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Question
by Vito Calderone 07 Feb '19

07 Feb '19

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

2 1

Running vina locally
by Sam Freeman-Fox 06 Feb '19

06 Feb '19

Hi, I am looking at running docking simulations locally, and see that with the vina command line execution (*vina* *docking* *receptor* *recmodel* <frameatom_spec.html> *ligand* *ligmodel* <frameatom_spec.html> *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

2 3

How to color density maps using markers?
by Ahmad Khalifa 05 Feb '19

05 Feb '19

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.

2 5

Help: 'broken pipe' error
by Mungo Carstairs (Staff) 04 Feb '19

04 Feb '19

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]<http://uod.ac.uk/sig-home> 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<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 2

Slicing/Subdividing Models in Chimera
by Mauser, Jonathon 04 Feb '19

04 Feb '19

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(a)winona.edu <mailto:jmauser@winona.edu>

2 3

Display showing a gap in my chain
by Ahmad Khalifa 04 Feb '19

04 Feb '19

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?

2 1

Combine atom-spec non-alphanumeric no-nunderscore character error
by Ahmad Khalifa 01 Feb '19

01 Feb '19

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.

2 5

question
by Craig Scoville 31 Jan '19

31 Jan '19

Dear Staff -- I am interested in using Chimera but have a question regarding its use. I am interested in looking at the shape of small polypeptides --usually ranging from 5-20 amino acids -- does this program allow me to input amino acid sequences and then look at confirmational shapes? make substitutions and then compare confirmational shapes? Does the proprietary nature of my work prohibit me from using Chimera? Sincerely, Dr Scoville

2 2

rmsd graph
by SEFA ÇELİK 31 Jan '19

31 Jan '19

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph(using the plotting in the MD Movie trajectory viewer). And I got the result. But, graph's x-axis "frame" and y-axis "rmsd" value. I want the x axis to be the "time". Briefly, I want to see how the value of rmsd changes with time. *I added files to the e-mail. Can you explain what "1001 frames" mean? And how do I convert "1001 frames" to time. I want to see the RMSD change by time.* Can you help with this? Could you explain in detail? Best regard Assoc Prof. Dr. Sefa Celik

2 3

Morph conformation - side chains
by arrafzaher＠campus.technion.ac.il 28 Jan '19

28 Jan '19

Hi, I noticed Morph conformation only compares backbone Is it possible to compare side chains conformation change Lets say enzyme vs. phosphorylated same enzyme on a tyrosine residue (TPO) Thanks Zaher

2 1