group at Scripps. Here is their website, and I see a download page: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 1, 2019, at 5:08 AM, Sam Freeman-Fox <16068657 at brookes.ac.uk> wrote: > > Hi, > I am looking at running docking simulations locally, and see that with the vina command line execution (vina docking receptor recmodel ligand ligmodel options) one of the available options is to change the backend from using the Opal web service to a local executable. > Could you advise on where I would be able to download such a local executable in order to get this to run. > Many Thanks, > Sam Freeman From jmauser at winona.edu Mon Feb 4 08:38:21 2019 From: jmauser at winona.edu (Mauser, Jonathon) Date: Mon, 4 Feb 2019 16:38:21 +0000 Subject: [Chimera-users] Slicing/Subdividing Models in Chimera Message-ID: Hello, I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of ?anatomical? cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. I have tried simply clipping into the model, which does essentially what I would like to do, but I don?t know how to delete everything that I?ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished? Thank you! Jon Jonathon Mauser, Ph.D. Assistant Professor Department of Chemistry Winona State University Office: Pasteur Hall 330 P: 507-457-5874 E: jmauser at winona.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Mon Feb 4 10:53:30 2019 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Mon, 4 Feb 2019 13:53:30 -0500 Subject: [Chimera-users] Display showing a gap in my chain Message-ID: After merging two structures in Coot, chimera is showing a chain break at one end where I merged my molecule. The other end is displayed correctly. How can I fix that? -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Mon Feb 4 13:21:12 2019 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Mon, 4 Feb 2019 13:21:12 -0800 Subject: [Chimera-users] Help: 'broken pipe' error In-Reply-To: References: Message-ID: <58290715-f13b-d288-7a85-83082622c769@cgl.ucsf.edu> Hi, Mungo. I tried using the RESTserver on a recent daily build, and it opening 4zhp worked fine. Since RESTserver hasn't changed in a very long time, I suspect the results would be the same with 1.13. The way I tested it is to start the RESTserver in Chimera, and then go to a browser to visit "http://localhost:PORT/static/cmdline.html" where PORT is the port number reported in the Reply Log. A form is displayed in the browser and I type in "open cifID:4zhp", which runs the command and displays Chimera messages in the browser rather than the Reply Log. I did notice that your tests show messages like: > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - whereas mine show: > 127.0.0.1 - - [04/Feb/2019 12:02:46] "POST /run HTTP/1.1" 200 - That looks to me like you are sending requests using http GET, whereas my tests are using POST. It /shouldn't/ make any difference, but would it be possible for you to test using POST to send requests to Chimera instead of GET? Conrad On 2/1/2019 2:43 AM, Mungo Carstairs (Staff) wrote: > Hi there, > > > I'm experimenting with Jalview /as Javascript/?talking to Chimera over > the latter's REST server. > > The first few 'list models' commands work fine, but when I send?a > command 'open cifID:4zhp' I (usually but not always) get an error > '[Errno?32]?Broken Pipe' in Chimera. Is there a clue in the stack traces > below as to the reason for this? Thanks. > > > Chimera 1.12 (build 41481) on OSX Sierra 10.12.6. > > > REST server on host 127.0.0.1 port 53135 > 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 - > Traceback (most recent call last): > ? File > "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", > line 50, in _checkThread > ? ? callable() > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 83, in run > ? ? _run(q, h, args) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 163, in _run > ? ? replyobj.error(str(v) + '\n') > ? File > "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line > 637, in error > ? ? _replyStack[-1].error(s) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 184, in writeLine > ? ? self.write(s) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 191, in write > ? ? self.f.write(s) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 328, in write > ? ? self.flush() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > thread callback: > error: [Errno 32] Broken pipe > > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > See reply log for Python traceback. > > > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 53326) > Traceback (most recent call last): > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 295, in _handle_request_noblock > ? ? self.process_request(request, client_address) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 321, in process_request > ? ? self.finish_request(request, client_address) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 334, in finish_request > ? ? self.RequestHandlerClass(request, client_address, self) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 657, in __init__ > ? ? self.finish() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 716, in finish > ? ? self.wfile.close() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 283, in close > ? ? self.flush() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > ---------------------------------------- > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - > Traceback (most recent call last): > ? File > "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", > line 50, in _checkThread > ? ? callable() > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 83, in run > ? ? _run(q, h, args) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 159, in _run > ? ? chimera.runCommand(cmd) > ? File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line > 2750, in runCommand > ? ? makeCommand(*args, **kw) > ? File > "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line > 69, in makeCommand > ? ? f(c, args) > ? File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", > line 20, in command > ? ? self.module("cmdline").process(cmdName, args) > ? File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 12, in process > ? ? doList(args) > ? File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 543, in doList > ? ? doExtensionFunc(func, otherArgs, **kwargs) > ? File > "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line > 451, in doExtensionFunc > ? ? extFunc(*tuple(processedArgs), **kw) > ? File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 192, in listr > ? ? replyobj.info(info) > ? File > "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line > 625, in info > ? ? _replyStack[-1].info(s) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 202, in message > ? ? self.writeLine(s) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 184, in writeLine > ? ? self.write(s) > ? File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 191, in write > ? ? self.f.write(s) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 328, in write > ? ? self.flush() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > thread callback: > error: [Errno 32] Broken pipe > > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > See reply log for Python traceback. > > > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 53329) > Traceback (most recent call last): > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 295, in _handle_request_noblock > ? ? self.process_request(request, client_address) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 321, in process_request > ? ? self.finish_request(request, client_address) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 334, in finish_request > ? ? self.RequestHandlerClass(request, client_address, self) > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 657, in __init__ > ? ? self.finish() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 716, in finish > ? ? self.wfile.close() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 283, in close > ? ? self.flush() > ? File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > ? ? self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > ---------------------------------------- > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET > /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET > /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - > > > Email signature > University of Dundee shield logo > > *Mungo Carstairs* > Jalview Computational Scientist > > The Barton Group > Division of Computational Biology > > School of Life Sciences > > University of Dundee, Dundee, Scotland, UK > > www.jalview.org > > www.compbio.dundee.ac.uk > g.m.carstairs at dundee.ac.uk > > University of Dundee Facebook University of > Dundee Twitter University of Dundee LinkedIn > University of Dundee YouTube > University of Dundee Instagram > University of Dundee Snapchat > > *We're Scottish University of the Year again!* > > The Times / Sunday Times Good University Guide 2016 and 2017 > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Mon Feb 4 13:26:51 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 4 Feb 2019 13:26:51 -0800 Subject: [Chimera-users] Display showing a gap in my chain In-Reply-To: References: Message-ID: Hi Ahmad, Probably you need to add the covalent bond between the carbonyl carbon at the end of one chain and the backbone nitrogen at the start of the other chain. Show all the atoms so that you can see them, select those two atoms, and then add a bond, e.g. with ?bond? command or in the ?Adjust Bonds? section of the Build Structure tool. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 4, 2019, at 10:53 AM, Ahmad Khalifa wrote: > > After merging two structures in Coot, chimera is showing a chain break at one end where I merged my molecule. The other end is displayed correctly. How can I fix that? From goddard at sonic.net Mon Feb 4 13:51:31 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 4 Feb 2019 13:51:31 -0800 Subject: [Chimera-users] Slicing/Subdividing Models in Chimera In-Reply-To: References: Message-ID: <6C38000A-6C7D-4686-8789-286012C31C15@sonic.net> Hi Jon, You won?t be able to get STL of a clipped molecule from Chimera ? as you observed you get the full molecule instead. The problem is that clip planes are just a graphical operation where the graphics decides not to display some of the pixels that would be behind or in front of a clip plane. But the STL format is a list of triangles. To make a list of triangles all the triangles cut by the clipping plane would have to be trimmed and the out of view triangles and partial triangles thrown away. Chimera does not do that. Often that is not enough as 3D printer software often requires the triangles are joined at their edges to form a closed mesh, and the tiniest gap causes the 3d printer software to fail (observed with old Catalyst software and uPrint printers). Clipping and getting closed triangles requires even fancier software ? this is typical of mechanical engineering CAD software. The one thing you can do to slice is and 3D print is use a surface calculated from a density map, and reduce the bounding box of the density map. The Chimera molmap command makes such density maps from molecules. But it won?t give ribbon or ball-and-stick type appearances. Lastly when cutting molecules you are likely to produce many disconnected fragments which will simply fall apart if you try to 3D print them after you dissolve the support material. Tom > On Feb 4, 2019, at 8:38 AM, Mauser, Jonathon wrote: > > Hello, > > I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of ?anatomical? cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. > > I have tried simply clipping into the model, which does essentially what I would like to do, but I don?t know how to delete everything that I?ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished? > > Thank you! > > Jon > > Jonathon Mauser, Ph.D. > Assistant Professor > Department of Chemistry > Winona State University > Office: Pasteur Hall 330 > P: 507-457-5874 > E: jmauser at winona.edu _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Feb 4 14:13:48 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 4 Feb 2019 14:13:48 -0800 Subject: [Chimera-users] Slicing/Subdividing Models in Chimera In-Reply-To: References: <6C38000A-6C7D-4686-8789-286012C31C15@sonic.net> Message-ID: <28A9AA31-F2FF-4045-A637-DA1204FBC36C@sonic.net> Hi Jon, The command to show a subregion of a volume looks like volume #1 region 0,0,0,85,100,50 where the 6 numbers are the two corners in grid index units. You would need to look at the size of your grid (shown in Volume Viewer) and specify a smaller size in this command. But using a command is a pretty difficult approach to cropping the volume, more commonly it would be done interactively with the mouse using the Volume Viewer menu Features / Subregion Selection. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html Tom > On Feb 4, 2019, at 2:04 PM, Mauser, Jonathon wrote: > > Thank you, Tom. What commands would I need to simply reduce the size of a density/surface model bounding box? > > From: Tom Goddard > Sent: Monday, February 4, 2019 3:52 PM > To: Mauser, Jonathon > Cc: chimera-users at cgl.ucsf.edu BB > > Subject: Re: [Chimera-users] Slicing/Subdividing Models in Chimera > > Hi Jon, > > You won?t be able to get STL of a clipped molecule from Chimera ? as you observed you get the full molecule instead. The problem is that clip planes are just a graphical operation where the graphics decides not to display some of the pixels that would be behind or in front of a clip plane. But the STL format is a list of triangles. To make a list of triangles all the triangles cut by the clipping plane would have to be trimmed and the out of view triangles and partial triangles thrown away. Chimera does not do that. Often that is not enough as 3D printer software often requires the triangles are joined at their edges to form a closed mesh, and the tiniest gap causes the 3d printer software to fail (observed with old Catalyst software and uPrint printers). Clipping and getting closed triangles requires even fancier software ? this is typical of mechanical engineering CAD software. > > The one thing you can do to slice is and 3D print is use a surface calculated from a density map, and reduce the bounding box of the density map. The Chimera molmap command makes such density maps from molecules. But it won?t give ribbon or ball-and-stick type appearances. > > Lastly when cutting molecules you are likely to produce many disconnected fragments which will simply fall apart if you try to 3D print them after you dissolve the support material. > > Tom > > > > On Feb 4, 2019, at 8:38 AM, Mauser, Jonathon wrote: > > Hello, > > I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of ?anatomical? cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. > > I have tried simply clipping into the model, which does essentially what I would like to do, but I don?t know how to delete everything that I?ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished? > > Thank you! > > Jon > > Jonathon Mauser, Ph.D. > Assistant Professor > Department of Chemistry > Winona State University > Office: Pasteur Hall 330 > P: 507-457-5874 > E: jmauser at winona.edu > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmauser at winona.edu Mon Feb 4 14:04:26 2019 From: jmauser at winona.edu (Mauser, Jonathon) Date: Mon, 4 Feb 2019 22:04:26 +0000 Subject: [Chimera-users] Slicing/Subdividing Models in Chimera In-Reply-To: <6C38000A-6C7D-4686-8789-286012C31C15@sonic.net> References: <6C38000A-6C7D-4686-8789-286012C31C15@sonic.net> Message-ID: Thank you, Tom. What commands would I need to simply reduce the size of a density/surface model bounding box? From: Tom Goddard Sent: Monday, February 4, 2019 3:52 PM To: Mauser, Jonathon Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Slicing/Subdividing Models in Chimera Hi Jon, You won?t be able to get STL of a clipped molecule from Chimera ? as you observed you get the full molecule instead. The problem is that clip planes are just a graphical operation where the graphics decides not to display some of the pixels that would be behind or in front of a clip plane. But the STL format is a list of triangles. To make a list of triangles all the triangles cut by the clipping plane would have to be trimmed and the out of view triangles and partial triangles thrown away. Chimera does not do that. Often that is not enough as 3D printer software often requires the triangles are joined at their edges to form a closed mesh, and the tiniest gap causes the 3d printer software to fail (observed with old Catalyst software and uPrint printers). Clipping and getting closed triangles requires even fancier software ? this is typical of mechanical engineering CAD software. The one thing you can do to slice is and 3D print is use a surface calculated from a density map, and reduce the bounding box of the density map. The Chimera molmap command makes such density maps from molecules. But it won?t give ribbon or ball-and-stick type appearances. Lastly when cutting molecules you are likely to produce many disconnected fragments which will simply fall apart if you try to 3D print them after you dissolve the support material. Tom On Feb 4, 2019, at 8:38 AM, Mauser, Jonathon wrote: Hello, I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of ?anatomical? cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. I have tried simply clipping into the model, which does essentially what I would like to do, but I don?t know how to delete everything that I?ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished? Thank you! Jon Jonathon Mauser, Ph.D. Assistant Professor Department of Chemistry Winona State University Office: Pasteur Hall 330 P: 507-457-5874 E: jmauser at winona.edu _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.m.carstairs at dundee.ac.uk Mon Feb 4 23:59:07 2019 From: g.m.carstairs at dundee.ac.uk (Mungo Carstairs (Staff)) Date: Tue, 5 Feb 2019 07:59:07 +0000 Subject: [Chimera-users] Help: 'broken pipe' error In-Reply-To: <58290715-f13b-d288-7a85-83082622c769@cgl.ucsf.edu> References: , <58290715-f13b-d288-7a85-83082622c769@cgl.ucsf.edu> Message-ID: Hi Conrad, I will see if I can change to POST. To explain a bit: Jalview (Java) application uses POST, we now have a Javascript version which for the moment is limited to sending GET requests, so I tweaked the code for that. I will see if I can persuade it to fake a POST instead and let you know what I find. Thanks, Mungo [University of Dundee shield logo] Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org www.compbio.dundee.ac.uk g.m.carstairs at dundee.ac.uk [University of Dundee Facebook] [University of Dundee Twitter] [University of Dundee LinkedIn] [University of Dundee YouTube] [University of Dundee Instagram] [University of Dundee Snapchat] We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: Conrad Huang Sent: 04 February 2019 21:21:12 To: Mungo Carstairs (Staff); chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Help: 'broken pipe' error Hi, Mungo. I tried using the RESTserver on a recent daily build, and it opening 4zhp worked fine. Since RESTserver hasn't changed in a very long time, I suspect the results would be the same with 1.13. The way I tested it is to start the RESTserver in Chimera, and then go to a browser to visit "http://localhost:PORT/static/cmdline.html" where PORT is the port number reported in the Reply Log. A form is displayed in the browser and I type in "open cifID:4zhp", which runs the command and displays Chimera messages in the browser rather than the Reply Log. I did notice that your tests show messages like: > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - whereas mine show: > 127.0.0.1 - - [04/Feb/2019 12:02:46] "POST /run HTTP/1.1" 200 - That looks to me like you are sending requests using http GET, whereas my tests are using POST. It /shouldn't/ make any difference, but would it be possible for you to test using POST to send requests to Chimera instead of GET? Conrad On 2/1/2019 2:43 AM, Mungo Carstairs (Staff) wrote: > Hi there, > > > I'm experimenting with Jalview /as Javascript/ talking to Chimera over > the latter's REST server. > > The first few 'list models' commands work fine, but when I send a > command 'open cifID:4zhp' I (usually but not always) get an error > '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces > below as to the reason for this? Thanks. > > > Chimera 1.12 (build 41481) on OSX Sierra 10.12.6. > > > REST server on host 127.0.0.1 port 53135 > 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 - > Traceback (most recent call last): > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", > line 50, in _checkThread > callable() > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 83, in run > _run(q, h, args) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 163, in _run > replyobj.error(str(v) + '\n') > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line > 637, in error > _replyStack[-1].error(s) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 184, in writeLine > self.write(s) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 191, in write > self.f.write(s) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 328, in write > self.flush() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > thread callback: > error: [Errno 32] Broken pipe > > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > See reply log for Python traceback. > > > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 53326) > Traceback (most recent call last): > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 295, in _handle_request_noblock > self.process_request(request, client_address) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 321, in process_request > self.finish_request(request, client_address) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 334, in finish_request > self.RequestHandlerClass(request, client_address, self) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 657, in __init__ > self.finish() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 716, in finish > self.wfile.close() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 283, in close > self.flush() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > ---------------------------------------- > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - > Traceback (most recent call last): > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", > line 50, in _checkThread > callable() > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 83, in run > _run(q, h, args) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 159, in _run > chimera.runCommand(cmd) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line > 2750, in runCommand > makeCommand(*args, **kw) > File > "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line > 69, in makeCommand > f(c, args) > File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", > line 20, in command > self.module("cmdline").process(cmdName, args) > File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 12, in process > doList(args) > File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 543, in doList > doExtensionFunc(func, otherArgs, **kwargs) > File > "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line > 451, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File > "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line > 192, in listr > replyobj.info(info) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line > 625, in info > _replyStack[-1].info(s) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 202, in message > self.writeLine(s) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 184, in writeLine > self.write(s) > File > "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", > line 191, in write > self.f.write(s) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 328, in write > self.flush() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > thread callback: > error: [Errno 32] Broken pipe > > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > See reply log for Python traceback. > > > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 53329) > Traceback (most recent call last): > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 295, in _handle_request_noblock > self.process_request(request, client_address) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 321, in process_request > self.finish_request(request, client_address) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 334, in finish_request > self.RequestHandlerClass(request, client_address, self) > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 657, in __init__ > self.finish() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", > line 716, in finish > self.wfile.close() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 283, in close > self.flush() > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", > line 307, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > ---------------------------------------- > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET > /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET > /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - > 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET > /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - > > > Email signature > University of Dundee shield logo > > *Mungo Carstairs* > Jalview Computational Scientist > > The Barton Group > Division of Computational Biology > > School of Life Sciences > > University of Dundee, Dundee, Scotland, UK > > www.jalview.org > > www.compbio.dundee.ac.uk > g.m.carstairs at dundee.ac.uk > > University of Dundee Facebook University of > Dundee Twitter University of Dundee LinkedIn > University of Dundee YouTube > University of Dundee Instagram > University of Dundee Snapchat > > *We're Scottish University of the Year again!* > > The Times / Sunday Times Good University Guide 2016 and 2017 > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Tue Feb 5 14:36:10 2019 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Tue, 5 Feb 2019 17:36:10 -0500 Subject: [Chimera-users] How to color density maps using markers? In-Reply-To: <1F39D860-03FF-4CB6-806D-103FECC5EDD8@cgl.ucsf.edu> References: <1F39D860-03FF-4CB6-806D-103FECC5EDD8@cgl.ucsf.edu> Message-ID: Thank you so much. I do have a follow up question. Is there a way to reverse color the densities that I didn't fit a model/markers in? I mean similar to a reverse selection type strategy to save time. On Fri, Jan 18, 2019 at 12:21 PM Elaine Meng wrote: > Hi Ahmad, > I believe you have to do it in one step. Color all the atomic models, > select all the atomic models at the same time, then do the coloring with > Color Zone. > Elaine > > > On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa > wrote: > > > > Thanks. When I try to color a different part of the map, it removes the > first color. How can I save the colors to the map? P.s. I use atomic models > for the coloring. > > > > On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng wrote: > > Hi Ahmad, > > There?s not really that many steps to it. You just need to select the > markers and then use the Color Zone tool. There is a little more > description here > > < > http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorzone > > > > > > ...and in the Color Zone manual page: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html > > > > > > As mentioned in that page, you can also do it with the ?scolor? command > ?zone? option. > > > > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa > wrote: > > > > > > I know I can use volume tracer to place markers in the density. There > was a tutorial explaining the use of these markers to color certain areas > of my density map, however I lost track of it. > > > > > > Best regards. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Feb 5 15:24:18 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 5 Feb 2019 15:24:18 -0800 Subject: [Chimera-users] How to color density maps using markers? In-Reply-To: References: <1F39D860-03FF-4CB6-806D-103FECC5EDD8@cgl.ucsf.edu> Message-ID: Sorry, no, not after the color zone. You could change the color of the whole surface before doing the color zone. Then after color zone, the non-zone parts of the surface will have the color you assigned the whole surface. Elaine > On Feb 5, 2019, at 2:36 PM, Ahmad Khalifa wrote: > > Thank you so much. I do have a follow up question. Is there a way to reverse color the densities that I didn't fit a model/markers in? I mean similar to a reverse selection type strategy to save time. > > On Fri, Jan 18, 2019 at 12:21 PM Elaine Meng wrote: > Hi Ahmad, > I believe you have to do it in one step. Color all the atomic models, select all the atomic models at the same time, then do the coloring with Color Zone. > Elaine > > > On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa wrote: > > > > Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring. > > > > On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng wrote: > > Hi Ahmad, > > There?s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here > > > > > > ...and in the Color Zone manual page: > > > > > > As mentioned in that page, you can also do it with the ?scolor? command ?zone? option. > > > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa wrote: > > > > > > I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it. > > > > > > Best regards. > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From 16068657 at brookes.ac.uk Wed Feb 6 06:32:56 2019 From: 16068657 at brookes.ac.uk (Sam Freeman-Fox) Date: Wed, 6 Feb 2019 14:32:56 +0000 Subject: [Chimera-users] Running vina locally In-Reply-To: <562F349D-9DFD-4BE2-8BF6-84AE4E4091AB@cgl.ucsf.edu> References: <562F349D-9DFD-4BE2-8BF6-84AE4E4091AB@cgl.ucsf.edu> Message-ID: Many thanks, a follow up question to this with regards to running autodock vina. Is it possible to stop the view dock results from automatically appearing after a dock? Looking through the user guide I cannot see an option but could be overlooking it! Thanks again, Sam Freeman On Fri, 1 Feb 2019 at 18:09, Elaine Meng wrote: > Hi Sam, > Autodock Vina is developed by the Trott group at Scripps. Here is their > website, and I see a download page: > > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 1, 2019, at 5:08 AM, Sam Freeman-Fox <16068657 at brookes.ac.uk> > wrote: > > > > Hi, > > I am looking at running docking simulations locally, and see that with > the vina command line execution (vina docking receptor recmodel ligand > ligmodel options) one of the available options is to change the backend > from using the Opal web service to a local executable. > > Could you advise on where I would be able to download such a local > executable in order to get this to run. > > Many Thanks, > > Sam Freeman > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Feb 6 09:13:20 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 6 Feb 2019 09:13:20 -0800 Subject: [Chimera-users] Running vina locally In-Reply-To: References: <562F349D-9DFD-4BE2-8BF6-84AE4E4091AB@cgl.ucsf.edu> Message-ID: Sorry no. I believe it is possible to run the command version ?vina? with ?wait true? in Chimera nogui mode, but then you have no GUI at all (no Chimera window, etc.). nogui mode is specified at Chimera startup: If you want full access to all Autodock Vina settings, including higher levels of sampling, I would encourage you to not use Chimera as the middleman and instead run your local Autodock Vina directly. With Chimera as the middleman, it is only in single-ligand mode with low sampling. Best, Elaine > On Feb 6, 2019, at 6:32 AM, Sam Freeman-Fox <16068657 at brookes.ac.uk> wrote: > > Many thanks, a follow up question to this with regards to running autodock vina. Is it possible to stop the view dock results from automatically appearing after a dock? Looking through the user guide I cannot see an option but could be overlooking it! > > Thanks again, > > Sam Freeman > > On Fri, 1 Feb 2019 at 18:09, Elaine Meng wrote: > Hi Sam, > Autodock Vina is developed by the Trott group at Scripps. Here is their website, and I see a download page: > > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 1, 2019, at 5:08 AM, Sam Freeman-Fox <16068657 at brookes.ac.uk> wrote: > > > > Hi, > > I am looking at running docking simulations locally, and see that with the vina command line execution (vina docking receptor recmodel ligand ligmodel options) one of the available options is to change the backend from using the Opal web service to a local executable. > > Could you advise on where I would be able to download such a local executable in order to get this to run. > > Many Thanks, > > Sam Freeman From calderone at cerm.unifi.it Thu Feb 7 03:04:01 2019 From: calderone at cerm.unifi.it (Vito Calderone) Date: Thu, 7 Feb 2019 12:04:01 +0100 Subject: [Chimera-users] Question Message-ID: <004801d4bed4$d83bf820$88b3e860$@cerm.unifi.it> I have superposed two structures and printed the attached figure with sequence superposition and Ca RMSD. Is there a list of residue by residue RMSD as well? I can?t find it anywhere apparently. Thanks Vito -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6ESR_DEFINITIVO_DEPOSITION_vs_3ttg.eps Type: application/postscript Size: 238330 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 7 13:02:56 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 7 Feb 2019 13:02:56 -0800 Subject: [Chimera-users] per-residue "RMSD" values from alignment In-Reply-To: <004801d4bed4$d83bf820$88b3e860$@cerm.unifi.it> References: <004801d4bed4$d83bf820$88b3e860$@cerm.unifi.it> Message-ID: <6366A42E-3F88-4374-940D-B05F0B748FB1@cgl.ucsf.edu> Hi Vito, (I changed the subject line because ?Question? is not useful to people searching the chimera-users archive.) You can save the per-residue ?RMSD? values to a text file. Since you have only two structures, the values are just the distance between the two CA atoms in that column of the sequence alignment. The RMSD values in the histogram above the sequences in Multalign Viewer are assigned as an attribute to the structure residues in each column, as explained here: You can write attribute values to file using Render by Attribute (Tools? Depiction? Render by Attribute). In that tool?s menu, choose ?File.. Save Attribute? and then specify which attribute to save. You want the attribute of ?residues? named ?mavRMSDca? (the ?mav? part means that it comes from Multalign Viewer). In the ?Models? section at the top of that dialog, you could just choose one model or the other to report the values with its residue numbers. If you choose both models, then you will get each distance twice because there are two residues (one from each structure) for each alignment column with the value. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 7, 2019, at 3:04 AM, Vito Calderone wrote: > > I have superposed two structures and printed the attached figure with sequence superposition and Ca RMSD. > Is there a list of residue by residue RMSD as well? I can?t find it anywhere apparently. > Thanks > > Vito > From bshaanan at bgu.ac.il Fri Feb 8 12:16:36 2019 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Fri, 8 Feb 2019 20:16:36 +0000 Subject: [Chimera-users] Strange and inconsistent Chimera behavior recently on W7/Nvidia OS Message-ID: <15cae60bef2645dda014f126f9e0a510@bgu.ac.il> Hi, I started to have strange and inconsistent behavior of chimera when I open PDB's. My system is W7 with Nvidia 840M graphics card (which has been functioning fine for nearly 3 years). I am running the latest daily build but noticed this strange behavior with previous versions as well as the production one. I attach 3 snip pictures, the first two are of pdb files opened, one OK (as usual) and the other distorted. The 3rd snip pictures is of the Nvidia debug when I start Chimera in command file as chimera.exe --debug-opengl. It became quite a lottery for me as for how pdb file will open. The .py files open OK so far as I recall. Please help me with this recent mystery. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture-chimera-snip1.PNG Type: image/png Size: 470195 bytes Desc: Capture-chimera-snip1.PNG URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture-chimera-snip2.PNG Type: image/png Size: 328963 bytes Desc: Capture-chimera-snip2.PNG URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture-snip3-debug-openGL.PNG Type: image/png Size: 257576 bytes Desc: Capture-snip3-debug-openGL.PNG URL: From meng at cgl.ucsf.edu Fri Feb 8 12:50:10 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 8 Feb 2019 12:50:10 -0800 Subject: [Chimera-users] Strange and inconsistent Chimera behavior recently on W7/Nvidia OS In-Reply-To: <15cae60bef2645dda014f126f9e0a510@bgu.ac.il> References: <15cae60bef2645dda014f126f9e0a510@bgu.ac.il> Message-ID: <76FB4330-B1BA-40CA-99FD-0DD70121DA4D@cgl.ucsf.edu> Hi Boaz, As far as I know we haven?t had anybody report this, but the type of distortion looks like when the ?horizontal field of view? angle is abnormally large. This parameter is in the Camera tab of the viewing tool, the same dialog that has the Side View, and can also be adjusted continuously if you drag to widen the ?vee? when the Side View side is set to ?top?. You can also change it with a command, e.g. set fieldOfView 20 There is no one default value for startup, but some calculation based on the window size and computer screen size occurs. I haven?t heard of it going berserk spontaneously, but maybe Chimera gets confused about what the window and/or screen size is at startup when you see that distortion. When that happens, at least for now as a stopgap, look in the Camera tool to see if it is abnormally large and if so, reset to something smaller, like what you get when the image looks normal. If it continues to happen spontaneously, please use menu: Help? Report a Bug so that it gets logged as an issue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2019, at 12:16 PM, Boaz Shaanan wrote: > > Hi, > I started to have strange and inconsistent behavior of chimera when I open PDB's. My system is W7 with Nvidia 840M graphics card (which has been functioning fine for nearly 3 years). I am running the latest daily build but noticed this strange behavior with previous versions as well as the production one. > > I attach 3 snip pictures, the first two are of pdb files opened, one OK (as usual) and the other distorted. The 3rd snip pictures is of the Nvidia debug when I start Chimera in command file as chimera.exe --debug-opengl. > > It became quite a lottery for me as for how pdb file will open. The .py files open OK so far as I recall. > > Please help me with this recent mystery. > Thanks, > Boaz From bshaanan at bgu.ac.il Fri Feb 8 13:48:36 2019 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Fri, 8 Feb 2019 21:48:36 +0000 Subject: [Chimera-users] Strange and inconsistent Chimera behavior recently on W7/Nvidia OS In-Reply-To: <76FB4330-B1BA-40CA-99FD-0DD70121DA4D@cgl.ucsf.edu> References: <15cae60bef2645dda014f126f9e0a510@bgu.ac.il>, <76FB4330-B1BA-40CA-99FD-0DD70121DA4D@cgl.ucsf.edu> Message-ID: <7f47d35407944c279d458ca3535033ef@bgu.ac.il> Thanks a lot Elaine for your prompt reply and help, Your suggestion "set fieldOfView 20" did the trick. It's the first time I come across such strange behavior and I have no idea what caused it. Best regards, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng Sent: Friday, February 8, 2019 10:50 PM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Strange and inconsistent Chimera behavior recently on W7/Nvidia OS Hi Boaz, As far as I know we haven?t had anybody report this, but the type of distortion looks like when the ?horizontal field of view? angle is abnormally large. This parameter is in the Camera tab of the viewing tool, the same dialog that has the Side View, and can also be adjusted continuously if you drag to widen the ?vee? when the Side View side is set to ?top?. You can also change it with a command, e.g. set fieldOfView 20 There is no one default value for startup, but some calculation based on the window size and computer screen size occurs. I haven?t heard of it going berserk spontaneously, but maybe Chimera gets confused about what the window and/or screen size is at startup when you see that distortion. When that happens, at least for now as a stopgap, look in the Camera tool to see if it is abnormally large and if so, reset to something smaller, like what you get when the image looks normal. If it continues to happen spontaneously, please use menu: Help? Report a Bug so that it gets logged as an issue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2019, at 12:16 PM, Boaz Shaanan wrote: > > Hi, > I started to have strange and inconsistent behavior of chimera when I open PDB's. My system is W7 with Nvidia 840M graphics card (which has been functioning fine for nearly 3 years). I am running the latest daily build but noticed this strange behavior with previous versions as well as the production one. > > I attach 3 snip pictures, the first two are of pdb files opened, one OK (as usual) and the other distorted. The 3rd snip pictures is of the Nvidia debug when I start Chimera in command file as chimera.exe --debug-opengl. > > It became quite a lottery for me as for how pdb file will open. The .py files open OK so far as I recall. > > Please help me with this recent mystery. > Thanks, > Boaz From junhasong at berkeley.edu Sun Feb 10 19:23:31 2019 From: junhasong at berkeley.edu (Jun Ha Song) Date: Mon, 11 Feb 2019 12:23:31 +0900 Subject: [Chimera-users] Does UCSF Chimera support RTX 2080 Ti? Message-ID: Dear RBVI, I am currently deciding which graphic card to upgrade to, and I wonder if UCSF Chimera support RTX2080Ti. Would there be any bugs due to graphic cards being RTX? Best, Junha. -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.elbaum at weizmann.ac.il Mon Feb 11 07:32:33 2019 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Mon, 11 Feb 2019 15:32:33 +0000 Subject: [Chimera-users] using a surface as a mask for a volume Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F439B0@IBWMBX01> Hi. I have a volume (EM tomography data) which I display together with a surface. I'd like to use that surface to mask away the volume elements that lie outside the surface boundary. Is it possible to define and display a restricted region this way? It's similar to Segment Map but without the segmentation step. thanks, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From mordred_ at hotmail.com Sat Feb 9 23:09:58 2019 From: mordred_ at hotmail.com (Alberto garcia lopez) Date: Sun, 10 Feb 2019 07:09:58 +0000 Subject: [Chimera-users] Hello chimera my name is Alberto, I would like to know if there is any way to see the double bonds in the structures. Message-ID: Enviado desde Correo para Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Feb 11 08:53:39 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 11 Feb 2019 08:53:39 -0800 Subject: [Chimera-users] using a surface as a mask for a volume In-Reply-To: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F439B0@IBWMBX01> References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F439B0@IBWMBX01> Message-ID: <83A586BE-CC65-49E0-931E-84207159A1C5@cgl.ucsf.edu> Hi Michael, Certainly, you can just use the ?mask? command to create a new map masked by the surface: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 11, 2019, at 7:32 AM, Michael Elbaum wrote: > > Hi. I have a volume (EM tomography data) which I display together with a surface. I'd like to use that surface to mask away the volume elements that lie outside the surface boundary. Is it possible to define and display a restricted region this way? It's similar to Segment Map but without the segmentation step. > thanks, > Michael From meng at cgl.ucsf.edu Mon Feb 11 08:54:37 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 11 Feb 2019 08:54:37 -0800 Subject: [Chimera-users] Hello chimera my name is Alberto, I would like to know if there is any way to see the double bonds in the structures. In-Reply-To: References: Message-ID: Hi Alberto, Sorry no, Chimera does not have an option to show double bonds differently than single bonds. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco From goddard at sonic.net Mon Feb 11 08:58:02 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 11 Feb 2019 08:58:02 -0800 Subject: [Chimera-users] Does UCSF Chimera support RTX 2080 Ti? In-Reply-To: References: Message-ID: <9CEB3A22-0C5B-4F70-8F55-12BFD38F80E9@sonic.net> Hi Junha, The 2080 Ti will work fine with Chimera. The main trouble with graphics cards are buggy drivers, especially a problem on cards no one uses. Not too many people use 2080 Ti, but it likely uses the drivers of the 2080, 2070, that are more widely used. The 2080 Ti is an expensive card $1200-1400. The claimed speed improvements over the 1080 and 1080 Ti are mostly measuring a new raytracing capability that almost no software uses, Chimera does not use it. In the future (probably at least a year away) we may try hardware raytracing in ChimeraX. Tom > On Feb 10, 2019, at 7:23 PM, Jun Ha Song wrote: > > Dear RBVI, > > I am currently deciding which graphic card to upgrade to, and I wonder if UCSF Chimera support RTX2080Ti. Would there be any bugs due to graphic cards being RTX? > > Best, > Junha. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.elbaum at weizmann.ac.il Mon Feb 11 13:02:38 2019 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Mon, 11 Feb 2019 21:02:38 +0000 Subject: [Chimera-users] using a surface as a mask for a volume In-Reply-To: <83A586BE-CC65-49E0-931E-84207159A1C5@cgl.ucsf.edu> References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F439B0@IBWMBX01>, <83A586BE-CC65-49E0-931E-84207159A1C5@cgl.ucsf.edu> Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F43EC2@IBWMBX01> Of course - silly me. I looked in the Volume Viewer Tools and didn't check the commands. Works like a charm. Michael ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Monday, February 11, 2019 18:53 To: Michael Elbaum Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] using a surface as a mask for a volume Hi Michael, Certainly, you can just use the ?mask? command to create a new map masked by the surface: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 11, 2019, at 7:32 AM, Michael Elbaum wrote: > > Hi. I have a volume (EM tomography data) which I display together with a surface. I'd like to use that surface to mask away the volume elements that lie outside the surface boundary. Is it possible to define and display a restricted region this way? It's similar to Segment Map but without the segmentation step. > thanks, > Michael From michael.elbaum at weizmann.ac.il Tue Feb 12 00:12:34 2019 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Tue, 12 Feb 2019 08:12:34 +0000 Subject: [Chimera-users] Volume Viewer Planes Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F44AB8@IBWMBX01> Hi. Here's an issue regarding the use of "Planes" in the Volume Viewer, not really a proper bug but often an inconvenience. When I choose a subset of Planes there is obviously some calculation, and the calculation has to be redone when I move the slider. For a large volume this can be very slow, especially for Surface rendering. If I use the number box to save time, the calculation updates for each change "instantaneously", meaning slowly. For example if I want to move from 110 to 85, the calculation updates for 11, 1, 8, and 85. I think it would be more efficient to wait for an Enter, or even just to add a delay of 2-3 seconds. I hope you can consider this in future versions. thanks, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Mon Feb 11 14:13:46 2019 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Mon, 11 Feb 2019 17:13:46 -0500 Subject: [Chimera-users] Linking structure to Multialign viewer Message-ID: I have multiple copies of the same structure open. How to link specific chains of model IDs to Multialign viewer, to be able to highlight sequence of the residues I select? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Feb 12 08:35:01 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 12 Feb 2019 08:35:01 -0800 Subject: [Chimera-users] Linking structure to Multialign viewer In-Reply-To: References: Message-ID: <5A5F8970-59E5-49B5-A0FA-56A667627D37@cgl.ucsf.edu> Hi Ahmad, If you click the ?Help? button on Multalign Viewer it will show the help for that tool. Here is the copy of the same information at our website: The ?Sequence-Structure Association? section in that page explains how to do this. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 11, 2019, at 2:13 PM, Ahmad Khalifa wrote: > > I have multiple copies of the same structure open. How to link specific chains of model IDs to Multialign viewer, to be able to highlight sequence of the residues I select? > Thanks. From goddard at sonic.net Tue Feb 12 10:44:23 2019 From: goddard at sonic.net (Tom Goddard) Date: Tue, 12 Feb 2019 10:44:23 -0800 Subject: [Chimera-users] Volume Viewer Planes In-Reply-To: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F44AB8@IBWMBX01> References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F44AB8@IBWMBX01> Message-ID: Hi Michael, I fixed this problem in ChimeraX just now ? it was a one line change. Chimera uses a different window toolkit (Tk) and it would take significant time to figure out the change and test it. I tried a few simple things that did not work. All our work is on ChimeraX now I?m not going to fix it in Chimera since I do not have time or funding to work on Chimera. Tom > On Feb 12, 2019, at 12:12 AM, Michael Elbaum wrote: > > Hi. Here's an issue regarding the use of "Planes" in the Volume Viewer, not really a proper bug but often an inconvenience. When I choose a subset of Planes there is obviously some calculation, and the calculation has to be redone when I move the slider. For a large volume this can be very slow, especially for Surface rendering. If I use the number box to save time, the calculation updates for each change "instantaneously", meaning slowly. For example if I want to move from 110 to 85, the calculation updates for 11, 1, 8, and 85. I think it would be more efficient to wait for an Enter, or even just to add a delay of 2-3 seconds. I hope you can consider this in future versions. > thanks, > Michael > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.elbaum at weizmann.ac.il Tue Feb 12 14:04:43 2019 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Tue, 12 Feb 2019 22:04:43 +0000 Subject: [Chimera-users] Volume Viewer Planes In-Reply-To: References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F44AB8@IBWMBX01>, Message-ID: <6908210B148F61A6.66d85d64-1606-435a-9321-049f830db30c@mail.outlook.com> No problem - I'm looking forward to getting started with ChimeraX. Doesn't make sense to put a lot of effort into fixing the old program if nobody complained till now. Regards, Michael Get Outlook for Android From: Tom Goddard Sent: Tuesday, February 12, 20:44 Subject: Re: [Chimera-users] Volume Viewer Planes To: Michael Elbaum Cc: chimera-users at cgl.ucsf.edu BB Hi Michael, I fixed this problem in ChimeraX just now ? it was a one line change. Chimera uses a different window toolkit (Tk) and it would take significant time to figure out the change and test it. I tried a few simple things that did not work. All our work is on ChimeraX now I?m not going to fix it in Chimera since I do not have time or funding to work on Chimera. Tom On Feb 12, 2019, at 12:12 AM, Michael Elbaum wrote: Hi. Here's an issue regarding the use of "Planes" in the Volume Viewer, not really a proper bug but often an inconvenience. When I choose a subset of Planes there is obviously some calculation, and the calculation has to be redone when I move the slider. For a large volume this can be very slow, especially for Surface rendering. If I use the number box to save time, the calculation updates for each change "instantaneously", meaning slowly. For example if I want to move from 110 to 85, the calculation updates for 11, 1, 8, and 85. I think it would be more efficient to wait for an Enter, or even just to add a delay of 2-3 seconds. I hope you can consider this in future versions. thanks, Michael _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From sun647 at purdue.edu Tue Feb 12 16:30:25 2019 From: sun647 at purdue.edu (Chen Sun) Date: Wed, 13 Feb 2019 00:30:25 +0000 Subject: [Chimera-users] Measure unmodeled density Message-ID: Dear Chimera users, I have a map with extra density in it and I'd like to know the volume of the extra density. So is there an existing command in Chimera that can measure the volume of unmodeled density? Best regards, Chen Chen Sun Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S.Martin Jischke Dr. West Lafayette, IN 47907 "The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts. --Bertrand Russell" -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Feb 13 08:45:28 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Feb 2019 08:45:28 -0800 Subject: [Chimera-users] Measure unmodeled density In-Reply-To: References: Message-ID: <1278DF5A-85AF-45FB-BE26-867D522796EE@cgl.ucsf.edu> Hi Chen, Not a single command, but may be possible with a few steps. (A) somehow remove the density for the modeled part to create a map that just has the unmodeled density (B) set contour level of the unmodeled-density map as you like, then use command ?measure volume? to measure isosurface-enclosed volume I?m guessing by ?modeled? you mean that you have atomic structures fitted in. In that case, two ways that might work for part ?A? are: - color all the atomic structures (could be all the same color), select all the atomic structures, use Color Zone and its ?Split Map? button. The ?unzone? part will be one of the resulting maps. - simulate density of atomic structures with ?molmap? and use ?vop subtract? to subtract it from the density, creating a new map of the unmodeled part. Might be tricky to decide what resolution value to use with molmap. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 12, 2019, at 4:30 PM, Chen Sun wrote: > > Dear Chimera users, > > I have a map with extra density in it and I'd like to know the volume of the extra density. So is there an existing command in Chimera that can measure the volume of unmodeled density? > > Best regards, > Chen > Chen Sun > Department of Biological Sciences > Purdue University > Hockmeyer Hall of Structural Biology > 240 S.Martin Jischke Dr. > West Lafayette, IN 47907 > > "The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts. --Bertrand Russell" From terre031 at r.umn.edu Wed Feb 13 11:53:06 2019 From: terre031 at r.umn.edu (Cassidy Terrell) Date: Wed, 13 Feb 2019 13:53:06 -0600 Subject: [Chimera-users] Question about AutoDock Message-ID: Hello, I am using the AutoDock feature in UCSF Chimera and after clicking "Apply" everything appears to work normally and then program says: E*xecution complete - check outputs to verify successful execution* In the past a ViewDock window with the results would automatically pop-up after the execution completed - however this is no longer happening and I do not know how to access the output files. The program did not write a *name.pdbqt *file - all other files are there though. Any suggestions for accessing the output file would be much appreciated!! -- Cassidy R. Terrell, Ph.D. Assistant Professor, Biochemistry University of Minnesota, Rochester 111 South Broadway Rochester, MN 55904 *Always believe something wonderful is about to happen* -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandru.buhimschi at yale.edu Wed Feb 13 14:50:05 2019 From: alexandru.buhimschi at yale.edu (Alexandru Buhimschi) Date: Wed, 13 Feb 2019 16:50:05 -0600 Subject: [Chimera-users] Troubleshooting Docking Problem Message-ID: Hello- I have been trying to perform a docking search for small molecule binding to a B-DNA double helix (e.g. 1ZFH). Unfortunately, when I set up the ligand and receptor, I receive the following error: IndexError: list index out of range Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages. cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. I am not sure what I can do to address this, but I have tried multiple DNA structures and the result appears to be the same. I have also encountered this error which I could not resolve either: ValueError: Could not find atomic number for Ha Ha > failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. Please let me know if there is anything I should do to address this issue. Best, Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Feb 13 15:27:28 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Feb 2019 15:27:28 -0800 Subject: [Chimera-users] Troubleshooting Docking Problem In-Reply-To: References: Message-ID: Hi Alex, If you look in the Help, you can see that there is an option (default true) in receptor prep to omit chains that are made up of anything other than standard amino acids. You could try changing that to ?false?. Even if you try that, I do not know if Autodock Vina is meant for use with nucleic acids. You may want to check their website for such information. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 13, 2019, at 2:50 PM, Alexandru Buhimschi wrote: > > Hello- > I have been trying to perform a docking search for small molecule binding to a B-DNA double helix (e.g. 1ZFH). Unfortunately, when I set up the ligand and receptor, I receive the following error: > > IndexError: list index out of range > Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages. > cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. > > I am not sure what I can do to address this, but I have tried multiple DNA structures and the result appears to be the same. > > I have also encountered this error which I could not resolve either: > ValueError: Could not find atomic number for Ha Ha > > failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. > > Please let me know if there is anything I should do to address this issue. > Best, > Alex From conrad at cgl.ucsf.edu Wed Feb 13 15:29:00 2019 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 13 Feb 2019 15:29:00 -0800 Subject: [Chimera-users] Question about AutoDock In-Reply-To: References: Message-ID: That's very odd. The Chimera tool is supposed to detect and download the data. If it doesn't take too long, can you please try running it again? When the request is sent, there should be a "status" URL displayed in the Reply Log. You can use a browser to visit that URL to check on the calculation. If you can send one of those URLs to me, I can try to do a little more investigation as to why Chimera is not behaving properly. Thanks. Conrad On 2/13/2019 11:53 AM, Cassidy Terrell wrote: > Hello, > > I am using the AutoDock feature in UCSF Chimera and after clicking > "Apply" everything appears to work normally and then program says: > E/xecution complete?- check outputs to verify successful execution/ > > In the past a ViewDock window with the results would automatically > pop-up after the execution completed - however this is no longer > happening and I do not know how to access the output files. The program > did not write a /name.pdbqt /file - all other files are there though. > > Any suggestions for accessing the output file would be much appreciated!! > > -- > Cassidy R. Terrell, Ph.D. > > Assistant Professor, Biochemistry > University of Minnesota, Rochester > 111 South Broadway > Rochester, MN 55904 > > /Always believe something wonderful is about to happen/ > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From terre031 at r.umn.edu Wed Feb 13 16:35:12 2019 From: terre031 at r.umn.edu (Cassidy Terrell) Date: Wed, 13 Feb 2019 18:35:12 -0600 Subject: [Chimera-users] Question about AutoDock In-Reply-To: References: Message-ID: Sure thing, here is what I found in the reply log: Autodock Vina ligand docking initiated for 4Q2U.pdb Opal service URL: http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2 Opal job URL: http://nbcr-222.ucsd.edu/opal-jobs/appvina_1.1.21550104273457-329691785 standard output ----- Inputs arguments: --receptor receptor.pdbqt --ligand ligand.pdbqt --config vina.conf --out results.pdbqt Your job 549453 ("vina.sub") has been submitted Job 549453 exited with exit code 1. ----- standard error ----- [no output] ----- Traceback (most recent call last): File "/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/WebServices/appWebService.py", line 172, in statusCB self.finishCB(self.backend, fileMap) File "/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/vina/ws.py", line 181, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service On Wed, Feb 13, 2019 at 5:55 PM Conrad Huang wrote: > That's very odd. The Chimera tool is supposed to detect and download > the data. If it doesn't take too long, can you please try running it > again? When the request is sent, there should be a "status" URL > displayed in the Reply Log. You can use a browser to visit that URL to > check on the calculation. If you can send one of those URLs to me, I > can try to do a little more investigation as to why Chimera is not > behaving properly. Thanks. > > Conrad > > On 2/13/2019 11:53 AM, Cassidy Terrell wrote: > > Hello, > > > > I am using the AutoDock feature in UCSF Chimera and after clicking > > "Apply" everything appears to work normally and then program says: > > E/xecution complete - check outputs to verify successful execution/ > > > > In the past a ViewDock window with the results would automatically > > pop-up after the execution completed - however this is no longer > > happening and I do not know how to access the output files. The program > > did not write a /name.pdbqt /file - all other files are there though. > > > > Any suggestions for accessing the output file would be much appreciated!! > > > > -- > > Cassidy R. Terrell, Ph.D. > > > > Assistant Professor, Biochemistry > > University of Minnesota, Rochester > > 111 South Broadway > > Rochester, MN 55904 > > > > /Always believe something wonderful is about to happen/ > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- Cassidy R. Terrell, Ph.D. Assistant Professor, Biochemistry University of Minnesota, Rochester 111 South Broadway Rochester, MN 55904 *Always believe something wonderful is about to happen* -------------- next part -------------- An HTML attachment was scrubbed... URL: From dziemian at ucalgary.ca Thu Feb 14 16:00:35 2019 From: dziemian at ucalgary.ca (Daniel Ziemianowicz) Date: Fri, 15 Feb 2019 00:00:35 +0000 Subject: [Chimera-users] rmf3 control in Chimera Message-ID: Hello, I can't find anything about this online, but I was told that there should be some control on the components of rmf3 files. Specifically, I would like to map my data onto an rmf structure from IMP. Normally I would use render/define attribute for some types of data and xlinkanalyzer plugin for crosslink data. However, I can't quite figure out how to control rmf structures in this same manner. I am hoping I could do something like this: given a bead with residue x and another bead containing residue y, I can map a crosslink to those beads. Likewise, with render by attribute, I can color the beads containing the relevant residues. The farthest I was able to get was reading the rmfalias documentation but that is also a bit confusing and I was not able to perform the aliasing - specifically it says rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ] as the command but then it gives an example filename/nodename1/nodename2/nodename3 which seems to contradict the "usage" format. Either way I was not able to select or alias-name the beads I would like. Below I attached an example of the hierarchy in my file, how can I select e.g. "13-22_bead" of "EED"? I hope this was not a confusing question, let me know if I need to clarify. I can also email Ben Webb from the Sali lab if this is more relevant for them. Thank you, Dan [cid:image001.png at 01D4C486.CABA8470] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 10788 bytes Desc: image001.png URL: From stevezchou at gmail.com Thu Feb 14 21:49:44 2019 From: stevezchou at gmail.com (Steve Chou) Date: Fri, 15 Feb 2019 00:49:44 -0500 Subject: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces? In-Reply-To: <59532975-44BA-4E97-B44A-A494BC9A5B22@cgl.ucsf.edu> References: <366B6724-FC09-4238-B0A0-80F1ADD20010@cgl.ucsf.edu> <59532975-44BA-4E97-B44A-A494BC9A5B22@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks for your detailed explanation! What's the format of the pseudobond file? Should it look like this? =============================== #1/A:13 at NE2 #1/A:502 at MG =============================== All the best, Steve On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng wrote: > Hi Steve, > Actually I?m surprised the Mg and water were included (even if present at > both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under ?Atoms in Common?: > > > > For the case where composition changes, you could add in a fake Mg ion and > water to the structure that?s missing them, but you?d have to decide where > to put them. Also it was my understanding that they had to be tethered to > the biopolymer chain (e.g. add distance measurement, which can then be > hidden), but maybe that requirement has changed, or the Mg does already > have a metal-coordination pseudobond to the biopolymer. > > Or if you don?t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 14, 2019, at 12:51 PM, Steve Chou wrote: > > > > Thanks, Elaine! > > You command "rainbow structures" works beautifully. > > There is "a Mg ion" and "a water molecule" in the two conformations. > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > Is there a way to morph the specific components properly? > > Steve > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Feb 15 08:31:02 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Feb 2019 08:31:02 -0800 Subject: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces? In-Reply-To: References: <366B6724-FC09-4238-B0A0-80F1ADD20010@cgl.ucsf.edu> <59532975-44BA-4E97-B44A-A494BC9A5B22@cgl.ucsf.edu> Message-ID: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it. You don?t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. Elaine > On Feb 14, 2019, at 9:49 PM, Steve Chou wrote: > > Hi Elaine, > Thanks for your detailed explanation! > What's the format of the pseudobond file? Should it look like this? > =============================== > #1/A:13 at NE2 #1/A:502 at MG > =============================== > All the best, > Steve > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng wrote: > Hi Steve, > Actually I?m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under ?Atoms in Common?: > > > > For the case where composition changes, you could add in a fake Mg ion and water to the structure that?s missing them, but you?d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. > > Or if you don?t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 14, 2019, at 12:51 PM, Steve Chou wrote: > > > > Thanks, Elaine! > > You command "rainbow structures" works beautifully. > > There is "a Mg ion" and "a water molecule" in the two conformations. > > (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. > > (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. > > Is there a way to morph the specific components properly? > > Steve > > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Feb 15 15:20:45 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Feb 2019 15:20:45 -0800 Subject: [Chimera-users] rmf3 control in Chimera In-Reply-To: References: Message-ID: <9E6BCBA7-1EA0-4ECF-9D2E-5893ADBC07B4@cgl.ucsf.edu> Hi Daniel, The "filename/nodename1/nodename2/nodename3? string is not an example of ?rmfalias" command you would give, but the aliases that would be created as a result of your using that command. rmfalias command: RMF Viewer GUI: The idea is that after creating those aliases with the ?rmfalias? command, you could use them in other commands like ?color,? etc. All the square brackets in the usage mean optional things. It looks like the thing you have highlighted is level 6 and maybe you want to omit some higher levels from the resulting aliases, so maybe something like rmfalias depth 7 skip_prefix 3 and then the aliases to use in other commands would be something like EED/Frag_3-78/Frag_3-78/3-22_bead for example, command: color red EED/Frag_3-78/Frag_3-78/3-22_bead I may be off by one in the numbers for the command options, but you can experiment and see what aliases you get (they are listed in the Reply Log) and adjust as needed. Once you have the aliases, another issue might be which commands will work on them. Several commands were implemented for atomic structures, and may only work at node levels implemented as atoms. For example, the ?distance? command adds a distance measurement between two atoms, and attribute assignment is to atoms, residues, or models. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 14, 2019, at 4:00 PM, Daniel Ziemianowicz wrote: > > Hello, > I can?t find anything about this online, but I was told that there should be some control on the components of rmf3 files. Specifically, I would like to map my data onto an rmf structure from IMP. Normally I would use render/define attribute for some types of data and xlinkanalyzer plugin for crosslink data. > > However, I can?t quite figure out how to control rmf structures in this same manner. I am hoping I could do something like this: given a bead with residue x and another bead containing residue y, I can map a crosslink to those beads. Likewise, with render by attribute, I can color the beads containing the relevant residues. > > The farthest I was able to get was reading the rmfalias documentation but that is also a bit confusing and I was not able to perform the aliasing ? specifically it says > > rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ] > > as the command but then it gives an example > > filename/nodename1/nodename2/nodename3 > > which seems to contradict the ?usage? format. Either way I was not able to select or alias-name the beads I would like. Below I attached an example of the hierarchy in my file, how can I select e.g. ?13-22_bead? of ?EED?? > > I hope this was not a confusing question, let me know if I need to clarify. I can also email Ben Webb from the Sali lab if this is more relevant for them. > > Thank you, > > Dan > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From michael.elbaum at weizmann.ac.il Sun Feb 17 07:36:25 2019 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Sun, 17 Feb 2019 15:36:25 +0000 Subject: [Chimera-users] linking plane slider among between volume models Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F4C434@IBWMBX01> Hi. I'm looking at volume and surface data simultaneously. I'd like to select a range of planes, and then when I change the selection to have it apply to both datasets. For example I'm looking at density in "solid" mode together with a smoothed isosurface. To keep them in step I should change the setting manually (in the gui) for each dataset individually. It's surprisingly easy to lose the precise overlap. It would be helpful to choose the datasets to which the planes parameters apply. Perhaps there's a non-gui way to do this? If not possible in Classic Chimera, then please just consider as a suggestion for ChimeraX. thanks, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jaime.RodriguezGuerra at uab.cat Mon Feb 18 04:13:10 2019 From: Jaime.RodriguezGuerra at uab.cat (=?utf-8?B?SmFpbWUgUm9kcsOtZ3Vlei1HdWVycmEgUGVkcmVnYWw=?=) Date: Mon, 18 Feb 2019 12:13:10 +0000 Subject: [Chimera-users] STL/OBJ 3D models exported by Chimera cannot be read in Office 2019 In-Reply-To: References: Message-ID: Oops, sorry, I just realized that it might be a problem with the Windows VM and the 3D drivers, because even the sample models provided by Microsoft cannot be displayed. Still, if somebody has access to a properly configured Office 2019 (or latest 365) installation, can you test the files I provided? Thanks again! El lun., 18 feb. 2019 a las 13:08, Jaime Rodr?guez-Guerra (>) escribi?: Hi, Chimera team! I have recently discovered that Office 2019 has support for 3D objects that can be rotated, animated, zoomed... So I was curious about the possibilities for our molecular presentations. I knew Chimera allows to export molecules to several 3D formats and crossed my fingers so there was at least one format supported by Office. - Good news: there are two! STL and OBJ are both exported by Chimera and supported by Office. - Bad news: while the files can be correctly "loaded" in Office, they are not displayed at all! "Image could not be shown". Is this something that must be addressed in Chimera or is Microsoft's fault? The error message is very succinct and does not provide more details. I have attached the files I created with Chimera just in case. Thank you very much! Jaime. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jaime.RodriguezGuerra at uab.cat Mon Feb 18 04:09:04 2019 From: Jaime.RodriguezGuerra at uab.cat (=?utf-8?B?SmFpbWUgUm9kcsOtZ3Vlei1HdWVycmEgUGVkcmVnYWw=?=) Date: Mon, 18 Feb 2019 12:09:04 +0000 Subject: [Chimera-users] STL/OBJ 3D models exported by Chimera cannot be read in Office 2019 Message-ID: Hi, Chimera team! I have recently discovered that Office 2019 has support for 3D objects that can be rotated, animated, zoomed... So I was curious about the possibilities for our molecular presentations. I knew Chimera allows to export molecules to several 3D formats and crossed my fingers so there was at least one format supported by Office. - Good news: there are two! STL and OBJ are both exported by Chimera and supported by Office. - Bad news: while the files can be correctly "loaded" in Office, they are not displayed at all! "Image could not be shown". Is this something that must be addressed in Chimera or is Microsoft's fault? The error message is very succinct and does not provide more details. I have attached the files I created with Chimera just in case. Thank you very much! Jaime. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3D-1RFO.mtl Type: application/octet-stream Size: 115 bytes Desc: 3D-1RFO.mtl URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3D-1RFO.stl Type: application/octet-stream Size: 2138484 bytes Desc: 3D-1RFO.stl URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3D-1RFO.obj Type: application/octet-stream Size: 1084912 bytes Desc: 3D-1RFO.obj URL: From stevezchou at gmail.com Fri Feb 15 15:02:51 2019 From: stevezchou at gmail.com (Steve Chou) Date: Fri, 15 Feb 2019 18:02:51 -0500 Subject: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces? In-Reply-To: References: <366B6724-FC09-4238-B0A0-80F1ADD20010@cgl.ucsf.edu> <59532975-44BA-4E97-B44A-A494BC9A5B22@cgl.ucsf.edu> Message-ID: Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13 at NE2 #1/A:704 at O #1/A:13 at NE2 #1/A:502 at MG #1/A:13 at NE2 #1/A:501 at PB #2/A:13 at NE2 #2/A:704 at O #2/A:13 at NE2 #2/A:502 at MG #2/A:13 at NE2 #2/A:501 at PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. ============================= (2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13 at NE2 #1/A:704 at O distance #1/A:13 at NE2 #1/A:502 at MG distance #1/A:13 at NE2 #1/A:501 at PB distance #2/A:13 at NE2 #2/A:704 at O distance #2/A:13 at NE2 #2/A:502 at MG distance #2/A:13 at NE2 #2/A:501 at PB ============================= I was able to see the distance labels in the two structure. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. > You'd make a plain text file with name *.pb with lines like that and open > it. > > You don?t have to read in pseudobonds from a file, however. If not too > many, probably easier just to add distance monitors. > > > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13 at NE2 #1/A:502 at MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng wrote: > > Hi Steve, > > Actually I?m surprised the Mg and water were included (even if present > at both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under ?Atoms in Common?: > > > > > > > > For the case where composition changes, you could add in a fake Mg ion > and water to the structure that?s missing them, but you?d have to decide > where to put them. Also it was my understanding that they had to be > tethered to the biopolymer chain (e.g. add distance measurement, which can > then be hidden), but maybe that requirement has changed, or the Mg does > already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don?t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- Steve Chou -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.sourav05 at gmail.com Sat Feb 16 23:51:55 2019 From: m.sourav05 at gmail.com (Sourav Mondal) Date: Sun, 17 Feb 2019 13:21:55 +0530 Subject: [Chimera-users] Error while doing autodock vina via chimera Message-ID: <5c69126e.1c69fb81.51d20.2dfd@mx.google.com> I was tring to dock the phytochemical (cid-3114) with protein (pdb id -5YFN) , this is the error I am getting. What is the reason for the error? How to overcome this error? Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: #0 LYS 1.C Chain-final residues that are actual C terminii: #0 MG 410.C Chain-final residues that are not actual C terminii: 396 hydrogen bonds Hydrogens added Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D Unable to assign MAP type to atom Mg Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb Status file contents: 1 1550389354.82 1550389354.92 Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 4016 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# WARNING: The search space volume > 27000 Angstrom^3 (See FAQ) Detected 8 CPUs WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs Reading input ... ----- Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.tapi at alice.it Mon Feb 18 07:43:57 2019 From: p.tapi at alice.it (p.tapi at alice.it) Date: Mon, 18 Feb 2019 16:43:57 +0100 (CET) Subject: [Chimera-users] Chimera laptop features required Message-ID: <16901473619.p.tapi@alice.it> Sir, I'm going to use USFC Chimera program working for La Sapienza University in Rome Italy ... before to get the program, I would like to understand the best recommended laptop features to easy run the program under Microsoft Windows WIN 10 platform .. May you answer me regarding the main laptop features ( CPU type, speed, RAM, SSD, screen resolution, etc ) you recommended ? What you suggestions ? Thanks in advance Regards Silvia Taglieri Rome Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Feb 19 09:18:36 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Feb 2019 09:18:36 -0800 Subject: [Chimera-users] Error while doing autodock vina via chimera In-Reply-To: <5c69126e.1c69fb81.51d20.2dfd@mx.google.com> References: <5c69126e.1c69fb81.51d20.2dfd@mx.google.com> Message-ID: <061BFBFD-4B84-4DB9-B146-B78A4E930007@cgl.ucsf.edu> Hi Sourav, As it says in the error message, the autodock prep cannot handle the MG or NAP residue in the receptor. Maybe it will work if you delete those residues first. If they are important for your docking calculations, you may need to find some other method (outside of Chimera). You could try running the Dock Prep tool before running the Autodock Vina tool in Chimera, but I don?t know if that will help. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 16, 2019, at 11:51 PM, Sourav Mondal wrote: > > I was tring to dock the phytochemical (cid-3114) with protein (pdb id -5YFN) , this is the error I am getting. What is the reason for the error? How to overcome this error? > > > Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments. > Automatically computing assignments using 'ksdssp' and parameter values: > energy cutoff -0.5 > minimum helix length 3 > minimum strand length 3 > Use command 'help ksdssp' for more information. > No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead > Chain-initial residues that are actual N terminii: > Chain-initial residues that are not actual N terminii: #0 LYS 1.C > Chain-final residues that are actual C terminii: #0 MG 410.C > Chain-final residues that are not actual C terminii: > 396 hydrogen bonds > Hydrogens added > Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb > Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B > Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D > Unable to assign MAP type to atom Mg > Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG > Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb > Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb > Status file contents: > 1 > 1550389354.82 > 1550389354.92 > > Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information > > Application stderr > ----- > > > Parse error on line 4016 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. > ----- > Application stdout > ----- > ################################################################# > # If you used AutoDock Vina in your work, please cite: # > # # > # O. Trott, A. J. Olson, # > # AutoDock Vina: improving the speed and accuracy of docking # > # with a new scoring function, efficient optimization and # > # multithreading, Journal of Computational Chemistry 31 (2010) # > # 455-461 # > # # > # DOI 10.1002/jcc.21334 # > # # > # Please see http://vina.scripps.edu for more information. # > ################################################################# > > WARNING: The search space volume > 27000 Angstrom^3 (See FAQ) > Detected 8 CPUs > WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs > Reading input ... ----- > > Sent from Mail for Windows 10 From meng at cgl.ucsf.edu Tue Feb 19 09:27:53 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Feb 2019 09:27:53 -0800 Subject: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces? In-Reply-To: References: <366B6724-FC09-4238-B0A0-80F1ADD20010@cgl.ucsf.edu> <59532975-44BA-4E97-B44A-A494BC9A5B22@cgl.ucsf.edu> Message-ID: This thread is not relevant to chimera-users. There were several more followup messages to this on chimerax-users, culminating in: (P.S. please do not send to both lists if the question is specific to Chimera or ChimeraX) > On Feb 15, 2019, at 3:02 PM, Steve Chou wrote: > > Hi Elaine, > (1) I tried to read the pseudobonds from a file (.pb) , > ========================= > #1/A:13 at NE2 #1/A:704 at O > #1/A:13 at NE2 #1/A:502 at MG > #1/A:13 at NE2 #1/A:501 at PB > > #2/A:13 at NE2 #2/A:704 at O > #2/A:13 at NE2 #2/A:502 at MG > #2/A:13 at NE2 #2/A:501 at PB > ========================= > the program reported an error. > ============================= > ValueError: not enough values to unpack (expected 2, got 0) > File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file > aspec1, aspec2 = line.split()[:2] > See log for complete Python traceback. > ============================= > > (2) Then I tried to add distances on the ChimeraX terminal > ============================= > distance #1/A:13 at NE2 #1/A:704 at O > distance #1/A:13 at NE2 #1/A:502 at MG > distance #1/A:13 at NE2 #1/A:501 at PB > > distance #2/A:13 at NE2 #2/A:704 at O > distance #2/A:13 at NE2 #2/A:502 at MG > distance #2/A:13 at NE2 #2/A:501 at PB > ============================= > I was able to see the distance labels in the two structure. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. > Steve > > On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it. > > You don?t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. > > > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13 at NE2 #1/A:502 at MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng wrote: > > Hi Steve, > > Actually I?m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under ?Atoms in Common?: > > > > > > > > For the case where composition changes, you could add in a fake Mg ion and water to the structure that?s missing them, but you?d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don?t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. > > > (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > -- > Steve Chou > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue Feb 19 10:34:19 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Feb 2019 10:34:19 -0800 Subject: [Chimera-users] linking plane slider among between volume models In-Reply-To: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F4C434@IBWMBX01> References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F4C434@IBWMBX01> Message-ID: Hi Michael, This has been implemented very recently in ChimeraX for a specialized case: certain segmentations associated with DICOM imaging data, for example, surfaces outlining a lesion in a CT scan. However, there is not (yet) a way for the user to control which datasets are synchronized. Sounds like this would be generally useful in a number of contexts, not just medical imaging data. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 17, 2019, at 7:36 AM, Michael Elbaum wrote: > > Hi. I'm looking at volume and surface data simultaneously. I'd like to select a range of planes, and then when I change the selection to have it apply to both datasets. For example I'm looking at density in "solid" mode together with a smoothed isosurface. To keep them in step I should change the setting manually (in the gui) for each dataset individually. It's surprisingly easy to lose the precise overlap. It would be helpful to choose the datasets to which the planes parameters apply. Perhaps there's a non-gui way to do this? If not possible in Classic Chimera, then please just consider as a suggestion for ChimeraX. > thanks, > Michael > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue Feb 19 11:49:49 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Feb 2019 11:49:49 -0800 Subject: [Chimera-users] linking plane slider among between volume models In-Reply-To: References: <77389ED5A5E5A947A5FEA1B9E8D512CB0195F4C434@IBWMBX01> Message-ID: <8B5950FB-D05F-4E8F-8B16-516F5E03665F@cgl.ucsf.edu> Although not as handy as automatically synchronized sliders, in either Chimera or ChimeraX, you can also specify multiple models (datasets) in a single ?volume? command that specifies which subregion or plane(s) to show, for example: volume all region 99,177,146,231,409,146 volume #2,4 region all volume #1-3 planes y,120 Elaine > On Feb 19, 2019, at 10:34 AM, Elaine Meng wrote: > > Hi Michael, > This has been implemented very recently in ChimeraX for a specialized case: certain segmentations associated with DICOM imaging data, for example, surfaces outlining a lesion in a CT scan. However, there is not (yet) a way for the user to control which datasets are synchronized. > > Sounds like this would be generally useful in a number of contexts, not just medical imaging data. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Feb 17, 2019, at 7:36 AM, Michael Elbaum wrote: >> >> Hi. I'm looking at volume and surface data simultaneously. I'd like to select a range of planes, and then when I change the selection to have it apply to both datasets. For example I'm looking at density in "solid" mode together with a smoothed isosurface. To keep them in step I should change the setting manually (in the gui) for each dataset individually. It's surprisingly easy to lose the precise overlap. It would be helpful to choose the datasets to which the planes parameters apply. Perhaps there's a non-gui way to do this? If not possible in Classic Chimera, then please just consider as a suggestion for ChimeraX. >> thanks, >> Michael From gregc at cgl.ucsf.edu Wed Feb 20 15:03:29 2019 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 20 Feb 2019 15:03:29 -0800 Subject: [Chimera-users] Chimera laptop features required In-Reply-To: <16901473619.p.tapi@alice.it> References: <16901473619.p.tapi@alice.it> Message-ID: <0092a45a-77ba-5db4-8174-74d17d8777dd@cgl.ucsf.edu> What you want to get depends on how much data you want to visualize at one time.? If you are only looking at small molecules, almost any laptop will do.? If you are looking at bigger systems, then a laptop might not be good enough. I don't think you can buy one anymore, but the best laptops were those with NVIDIA Quadro (not NVS) graphics and a 3D stereo display (120Mhz, 3D glasses).? Chimera needs workstation graphics (NVIDIA Quadro or AMD FirePro/FireGL), to support 3D stereo viewing. For most people, any decent gaming laptop will do.? My order of optimization would start the the graphics.? Stay away from Intel graphics, go for NVIDIA or AMD graphics -- the higher end, the better; and the more dedicated graphics memory, the better.? Next, pick a fast CPU -- some parts of Chimera are single-core CPU bound.? Next, more memory is better, 4GB for small data, 8/16/32 for larger data.? Screen resolution isn't that important -- higher screen resolutions need better graphics to keep the 3D interactive, and you can always use F11 to switch into and out of fullscreen graphics.? And a SSD is very, very nice, it will improve the overall responsiveness of the computer, but is not critical for Chimera. But some people are happy with laptops that have Intel graphics. Again, it depends on how much data you want to visualize at one time.? Ideally, you would demo the laptop you want to buy with your data before buying it.? Next best thing would be to try out your friend's laptop. You can see user-submitted Chimera benchmark results at http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks.? There aren't many results for recent graphics cards.? Please submit the results for the system you end up getting. ??? Best of luck, ??? Greg On 2/18/19 7:43 AM, p.tapi at alice.it wrote: > Sir, > I'm going to use *USFC Chimera* program working for /*La Sapienza > University in Rome Italy*/ ... > before to get the program, I would like to understand the best > recommended laptop features to easy run the program under *Microsoft > Windows WIN 10 platform *? .. > > May you answer me? regarding the *main laptop features* ( CPU type, > speed, RAM, SSD, screen resolution, etc ) *you recommended* ? What you > suggestions ? > > Thanks in advance > Regards > > Silvia Taglieri > Rome Italy > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Feb 20 15:25:00 2019 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 20 Feb 2019 15:25:00 -0800 Subject: [Chimera-users] STL/OBJ 3D models exported by Chimera cannot be read in Office 2019 In-Reply-To: References: Message-ID: <64faeff9-e173-710c-42fd-f5b1b9448014@cgl.ucsf.edu> Sorry, don't have Office 2019, but your STL file looked good in MeshLab.? Look at the "3-D Models make with Chimera" web page, https://www.rbvi.ucsf.edu/Outreach/technotes/ModelGallery/index.html for more STL related information.? In particular, it links to Eduardo's Guide for 3D Printing, http://www.munfred.com/proteins.html.? And that page has a section on using Netfabb to fix the STL models.? Microsoft also provides a free service to repair STL files, https://modelrepair.azurewebsites.net/.? Perhaps if Microsoft repaired the STL file, Office would be able to display it. ??? Best wishes, ??? Greg On 2/18/19 4:13 AM, Jaime Rodr?guez-Guerra Pedregal wrote: > Oops, sorry, I just realized that it might be a problem with the > Windows VM and the 3D drivers, because even the sample models provided > by Microsoft cannot be displayed. Still, if somebody has access to a > properly configured Office 2019 (or latest 365) installation, can you > test the files I provided? Thanks again! > > El lun., 18 feb. 2019 a las 13:08, Jaime Rodr?guez-Guerra > ( >) escribi?: > > Hi, Chimera team! > > I have recently discovered that Office 2019 has support for 3D > objects that can be rotated, animated, zoomed... So I was curious > about the possibilities for our molecular presentations. I knew > Chimera allows to export molecules to several 3D formats and > crossed my fingers so there was at least one format supported by > Office. > > - Good news: there are two! STL and OBJ are both exported by > Chimera and supported by Office. > > - Bad news: while the files can be correctly "loaded" in Office, > they are not displayed at all! "Image could not be shown". > > Is this something that must be addressed in Chimera or is > Microsoft's fault? The error message is very succinct and does not > provide more details. I have attached the files I created with > Chimera just in case. > > Thank you very much! > Jaime. > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From masoud.aliyar at gmail.com Thu Feb 21 07:36:05 2019 From: masoud.aliyar at gmail.com (masoud aliyar) Date: Thu, 21 Feb 2019 19:06:05 +0330 Subject: [Chimera-users] Broad selection with command Message-ID: I use "zonesel" command to select SOL residues around ligand. but this command did not select entire residue and just select atoms that are the given zone.how can I use command-line to broaden residue selection and select entire residue atoms?. I know I can use the keyboard to broaden selection, but I want to use the command-line -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 21 08:17:29 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Feb 2019 08:17:29 -0800 Subject: [Chimera-users] Broad selection with command In-Reply-To: References: Message-ID: Hello, The command to broaden selection is ?select up?, see: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 21, 2019, at 7:36 AM, masoud aliyar wrote: > > I use "zonesel" command to select SOL residues around ligand. but this command did not select entire residue and just select atoms that are the given zone.how can I use command-line to broaden residue selection and select entire residue atoms?. I know I can use the keyboard to broaden selection, but I want to use the command-line From soemya at kemi.dtu.dk Thu Feb 21 01:44:16 2019 From: soemya at kemi.dtu.dk (Sowmya Indrakumar) Date: Thu, 21 Feb 2019 09:44:16 +0000 Subject: [Chimera-users] Chimera PDB2PQR In-Reply-To: References: Message-ID: <993808d090a2402fa591268daec8506f@kemi.dtu.dk> Dear Developers, I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. Thanks a lot for your help! Regards Sowmya [cid:cdf013bd-01d5-4d3d-9dd2-554c27674417] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedImage.png Type: image/png Size: 80063 bytes Desc: pastedImage.png URL: From walke284 at msu.edu Thu Feb 21 05:22:28 2019 From: walke284 at msu.edu (Walker, Kevin) Date: Thu, 21 Feb 2019 13:22:28 +0000 Subject: [Chimera-users] ViewDock tool not showing PDBQT vina output file Message-ID: The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. Windows 10 64-bit Chimera 1.13 Graphics Card: AMD Radeon 480 Memory: 11 GB -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovannyrincons at gmail.com Thu Feb 21 03:50:20 2019 From: giovannyrincons at gmail.com (Giovanny Rincon S) Date: Thu, 21 Feb 2019 12:50:20 +0100 Subject: [Chimera-users] Chimera Message-ID: Hello, I am a graduate student in Balearic Islands, I am doing a protein study with Chimera, I wanted to ask if it is possible to change the background color to White. Thank you so Much From pett at cgl.ucsf.edu Thu Feb 21 10:22:36 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 21 Feb 2019 10:22:36 -0800 Subject: [Chimera-users] ViewDock tool not showing PDBQT vina output file In-Reply-To: References: Message-ID: <521E3FAA-E01D-4660-8F2E-900DE210D984@cgl.ucsf.edu> Hi Kevin, I have one further thing for you to try: remove your preferences file. You can find the location of you preferences file by bringing up the Preferences dialog (Favorites?Preferences) and then change the ?Category? in the dialog to ?Preferences?. The location of your preferences file will then be shown near the top of the dialog. Remove (or rename) that file, and then restart Chimera. If that does not help, please use Help?Report A Bug to submit a bug report and attach the problematic PDBQT file. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Feb 21, 2019, at 5:22 AM, Walker, Kevin wrote: > > The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. > > The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. > > Windows 10 64-bit > Chimera 1.13 > Graphics Card: AMD Radeon 480 > Memory: 11 GB > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeffrey.schineller at humboldt.edu Thu Feb 21 10:33:57 2019 From: jeffrey.schineller at humboldt.edu (Jeffrey B Schineller) Date: Thu, 21 Feb 2019 10:33:57 -0800 Subject: [Chimera-users] Chimera In-Reply-To: References: Message-ID: Hi Giovanny, Choose command line under the favorites menu and enter: set bgcolor white on the command line at the bottom of the screen. Dr. Jeffrey Schineller Department of Chemistry Humboldt State University 1 Harpst Street Arcata, CA 95521 On Thu, Feb 21, 2019 at 10:17 AM Giovanny Rincon S > wrote: Hello, I am a graduate student in Balearic Islands, I am doing a protein study with Chimera, I wanted to ask if it is possible to change the background color to White. Thank you so Much _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From masoud.aliyar at gmail.com Thu Feb 21 11:20:08 2019 From: masoud.aliyar at gmail.com (masoud aliyar) Date: Thu, 21 Feb 2019 22:50:08 +0330 Subject: [Chimera-users] Broad selection with command In-Reply-To: References: Message-ID: Hello Yes, it does. thank you so much, it's helpfull On Thu, Feb 21, 2019 at 7:47 PM Elaine Meng wrote: > Hello, > The command to broaden selection is ?select up?, see: > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Feb 21, 2019, at 7:36 AM, masoud aliyar > wrote: > > > > I use "zonesel" command to select SOL residues around ligand. but this > command did not select entire residue and just select atoms that are the > given zone.how can I use command-line to broaden residue selection and > select entire residue atoms?. I know I can use the keyboard to broaden > selection, but I want to use the command-line > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From masoud.aliyar at gmail.com Thu Feb 21 11:40:10 2019 From: masoud.aliyar at gmail.com (masoud aliyar) Date: Thu, 21 Feb 2019 23:10:10 +0330 Subject: [Chimera-users] Chimera In-Reply-To: References: Message-ID: hello you can go action tab --> color --> all options --> background --> more --> click on the squere in right of background colore and set value 1 for R,G and B. then click close and save On Thu, Feb 21, 2019 at 10:08 PM Jeffrey B Schineller < jeffrey.schineller at humboldt.edu> wrote: > Hi Giovanny, > > Choose command line under the favorites menu and enter: set bgcolor > white on the command line at the bottom of the screen. > > Dr. Jeffrey Schineller > Department of Chemistry > Humboldt State University > 1 Harpst Street > Arcata, CA 95521 > > > On Thu, Feb 21, 2019 at 10:17 AM Giovanny Rincon S < > giovannyrincons at gmail.com> wrote: > >> Hello, >> >> I am a graduate student in Balearic Islands, I am doing a protein study >> with Chimera, I wanted to ask if it is possible to change the background >> color to White. >> >> Thank you so Much >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 21 11:54:09 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Feb 2019 11:54:09 -0800 Subject: [Chimera-users] Chimera PDB2PQR In-Reply-To: <993808d090a2402fa591268daec8506f@kemi.dtu.dk> References: <993808d090a2402fa591268daec8506f@kemi.dtu.dk> Message-ID: <3E047F24-600A-414D-87C5-63B1300FF2C0@cgl.ucsf.edu> Hi Sowmya, This calculation is not done inside of Chimera but at a webserver run by another group: So reinstalling Chimera would not be expected to have any effect on this. You could try running that webservice directly from the link above, but it will probably give the same results. I also saw this behavior even when I tried pH 1 and 12, which I would expect to give some difference, and even when I used the newer version of that webserver: I don?t know why there is no change in the total charge. However, it might change if you choose a different forcefield (e.g. AMBER instead of PARSE), but I did not try that. Maybe PARSE doesn?t include hydrogens. You could try using a different force field, and if that doesn?t help, maybe ask your question on the pdb2pqr-users mailing list (link at the bottom of the webserver page). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 21, 2019, at 1:44 AM, Sowmya Indrakumar wrote: > > Dear Developers, > I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. > Thanks a lot for your help! > Regards > Sowmya > From walker at chemistry.msu.edu Thu Feb 21 10:32:56 2019 From: walker at chemistry.msu.edu (Kevin D. Walker) Date: Thu, 21 Feb 2019 18:32:56 +0000 Subject: [Chimera-users] ViewDock tool not showing PDBQT vina output file In-Reply-To: <521E3FAA-E01D-4660-8F2E-900DE210D984@cgl.ucsf.edu> References: <521E3FAA-E01D-4660-8F2E-900DE210D984@cgl.ucsf.edu> Message-ID: Hi Eric, I figured it out. My 4K screen was placing the View Dock dialog box off screen. I realized this after I updated the video card driver (as a matter of course) and the video resolution changed to very high numbers. When that happened, I was able to see everything that was ?on? the desktop that was previously off screen. This threw me for a long loop. Kevin From: Eric Pettersen Sent: Thursday, February 21, 2019 1:23 PM To: Walker, Kevin Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] ViewDock tool not showing PDBQT vina output file Hi Kevin, I have one further thing for you to try: remove your preferences file. You can find the location of you preferences file by bringing up the Preferences dialog (Favorites?Preferences) and then change the ?Category? in the dialog to ?Preferences?. The location of your preferences file will then be shown near the top of the dialog. Remove (or rename) that file, and then restart Chimera. If that does not help, please use Help?Report A Bug to submit a bug report and attach the problematic PDBQT file. ?Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 21, 2019, at 5:22 AM, Walker, Kevin > wrote: The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. Windows 10 64-bit Chimera 1.13 Graphics Card: AMD Radeon 480 Memory: 11 GB _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From sra42 at case.edu Thu Feb 21 12:08:14 2019 From: sra42 at case.edu (Shishir Adhikari) Date: Thu, 21 Feb 2019 15:08:14 -0500 Subject: [Chimera-users] Measure angle and effect length Message-ID: Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From sowmyaiisc at gmail.com Thu Feb 21 12:23:37 2019 From: sowmyaiisc at gmail.com (Sowmya Indrakumar) Date: Thu, 21 Feb 2019 21:23:37 +0100 Subject: [Chimera-users] Chimera PDB2PQR In-Reply-To: <3E047F24-600A-414D-87C5-63B1300FF2C0@cgl.ucsf.edu> References: <993808d090a2402fa591268daec8506f@kemi.dtu.dk> <3E047F24-600A-414D-87C5-63B1300FF2C0@cgl.ucsf.edu> Message-ID: <4BD4B48C-8D07-4214-82C1-7F128C665F1C@gmail.com> Hi Elaine, Thanks a lot for your comments on this. I did try all that you mentioned. Finally, running the pqb2pqr locally on Linux to generate pqr worked fine. But running the same on windows did not work for me. I used the generated pqr in chimera, that looks alright. I do not know what sure why it does not run properly on windows. Would be nice to get feedback on the same from the developers. Best, Sowmya Sent from my iPhone > On 21 Feb 2019, at 20.54, Elaine Meng wrote: > > Hi Sowmya, > This calculation is not done inside of Chimera but at a webserver run by another group: > > > > So reinstalling Chimera would not be expected to have any effect on this. > > You could try running that webservice directly from the link above, but it will probably give the same results. I also saw this behavior even when I tried pH 1 and 12, which I would expect to give some difference, and even when I used the newer version of that webserver: > > > > I don?t know why there is no change in the total charge. However, it might change if you choose a different forcefield (e.g. AMBER instead of PARSE), but I did not try that. Maybe PARSE doesn?t include hydrogens. > > You could try using a different force field, and if that doesn?t help, maybe ask your question on the pdb2pqr-users mailing list (link at the bottom of the webserver page). > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Feb 21, 2019, at 1:44 AM, Sowmya Indrakumar wrote: >> >> Dear Developers, >> I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. >> Thanks a lot for your help! >> Regards >> Sowmya >> > From pett at cgl.ucsf.edu Thu Feb 21 15:31:09 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 21 Feb 2019 15:31:09 -0800 Subject: [Chimera-users] ViewDock tool not showing PDBQT vina output file In-Reply-To: References: <521E3FAA-E01D-4660-8F2E-900DE210D984@cgl.ucsf.edu> Message-ID: <5B0AD0C2-4189-4E78-B2D9-E8BD1017890E@cgl.ucsf.edu> I?m glad you were able to work it out. It would have been hard to debug! :-) ?Eric > On Feb 21, 2019, at 10:32 AM, Kevin D. Walker wrote: > > Hi Eric, > > I figured it out. My 4K screen was placing the View Dock dialog box off screen. I realized this after I updated the video card driver (as a matter of course) and the video resolution changed to very high numbers. When that happened, I was able to see everything that was ?on? the desktop that was previously off screen. This threw me for a long loop. > > Kevin > > From: Eric Pettersen > Sent: Thursday, February 21, 2019 1:23 PM > To: Walker, Kevin > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] ViewDock tool not showing PDBQT vina output file > > Hi Kevin, > I have one further thing for you to try: remove your preferences file. You can find the location of you preferences file by bringing up the Preferences dialog (Favorites?Preferences) and then change the ?Category? in the dialog to ?Preferences?. The location of your preferences file will then be shown near the top of the dialog. Remove (or rename) that file, and then restart Chimera. > If that does not help, please use Help?Report A Bug to submit a bug report and attach the problematic PDBQT file. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Feb 21, 2019, at 5:22 AM, Walker, Kevin > wrote: > > The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. > > The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. > > Windows 10 64-bit > Chimera 1.13 > Graphics Card: AMD Radeon 480 > Memory: 11 GB > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 21 15:48:49 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Feb 2019 15:48:49 -0800 Subject: [Chimera-users] Measure angle and effect length In-Reply-To: References: Message-ID: <6C231E5F-DC09-464E-A847-9249BB097613@cgl.ucsf.edu> Hi, There is no single ?correct way,? which is why the options are options. You have to decide for yourself because it all depends how you want to define those measurements based on your scientific judgment. Lengths (distances) could be measured between 2 atoms, and angles between 3 atoms, or you could calculate axes or planes from the two domains and then get the angle between them. However, if you calculate axes or planes, you have to decide which atoms to use to define each of those things. Distances, angles, axes, planes, etc. are all described here in the ?Structure Measurements? page: The meaning of mass weighting and helical correction for axis calculation are also described in that same page (which you would see if you just clicked ?Help? on the dialog). You cannot control axis length, it just extends as far as the farthest atoms used to calculate it, so for length measurements you might as well just pick two atoms and measure the distance between them. Personally, I always use helical correction. You can try both ways, it might not make much difference except for short helices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 21, 2019, at 12:08 PM, Shishir Adhikari wrote: > > Hi, > What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? > What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? > Thanks From meng at cgl.ucsf.edu Thu Feb 21 16:00:17 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Feb 2019 16:00:17 -0800 Subject: [Chimera-users] Measure angle and effect length In-Reply-To: <6C231E5F-DC09-464E-A847-9249BB097613@cgl.ucsf.edu> References: <6C231E5F-DC09-464E-A847-9249BB097613@cgl.ucsf.edu> Message-ID: <1A3E162F-D641-416D-9432-DEFA9196F944@cgl.ucsf.edu> Another possibility is to use the command ?measure inertia? to report principal axes in the Reply Log, but again you would have to decide/specify which atoms to use in the calculation. Elaine > On Feb 21, 2019, at 3:48 PM, Elaine Meng wrote: > > Hi, > There is no single ?correct way,? which is why the options are options. You have to decide for yourself because it all depends how you want to define those measurements based on your scientific judgment. Lengths (distances) could be measured between 2 atoms, and angles between 3 atoms, or you could calculate axes or planes from the two domains and then get the angle between them. However, if you calculate axes or planes, you have to decide which atoms to use to define each of those things. Distances, angles, axes, planes, etc. are all described here in the ?Structure Measurements? page: > > > The meaning of mass weighting and helical correction for axis calculation are also described in that same page (which you would see if you just clicked ?Help? on the dialog). You cannot control axis length, it just extends as far as the farthest atoms used to calculate it, so for length measurements you might as well just pick two atoms and measure the distance between them. > > Personally, I always use helical correction. You can try both ways, it might not make much difference except for short helices. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Feb 21, 2019, at 12:08 PM, Shishir Adhikari wrote: >> >> Hi, >> What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? >> What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? >> Thanks > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From bshaanan at bgu.ac.il Thu Feb 21 15:42:00 2019 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Thu, 21 Feb 2019 23:42:00 +0000 Subject: [Chimera-users] Defining CMYK color scheme for color actions Message-ID: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il> Hi, Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? Thanks for you advice, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 From pett at cgl.ucsf.edu Thu Feb 21 16:10:52 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 21 Feb 2019 16:10:52 -0800 Subject: [Chimera-users] Defining CMYK color scheme for color actions In-Reply-To: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il> References: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il> Message-ID: Hi Boaz, That means that the saved image should use the CMYK color space, not that you have to specify CMYK colors as you create the image. From the Save Image Help/Tips page: Color space <>. Some publications require images to be in the CMYK color space. Chimera currently saves images in only the RGB color space, so a separate application such as Adobe Photoshop? must be used to switch between the two. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Feb 21, 2019, at 3:42 PM, Boaz Shaanan wrote: > > Hi, > > Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? > Thanks for you advice, > > Boaz > > > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan at bgu.ac.il > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From bshaanan at bgu.ac.il Thu Feb 21 16:20:40 2019 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Fri, 22 Feb 2019 00:20:40 +0000 Subject: [Chimera-users] Defining CMYK color scheme for color actions In-Reply-To: References: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il>, Message-ID: <847c7f3b-2a0a-46bf-8cdd-78f04f783f2e@email.android.com> An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Thu Feb 21 21:32:26 2019 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 21 Feb 2019 21:32:26 -0800 Subject: [Chimera-users] Defining CMYK color scheme for color actions In-Reply-To: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il> References: <47c7b5b83c1b4598847b8ed9051f3869@bgu.ac.il> Message-ID: CMYK is just an another way of encoding colors.? All of the computer graphics uses RGB colors, even if you specify it with CMYK values.?? All printers print CMYK images, so the printer software does the conversion if you don't.? Most publishers now accept RGB images and do the conversion themselves because they'll need the RGB version for the web. Even if the publisher accepts RGB images, to ensure that your images are suitable for printing, you should print your images and see how the color is different from the screen version.? The color gamut of screens and printers overlap, but there are major differences, in particular, screens show much brighter colors. Often, things that are obviously different on the screen, are not as different when printed.? Then you can revise the colors if need be.? And, almost 9% of the population has some degree of color blindness, so use your colleagues to test your images too. If the publisher really needs a CMYK image, then you should use Adobe Photoshop, or some other image editor, to convert your saved image from RGB to CYMK.? To get the printed colors as close to the colors you're seeing, you'll need to associate a color profile with the image.? People that really worry about color, calibrate their monitors, and use the profile generated by the calibration tool.? In molecular graphics, we are not such people.? If you don't have a color profile for your screen, use the sRGB color profile.? Next, you need to pay attention to which version of CMYK your publisher wants.? US and European publishers have slightly different versions -- if I recall correctly, the European CYMK is better at showing shades of red.? If you are printing the image on your own printer, you should use the color profile for your printer instead of one of the standard CMYK ones if you have it. Adobe Photoshop has a way to view the transformed image on your screen, instead of having to print it -- presumably other image editors do too. Bottom line, give the publisher the RGB image and let the publisher sweat the details. ??? Hope this? helps, ??? Greg On 2/21/2019 3:42 PM, Boaz Shaanan wrote: > Hi, > > Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? > Thanks for you advice, > > Boaz > > > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan at bgu.ac.il > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From masoud.aliyar at gmail.com Fri Feb 22 12:39:18 2019 From: masoud.aliyar at gmail.com (masoud aliyar) Date: Sat, 23 Feb 2019 00:09:18 +0330 Subject: [Chimera-users] how to hide just H-bonds between water molecules with themselves? Message-ID: Hello I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don?t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 ********************* The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame. second, if I set selection mode on append and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict both ********************* The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don?t want it. How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain? Thank you, everyone, -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Feb 22 13:08:46 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 22 Feb 2019 13:08:46 -0800 Subject: [Chimera-users] how to hide just H-bonds between water molecules with themselves? In-Reply-To: References: Message-ID: <8824935D-1DE8-41CC-B65A-41EC813EAF8F@cgl.ucsf.edu> Hello Masoud, If I understand correctly, you want all H-bonds among 3 residues, ligand, water except not the water-water ones. I guess SOL is your waters? You could try sel :38:53:147:279 findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 Then SOL (water) is only in the second set of atoms and you will only get H-bonds between the two sets. The zonesel part may take some time too. If you only want to show the waters that are h-bonding to those residues and ligand at each step, you could instead use findhbond option ?reveal true? to display them. Also if the selected residues stay the same, you wouldn?t put that in your script unless you are also unselecting them at each frame. In other words, just do this one time: sel :38:53:147:279 ?then in per-frame script: ~disp :SOL findhbond linew 3 color blue selRestrict :SOL:38:53:147:279 reveal true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 22, 2019, at 12:39 PM, masoud aliyar wrote: > > Hello > > I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don?t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script: > > ********************* > > ~display :SOL > > zonesel :279 3 :SOL > > select up > > display sel > > select :38:53:147:279 > > findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 > > ********************* > > The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame. > > second, if I set selection mode on append and write this script: > > ********************* > > ~display :SOL > > zonesel :279 3 :SOL > > select up > > display sel > > select :38:53:147:279 > > findhbond linewidth 3 color blue selRestrict both > > ********************* > > The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don?t want it. > > How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain? > Thank you, everyone, From prasad.ssva at gmail.com Fri Feb 22 20:16:05 2019 From: prasad.ssva at gmail.com (prasad ssv) Date: Sat, 23 Feb 2019 09:46:05 +0530 Subject: [Chimera-users] Hi good morning Message-ID: How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6? -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Feb 22 22:12:23 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 22 Feb 2019 22:12:23 -0800 Subject: [Chimera-users] Hi good morning In-Reply-To: References: Message-ID: <5793008A-6BE9-45BD-9F63-29DB10A149FC@cgl.ucsf.edu> Hello, The Mol2 saving dialog has an option to save all models to "a single file [individual @MOLECULE sections]? If you are preparing the structures with Dock Prep, the Mol2 saving dialog will automatically appear after the other steps are done. The format needed for DOCK6 is described in the DOCK6 manual. Depending on what DOCK6 options you use, you may need to edit the Mol2 file yourself after Chimera writes it, such as to add SOLVATION or AMBER_SCORE_ID for certain types of scoring, as mentioned in this page: If you have questions specifically about DOCK6, the best place to ask is on the dock-fans mailing list: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 22, 2019, at 8:16 PM, prasad ssv wrote: > > How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6? From meng at cgl.ucsf.edu Mon Feb 25 12:59:48 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Feb 2019 12:59:48 -0800 Subject: [Chimera-users] Morph Help In-Reply-To: <3FD0E639-76B6-46D0-92CB-999BC1CEB44F@baylor.edu> References: <3FD0E639-76B6-46D0-92CB-999BC1CEB44F@baylor.edu> Message-ID: <6E209DAD-9CC0-424C-8346-755D5E751589@cgl.ucsf.edu> Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I?ve worked on, however). ChimeraX also allows changing hinge spacing. (1b) Chimera has an option to minimize each frame, but it also has limited ability to ?rescue? bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to ?guide? the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users at cgl.ucsf.edu or chimerax-users at cgl.ucsf.edu (depending on which program you?re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 25, 2019, at 12:30 PM, Paul, Debamita wrote: > > Hi, > > I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up. > > Thanks > Debamita From murpholinox at gmail.com Mon Feb 25 20:31:20 2019 From: murpholinox at gmail.com (Murpholino Peligro) Date: Mon, 25 Feb 2019 22:31:20 -0600 Subject: [Chimera-users] Installation problem on Fedora 29 Message-ID: [murphy at eva02 Downloads]$ ./chimera.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs at lists.wku.edu). Original path: '/home/murphy/Downloads' inflating: chimera_install_6JK7q6/installer inflating: chimera_install_6JK7q6/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-1.13.1 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/murphy/.local/UCSF-Chimera64-1.13.1' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org). Install desktop menu and icon? yes Traceback (most recent call last): File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/__main__.py", line 73, in value = chimeraInit.init(sys.argv) File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimeraInit.py", line 666, in init import chimera File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", line 2777, in from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/__init__.py", line 14, in from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/save.py", line 13, in from chimera import replyobj, selection, SessionPDBio, version File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/replyobj.py", line 24, in import Tkinter File "/home/murphy/.local/UCSF-Chimera64-1.13.1/lib/python2.7/lib-tk/Tkinter.py", line 39, in import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_6JK7q6' Installation is done; press return. Help please. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Feb 26 09:00:58 2019 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 26 Feb 2019 09:00:58 -0800 Subject: [Chimera-users] Installation problem on Fedora 29 In-Reply-To: References: Message-ID: <59431c4e-5241-561b-a026-136635ed2124@cgl.ucsf.edu> I believe? your trying to install Chimera on a very recent version of Fedora?? Regardless, this bug should be fixed in the daily build.? If not, please let me know. ??? -- Greg On 2/25/2019 8:31 PM, Murpholino Peligro wrote: > [murphy at eva02 Downloads]$ ./chimera.bin > UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs at lists.wku.edu > ). > Original path: '/home/murphy/Downloads' > ? inflating: chimera_install_6JK7q6/installer > ? inflating: chimera_install_6JK7q6/chimera.bin > > Enter install location: ~/.local/UCSF-Chimera64-1.13.1 > Extracting files.? This may take a few minutes. > Executing command: './chimera.bin -q -d > /home/murphy/.local/UCSF-Chimera64-1.13.1' > UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org). > > Install desktop menu and icon? yes > Traceback (most recent call last): > ? File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/__main__.py", > line 73, in > ??? value = chimeraInit.init(sys.argv) > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimeraInit.py", line > 666, in init > ??? import chimera > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", > line 2777, in > ??? from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/__init__.py", > line 14, in > ??? from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/save.py", > line 13, in > ??? from chimera import replyobj, selection, SessionPDBio, version > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/replyobj.py", > line 24, in > ??? import Tkinter > ? File > "/home/murphy/.local/UCSF-Chimera64-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in > ??? import _tkinter # If this fails your Python may not be configured > for Tk > ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: > FT_Done_MM_Var > ERROR in chimera_final_install: unable to install desktop icon: > result code from installer: 256 > Installer returned unexpected return code '256' > Cleaning up extract dir, 'chimera_install_6JK7q6' > Installation is done; press return. > > Help please. > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From trangiakhai97 at gmail.com Tue Feb 26 22:23:40 2019 From: trangiakhai97 at gmail.com (=?UTF-8?B?S2jhuqNpIFRy4bqnbiBHaWE=?=) Date: Wed, 27 Feb 2019 13:23:40 +0700 Subject: [Chimera-users] Chimera using question Message-ID: Dear Mr/Mrs, I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? I am looking forward for your replying. Thank you. Best regards, Khai. -------------- next part -------------- An HTML attachment was scrubbed... URL: From btemban at yahoo.com Wed Feb 27 08:16:24 2019 From: btemban at yahoo.com (temban billyhp) Date: Wed, 27 Feb 2019 16:16:24 +0000 (UTC) Subject: [Chimera-users] Seeking for help References: <1201831653.6005947.1551284184681.ref@mail.yahoo.com> Message-ID: <1201831653.6005947.1551284184681@mail.yahoo.com> SirI prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you.?Best wishes.? Sent from Yahoo Mail on Android -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Feb 27 09:02:30 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 27 Feb 2019 09:02:30 -0800 Subject: [Chimera-users] Error with Autodock Vina prep on DNA In-Reply-To: <1201831653.6005947.1551284184681@mail.yahoo.com> References: <1201831653.6005947.1551284184681.ref@mail.yahoo.com> <1201831653.6005947.1551284184681@mail.yahoo.com> Message-ID: <4460750D-8ACF-4C1C-8DA8-0881D8A19E1D@cgl.ucsf.edu> (I changed the Subject line because the original one was not useful for other people on the mailing list) Please see this recent answer to a similar question: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 27, 2019, at 8:16 AM, temban billyhp wrote: > > Sir > I prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you. > Best wishes. From meng at cgl.ucsf.edu Wed Feb 27 09:28:51 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 27 Feb 2019 09:28:51 -0800 Subject: [Chimera-users] writing multiple chains from Modeller to one PDB In-Reply-To: References: Message-ID: <1ECAA5B1-A37B-436B-AA8E-F3200C57EE3C@cgl.ucsf.edu> Dear Khai, (I changed the Subject line because the original one was not useful for other people on the mailing list) The problem may be because the chains that come back from Modeller do not have any chain IDs. After you get more models back from Modeller with the missing residues added, you would combine them and assign chain IDs, then save the PDB file. I give a detailed example below: I opened a structure 1www that has two chains with missing residues (V and W) and I made 5 models of V with missing residues added and 5 models of W with missing residues added. I looked in the Model Panel (open from Favorites menu) and I can see that there is #0 the original model #1.1-5 the models of chain V #2.1-5 the models of chain W Model Panel: I decided to use #1.1 and #2.4 as the chain models to combine into a new model, so in Model Panel I chose just those two (click the name of one, Ctrl-click the name of the other one) and clicked the ?copy/combine?? function on the right. Then in the Copy/Combine dialog I chose ?rename them uniquely? for assigning two different chain IDs. You can enter a name for new model that will be shown in the Model Panel, or else it will just be the default name ?combination?. Now I see there is a new model #3 named combination, so in Model Panel you can just choose that one and then click the ?write PDB? function on the right to save it as a PDB file. Now when I close everything and then reopen the PDB file I saved, it shows both chains and they are A and B (not V and W because Modeller lost that information). If you don?t like which chain is A and which is B, or you want to assign other different IDs like V and W, you could change chain IDs (menu: Tools? Structure Editing? Change Chain IDs) and then write another PDB. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 26, 2019, at 10:23 PM, Kh?i Tr?n Gia wrote: > > Dear Mr/Mrs, > I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? > I am looking forward for your replying. > Thank you. > Best regards, > Khai. From murpholinox at gmail.com Wed Feb 27 23:15:52 2019 From: murpholinox at gmail.com (Murpholino Peligro) Date: Thu, 28 Feb 2019 01:15:52 -0600 Subject: [Chimera-users] Can Chimera read electron density difference map files from RIDL? Message-ID: Here is what RIDL is https://github.com/GarmanGroup/RIDL I can open the map in coot specifying is a difference map and it opens nicely over the protein. In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P ... Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From prasad.ssva at gmail.com Thu Feb 28 05:41:16 2019 From: prasad.ssva at gmail.com (prasad ssv) Date: Thu, 28 Feb 2019 19:11:16 +0530 Subject: [Chimera-users] Morph Help In-Reply-To: <6E209DAD-9CC0-424C-8346-755D5E751589@cgl.ucsf.edu> References: <3FD0E639-76B6-46D0-92CB-999BC1CEB44F@baylor.edu> <6E209DAD-9CC0-424C-8346-755D5E751589@cgl.ucsf.edu> Message-ID: > > hi > good evening i have sdf files,i converted all those sdf files into single mol2 files..there is a option - a single file [individual @MOLECULE sections] - multiple files [file name must contain $name or $number] - a single file [combined @MOLECULE section] may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dp248 at cornell.edu Thu Feb 28 07:14:51 2019 From: dp248 at cornell.edu (Debamita Paul) Date: Thu, 28 Feb 2019 09:14:51 -0600 Subject: [Chimera-users] Chimera Help Message-ID: morphg5-xtal_0222_new.pdb morphg5-xtal_0222_new.pdb Hi Dr. Meng, I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6cfi_model_clean.pdb Type: application/octet-stream Size: 866892 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 64_IB_DP-coot-0.pdb Type: application/octet-stream Size: 899709 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Feb 28 09:13:38 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Feb 2019 09:13:38 -0800 Subject: [Chimera-users] saving Mol2 files with $name or $number In-Reply-To: References: <3FD0E639-76B6-46D0-92CB-999BC1CEB44F@baylor.edu> <6E209DAD-9CC0-424C-8346-755D5E751589@cgl.ucsf.edu> Message-ID: <977DA4A5-3CB1-43FA-BA51-F5C4FF73B8CE@cgl.ucsf.edu> Hi Prasad, I don?t know what other words to use ? it is exactly as the description says. First decide if you want one file or multiple files. If you want one file, choose whether you want all in one molecule or individual molecule sections, then choose location and enter the filename. (Most people want individual molecules, but we are giving you the choice.) If you want multiple files, choose location, but there is only one place to enter name (even though the result will have multiple names) so you have to enter something that literally includes ?$name? or ?$number?. Example: If you have two files that are models #1 and #2 in Chimera and you choose to save multiple files and enter file name: blahblah$number.mol2 ? then you will get two files, blahblah1.mol2 and blahblah2.mol2 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 28, 2019, at 5:41 AM, prasad ssv wrote: > > hi > good evening > i have sdf files,i converted all those sdf files into single mol2 files..there is a option > ? a single file [individual @MOLECULE sections] > ? multiple files [file name must contain $name or $number] > ? a single file [combined @MOLECULE section] > may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that. From meng at cgl.ucsf.edu Thu Feb 28 09:27:27 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Feb 2019 09:27:27 -0800 Subject: [Chimera-users] Can Chimera read electron density difference map files from RIDL? In-Reply-To: References: Message-ID: <75B50F45-9265-400B-B799-FFFC06D39AB0@cgl.ucsf.edu> Hi Murpholino, It sounds like you answered your own question, since you say the map opened. What is the problem? Does it look weird? For us to say anything, you would need to be more specific about what you are trying to do, or what behaviors you are trying to get. Chimera and Coot are two different programs, so the way they behave is different, and one may have features the other does not. Since you said ?opens nicely over the protein? in Coot, maybe you need to use Chimera command ?vop cover? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 27, 2019, at 11:15 PM, Murpholino Peligro wrote: > > Here is what RIDL is https://github.com/GarmanGroup/RIDL > I can open the map in coot specifying is a difference map and it opens nicely over the protein. > > In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P > ... > > Thanks > From meng at cgl.ucsf.edu Thu Feb 28 09:55:58 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Feb 2019 09:55:58 -0800 Subject: [Chimera-users] Morph Help In-Reply-To: References: Message-ID: <915F90B5-B0FC-44B6-B4CB-F47CE006B424@cgl.ucsf.edu> Hello, As mentioned in the previous reply ... sometimes it can be difficult to get what you want with morphing, and it may be a several-day project. We do not have time to consult on everybody?s specific morphing problem, so in that reply I had suggested some things you could try. However, my guess is that you simply did not superimpose the structures first. It is explained in the Help that you have to superimpose the structures first, so it would have saved you (and me) a lot of time if you read that information first. Also your coot structure has a crazy long bond between residue 502 C and 503 N that it would look better if you deleted. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 28, 2019, at 7:14 AM, Debamita Paul wrote: > > morphg5-xtal_0222_new.pdb > morphg5-xtal_0222_new.pdbHi Dr. Meng, > > I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph > <6cfi_model_clean.pdb><64_IB_DP-coot-0.pdb> From prasad.ssva at gmail.com Thu Feb 28 20:49:19 2019 From: prasad.ssva at gmail.com (prasad ssv) Date: Fri, 1 Mar 2019 10:19:19 +0530 Subject: [Chimera-users] saving Mol2 files with $name or $number In-Reply-To: <977DA4A5-3CB1-43FA-BA51-F5C4FF73B8CE@cgl.ucsf.edu> References: <3FD0E639-76B6-46D0-92CB-999BC1CEB44F@baylor.edu> <6E209DAD-9CC0-424C-8346-755D5E751589@cgl.ucsf.edu> <977DA4A5-3CB1-43FA-BA51-F5C4FF73B8CE@cgl.ucsf.edu> Message-ID: okay, thank you for your approach towards my problem.its been solved. i have individual mol2 files in single file.please check my combined file is that file okay for docking by using dock6 suite.file is attched below thanking you, On Thu, Feb 28, 2019 at 10:43 PM Elaine Meng wrote: > Hi Prasad, > I don?t know what other words to use ? it is exactly as the description > says. First decide if you want one file or multiple files. If you want > one file, choose whether you want all in one molecule or individual > molecule sections, then choose location and enter the filename. (Most > people want individual molecules, but we are giving you the choice.) If you > want multiple files, choose location, but there is only one place to enter > name (even though the result will have multiple names) so you have to enter > something that literally includes ?$name? or ?$number?. > > Example: > If you have two files that are models #1 and #2 in Chimera and you choose > to save multiple files and enter file name: > blahblah$number.mol2 > ? then you will get two files, blahblah1.mol2 and blahblah2.mol2 > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 28, 2019, at 5:41 AM, prasad ssv wrote: > > > > hi > > good evening > > i have sdf files,i converted all those sdf files into single mol2 > files..there is a option > > ? a single file [individual @MOLECULE sections] > > ? multiple files [file name must contain $name or $number] > > ? a single file [combined @MOLECULE section] > > may i know meaning of these option and i would like to know file name > must contain $name or $number may i know how to write that. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lig2_charged-single-file-individual.mol2 Type: application/octet-stream Size: 18819 bytes Desc: not available URL: From trangiakhai97 at gmail.com Thu Feb 28 20:17:57 2019 From: trangiakhai97 at gmail.com (=?UTF-8?B?S2jhuqNpIFRy4bqnbiBHaWE=?=) Date: Fri, 1 Mar 2019 11:17:57 +0700 Subject: [Chimera-users] writing multiple chains from Modeller to one PDB In-Reply-To: <1ECAA5B1-A37B-436B-AA8E-F3200C57EE3C@cgl.ucsf.edu> References: <1ECAA5B1-A37B-436B-AA8E-F3200C57EE3C@cgl.ucsf.edu> Message-ID: Dear Meng, Your guiding is very helpful to me. It unties the knot for me. Thank you very much!! Best regards, Khai. V?o Th 5, 28 thg 2, 2019 va?o lu?c 00:28 Elaine Meng ?? vi?t: > Dear Khai, > (I changed the Subject line because the original one was not useful for > other people on the mailing list) > > The problem may be because the chains that come back from Modeller do not > have any chain IDs. After you get more models back from Modeller with the > missing residues added, you would combine them and assign chain IDs, then > save the PDB file. I give a detailed example below: > > I opened a structure 1www that has two chains with missing residues (V and > W) and I made 5 models of V with missing residues added and 5 models of W > with missing residues added. > > I looked in the Model Panel (open from Favorites menu) and I can see that > there is > #0 the original model > #1.1-5 the models of chain V > #2.1-5 the models of chain W > > Model Panel: > > > I decided to use #1.1 and #2.4 as the chain models to combine into a new > model, so in Model Panel I chose just those two (click the name of one, > Ctrl-click the name of the other one) and clicked the ?copy/combine?? > function on the right. > > Then in the Copy/Combine dialog I chose ?rename them uniquely? for > assigning two different chain IDs. You can enter a name for new model that > will be shown in the Model Panel, or else it will just be the default name > ?combination?. > > Now I see there is a new model #3 named combination, so in Model Panel you > can just choose that one and then click the ?write PDB? function on the > right to save it as a PDB file. Now when I close everything and then > reopen the PDB file I saved, it shows both chains and they are A and B (not > V and W because Modeller lost that information). > > If you don?t like which chain is A and which is B, or you want to assign > other different IDs like V and W, you could change chain IDs (menu: Tools? > Structure Editing? Change Chain IDs) and then write another PDB. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 26, 2019, at 10:23 PM, Kh?i Tr?n Gia > wrote: > > > > Dear Mr/Mrs, > > I am a person using Chimera to adding missing residues to a protein from > Protein Data Bank. My protein has 2 chains: A and B which both have missing > residues. I have used Chimera tools compliment with Modeller to adding > missing residues in both chain. The problem is I want to save the whole > protein which consists of 2 fixed chains, however when I saved with PDB it > only show 1 chain. How can I do that? > > I am looking forward for your replying. > > Thank you. > > Best regards, > > Khai. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: