- Chimera-users - RBVI Mailing Lists

Chimera PDB2PQR
by Sowmya Indrakumar 21 Feb '19

21 Feb '19

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]

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Chimera
by Giovanny Rincon S 21 Feb '19

21 Feb '19

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

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Broad selection with command
by masoud aliyar 21 Feb '19

21 Feb '19

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

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STL/OBJ 3D models exported by Chimera cannot be read in Office 2019
by Jaime Rodríguez-Guerra Pedregal 20 Feb '19

20 Feb '19

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.

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Chimera laptop features required
by p.tapi＠alice.it 20 Feb '19

20 Feb '19

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

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linking plane slider among between volume models
by Michael Elbaum 19 Feb '19

19 Feb '19

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

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Re: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces?
by Steve Chou 19 Feb '19

19 Feb '19

Hi Elaine, Thanks for your detailed explanation! What's the format of the pseudobond file? Should it look like this? =============================== #1/A:13@NE2 #1/A:502@MG =============================== All the best, Steve On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> 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”: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > 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 <stevezchou(a)gmail.com> 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 > > > >

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Error while doing autodock vina via chimera
by Sourav Mondal 19 Feb '19

19 Feb '19

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

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rmf3 control in Chimera
by Daniel Ziemianowicz 15 Feb '19

15 Feb '19

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@01D4C486.CABA8470]

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Question about AutoDock
by Cassidy Terrell 13 Feb '19

13 Feb '19

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*

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Troubleshooting Docking Problem
by Alexandru Buhimschi 13 Feb '19

13 Feb '19

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

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Measure unmodeled density
by Chen Sun 13 Feb '19

13 Feb '19

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"

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Volume Viewer Planes
by Michael Elbaum 12 Feb '19

12 Feb '19

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

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Linking structure to Multialign viewer
by Ahmad Khalifa 12 Feb '19

12 Feb '19

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.

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using a surface as a mask for a volume
by Michael Elbaum 11 Feb '19

11 Feb '19

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

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Does UCSF Chimera support RTX 2080 Ti?
by Jun Ha Song 11 Feb '19

11 Feb '19

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.

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Hello chimera my name is Alberto, I would like to know if there is any way to see the double bonds in the structures.
by Alberto garcia lopez 11 Feb '19

11 Feb '19

Enviado desde Correo<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

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Strange and inconsistent Chimera behavior recently on W7/Nvidia OS
by Boaz Shaanan 08 Feb '19

08 Feb '19

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(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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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

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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

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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.

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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

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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>

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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?

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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.

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