- Chimera-users - RBVI Mailing Lists

broken lines
by shazia sabir 29 May '16

29 May '16

Hi dear All, Why chimera is showing broken lines (region encircled in red at one area). What can we predict from structure. I attached sequence of structure that shows amino acid is there(gey region in sequence). Regards, shazia.

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Modeller awareness of other proteins
by Eiros Zamora, Juan 26 May '16

26 May '16

Dear Chimera experts, I’ve got a system of three interacting proteins, and each of them is missing some linker regions in the crystal structure. I’ve succesfully used the Modeller interface in Chimera to add these regions, but the problem I’m facing now is that it adds the residues without considering that other atoms from another protein of the system are in the way. Is there a way to tell Modeller to be sensitive to other structures nearby? Thanks for any comments, [Imperial College London] <http://www.icb-cdt.co.uk/> Juan Eiros Zamora / PhD Student je714(a)ic.ac.uk<mailto:je714@ic.ac.uk> / +44 (0) 7783018326 Imperial College London Imperial College Road SW7 2AZ | UK http://www.icb-cdt.co.uk/

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Evolutional-based analysis in Chimera
by James Starlight 25 May '16

25 May '16

Dear Chimera Users! For my particular analysis I have 2 homologue membrane proteins (one is bacterial, and another one- mammalian cytocrome-C oxydase) each bound to same smaller (ligand) protein called for simplicity "the_guy". For that particular case the conservation in sequence of both protein is quite low however 1) the overall fold of both proteins especially within the membrane-embedded region as well as 2) ligand-bound (which is mostly the water exposed loops) region are quite similar. Now using some Chimera tool I need to estimate binding interfaces of two homologous proteins in terms of the conservation of the resides involved in binding of the_guy. Then I need to make more complex task- performing the same evolutional analysis but comparing 2 ensembles extracted from the MD trajectory represent simulation of binding of each of the protein with the_guy to track correlations of the statistics between the residues involved in the binding during MD as well as overall conservation for particular fold. Does the "Evolutionary tracing" might be useful here? Thanks for help! Gleb

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PDB post-processing
by James Starlight 25 May '16

25 May '16

Dear Chimera users! After some post-processing of MD simulation I have extracted from the trajectory several snapshots as individual pdbs which I need to 1- to re-assign information regarding chain letters (which was lost after some operations on pdbs) for all of those structures assuming that within each of these pdbs residues are ordered correctly e.g from (1-104 which should be chain A) than from 1-100 (it should be chain B), than 1-70 (in should be chain C) etc. 2- superimpose and combine all of the pdbs within one model in nmr-like format. Thanks for help!

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Long-ranged electrostatics analysis
by James Starlight 25 May '16

25 May '16

Dear Chimera users! I am analysing several snapshots etracted from the full atomistic md simulation of protein-protein assosiation. I wounder to ask what are the Chiemra plugins might be useful to study long-rang electrostatic effect mediated initial recognition of both proteins in this system besides APBS caclucation which is more focused on short-ranged electrostatics. Thanks for help! Gleb

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Script to open density from Coot in Chimera.
by Oliver Clarke 23 May '16

23 May '16

Hi all, Posting this in case it is useful to anyone else who uses both programs. This script will allow Coot to open the currently displayed molecules/maps in Chimera, and adjust display settings appropriately for taking a picture of electron density. Either put the appended code in your coot.py and use from the scripting interface, or place this longer script ( https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0) in your ~/.coot-preferences directory, which will add a new "Custom" menu including this option under the "Display" submenu (as well as a bunch of other stuff, and some extra custom key bindings). The orientation of the molecules should be correct after loading in Chimera, but the zoom and clipping may require some adjustment (I am not sure exactly how to match these precisely between the two programs). The script will only load a fragment of the maps (the same region that is displayed in Coot), but this has the advantage that it takes advantage of Coot's ability to deal with crystal symmetry, so it can be used at crystal contacts with no problems. Let me know if you run into any bugs! Cheers, Oli. Code: #Open displayed models and maps in Chimera, set map levels and view def open_in_chimera(): if find_exe("chimera"): #If chimera exists do stuff, else raise an error import subprocess pwd=os.getcwd() #Dir from which coot was launched cofr=rotation_centre() #3-membered list [x,y,z] make_directory_maybe("coot-chimera") #Put coot droppings here coot_chimera_path=pwd+"/coot-chimera/" check_path=coot_chimera_path+"chimera_launcher.cmd" #Chimera run script that will be written later check_path2=coot_chimera_path+"matrix.txt" #Orientation matrix for chimera input view_number=add_view_here("tmp") # initial_zoom=zoom_factor() #Coot's zoom factor. 100 is the initial state, zooming out gets larger, in gets smaller. # reset_view() zoom=zoom_factor() # go_to_view_number(view_number,1) # scale_factor=initial_zoom/base_zoom # chimera_scale=base_zoom/initial_zoom chimera_scale=100.0/zoom #Approx - breaks down when initial views upon loading mol in Coot or Chimera are different map_radius=get_map_radius() #We'll use this to export a map_radius sized fragment if os.path.isfile(check_path): #if chimera script exists, delete it. os.remove(check_path) if os.path.isfile(check_path2): #same for matrix.txt os.remove(check_path2) map_list=map_molecule_list() mol_list=model_molecule_list() matrix_list=view_matrix() #9-membered list of rotation matrix elements. with open(check_path2,"a") as matrix_file: #Write orientation matrix (specify first pdb as model, then use matrixcopy to apply to all others). Translation vector in last column is 0,0,0 because we will take care of that separately. matrix_file.write("Model {model_id}.0\n".format(model_id=mol_list[0])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[0],b=matrix_list[1],c=matrix_list[2])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[3],b=matrix_list[4],c=matrix_list[5])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[6],b=matrix_list[7],c=matrix_list[8])) with open(check_path,"a") as cmd_file: #Start writing stuff to chimera launch script. for mol_id in model_molecule_list(): if mol_is_displayed(mol_id): file_name=coot_chimera_path+"mol_{mol_id}.pdb".format(mol_id=mol_id) write_pdb_file(mol_id,file_name) path_to_file=file_name model_id=mol_id cmd_file.write("open #{model_id} {mol}\n".format(model_id=model_id,mol=path_to_file)) cmd_file.write("color gold #{model_id}; color byhet #{model_id}; ca_and_sidechains #{model_id}; disp ~protein\n".format(model_id=model_id)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{mol_id}\n".format(mol_id0=mol_list[0],mol_id=model_id)) map_id0=mol_id for map_id in map_molecule_list(): if map_is_displayed(map_id): map_level=get_contour_level_absolute(map_id) if map_is_difference_map(map_id): model_id=map_id0+map_id #make sure that the assigned model number of each map is unique and does not overlap with those of pdbs. if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"diff_map_{model_id}.mrc".format(model_id=model_id) path_to_file=file_name export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) cmd_file.write("open #{model_id} {diff_map} \n".format(model_id=model_id,diff_map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level -{map_level} color #da1200000000 level {map_level} color #0000bda00000 \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) else: model_id=map_id0+map_id if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"map_{model_id}.mrc".format(model_id=model_id) export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) path_to_file=file_name cmd_file.write("open #{model_id} {map} \n".format(model_id=model_id,map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level {map_level} \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) cmd_file.write("~sel; cofr {x},{y},{z} coordinatesystem #{mol_id0}; ac mc; center sel; cofr sel; clip hither 5 fromCenter true; clip yon -5 fromCenter true; cofr view; ~set showcofr; del sel; scale {chimera_scale}".format(x=cofr[0],y=cofr[1],z=cofr[2],mol_id0=mol_list[0],chimera_scale=chimera_scale)) chimera_exe=find_exe("chimera") info_dialog("Opening in Chimera...\nOrientation should be right but you will probably need to \nadjust the scale and clipping to get the same view as in Coot. \n If you can't see anything, try zooming out.") subprocess.Popen(["chimera",check_path]) else: info_dialog("Sorry, you need UCSF Chimera installed and accessible from the terminal for this to work!") #This works okay, though adjustment of zoom and clipping still not ideal. #would it be possible to add a subprocess.communicate() to use Coot as a controller for Chimera?

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Chimera does not start with mesa-11.2.2
by Jaime Rodríguez-Guerra Pedregal 23 May '16

23 May '16

Hi guys, just to let you know that mesa-11.2.2 is messing with Chimera startup sequence.: $ chimera --debug initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: i965_dri.so libGL error: driver pointer missing libGL error: failed to load driver: i965 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1410 Current serial number in output stream: 1411 $ `chimera --root`/bin/linuxdist /etc/os-release: NAME="Antergos Linux" VERSION="2015.11-ISO-Rolling" ID="antergos" ID_LIKE="arch" PRETTY_NAME="Antergos Linux" CPE_NAME="cpe:/o:antergosproject:antergos:2015.11" ANSI_COLOR="1;34;40" HOME_URL="https://antergos.com/" SUPPORT_URL="https://forum.antergos.com/" BUG_REPORT_URL="https://github.com/antergos" /etc/arch-release: Antergos Linux release 2015.11 (ISO-Rolling) /proc/cpuinfo: cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz (x86_64) cpu MHz: 3884.625 cache: 8192 KB /proc/meminfo: MemTotal: 16296392 kB Graphics: 00:02.0 VGA compatible controller: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller (rev 06) 01:00.0 VGA compatible controller: NVIDIA Corporation GM204 [GeForce GTX 970] (rev a1) I had to rollback to mesa-11.2.1 to make it work again. Cheers, Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

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How to convert Coot rotation matrix to something Chimera can read?
by Oliver Clarke 19 May '16

19 May '16

Hi all, I'd like to write a little python function in coot to open the current view with Chimera, because manually replicating in Chimera views that were identified in Coot is a little painful. The file handling aspects of this seem straightforward - the one aspect I haven't quite got yet is how to set the view in Chimera to match that seen in Coot. I would like to load up all molecules/maps that are displayed in coot, in their default orientations, and then apply the view matrix from coot using matrixset to get the equivalent view. Coot outputs a 3X3 rotation matrix which seems to be the same as that generated for an equivalent view by matrixget in Chimera, except that in Chimera the matrix is 3X4, with the last column representing the translation vector. This I cannot access directly within coot, but I can probably calculate it if I know what it represents. This is probably a stupid question, but is this simply the vector from the origin to the current center of rotation? Or is it something else? Cheers, Oliver.

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Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 16 May '16

16 May '16

update: with the up-to-date chimera Trajectory is loaded fine now the question is related to the analysis of the binding interface. is it possible to make contact maps plots based on the 2 selections from the input trajectory assuming that I am using martini CG model? Gleb 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > OK will try to update Chimera today ! > > What chimera's tools could be useful for the contact map based > analysis of md trajectories related to my case ? E.g to determine > binding interface between 2 proteins from long md simulation. > > Gleb > > 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >> Hi Gleb, >> If you are using Gromacs 5 trajectories, you have to be using at least >> version 1.10.2 of Chimera. If you are using that version (or later), please >> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach >> your topology file to the bug report. Thanks! >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >> Dear Chimera users! >> >> >> I am in charge with the analysis of protein-protein association during >> long molecular dynamic simulation where my system was parametrized >> using MARTINI CG force field. In particularly I am interesting to >> find residues on one of the protein which are crustal for the binding >> interface established during this MD. >> For that purpose I am trying to use Chimera to load trajectory and >> corresponded tpr file using MD movie plugin and than to >> map contact maps produced by Gromacs onto the 3D structure using Chimera. >> The problem that Chimera does not recognize properly the trajectory >> and topology. Briefly I have removed all solvent from both files >> before loading them to the Chimera using editconf and gmx convert-tpr >> obtaining eventually trajectory and topology with the same number of >> atoms. >> >> >> Than when I load it to Chimera that is the error which MD movie sent me: >> >> VERSION 5.0.2 >> using floats >> version 100, generation 26 >> 8 atoms >> Traceback (most recent call last): >> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >> line 1747, in __call__ >> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command >> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK >> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 56, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 67, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 345, in _readTopology >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 338, in _readString >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> EOFError >> EOFError >> >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> >> See reply log for Python traceback. >> >> Will be thankful for any suggestions! >> >> Gleb >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >>

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question
by zona cat 14 May '16

14 May '16

Good afternoon, My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue. Thank you very much,Dan

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Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 13 May '16

13 May '16

Dear Chimera users! I am in charge with the analysis of protein-protein association during long molecular dynamic simulation where my system was parametrized using MARTINI CG force field. In particularly I am interesting to find residues on one of the protein which are crustal for the binding interface established during this MD. For that purpose I am trying to use Chimera to load trajectory and corresponded tpr file using MD movie plugin and than to map contact maps produced by Gromacs onto the 3D structure using Chimera. The problem that Chimera does not recognize properly the trajectory and topology. Briefly I have removed all solvent from both files before loading them to the Chimera using editconf and gmx convert-tpr obtaining eventually trajectory and topology with the same number of atoms. Than when I load it to Chimera that is the error which MD movie sent me: VERSION 5.0.2 using floats version 100, generation 26 8 atoms Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 345, in _readTopology File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 338, in _readString File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError EOFError EOFError File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError See reply log for Python traceback. Will be thankful for any suggestions! Gleb

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Suggestion for ChimeraX - interruptible Matchmaker?
by Oliver Clarke 13 May '16

13 May '16

Hi, Matchmaker takes a *really* long time when dealing with long chains, particularly if it has been (unwisely/accidentally) directed to find the best matching pair of chains. This is as expected, but as Chimera is unresponsive while this happens, if the wrong matchmaker parameters are accidentally selected, there is no way to recover the session except by waiting for the operation to complete or force-quitting the app. If feasible, maybe in ChimeraX it would be useful to execute this operation in a manner that allows for cancelling a structural alignment in progress? And perhaps displaying an estimate of time to completion in the taskbar? Cheers, Oli.

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Averaging multiple structures
by Yehuda Halfon 12 May '16

12 May '16

Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda

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building and positioning disordered sequence
by thereal sisterdot 11 May '16

11 May '16

Dear Chimera Users, i would like to do something in chimera, that is not exactly science but more graphics :-) i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence. now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines. its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible. any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-) THANKS A LOT!!! sisterdot

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Join models
by shazia sabir 10 May '16

10 May '16

Hi dear all, I have to join two models in one single model. For this I have to select N and C terminal of each of the model. But I couldn't find a way how to select/pick atom from N terminal of one model and C terminal of the other model. Please can anyone help me on that? kind Regards, Shazia.

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surfaces
by A G Szabo 10 May '16

10 May '16

I am trying to represent a large homodimer with 840 residues per subunit, as a surface. On a smaller protein, 350 residues I was able to get a surface representation and color different domains. When I try to produce the surface representation of the larger molecule, I receive an error message saying that I have to split it because it is too large a molecule. So how do I do that? Thanks AGS

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repeat question
by A G Szabo 10 May '16

10 May '16

I am trying to make the sphere of an ion in an active site larger than what appears in the structure. I asked a similar question back in December, and on checking my notes I tried to use the command setattr ballScale 0.5 I first selected the ion using control<click). The ion was selected. I then tried the command line as I show it above. Nothing appeared to happen. Indeed I tried to do the same for an atom of a residue that I had selected using control <click> again nothing. I must have forgotten something. A message from Elaine suggested that I use setattr m ballScale 0.5 Am I supposed to select the residue and leave out the m? Thanks for your patience. Arthur Szabo

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opengl error with quadro k620
by Krishnan, Raman 10 May '16

10 May '16

[cid:image001.jpg@01D1A9F2.DB70AF30] Get this error on running chimera -debug-opengl option. Using quadrok620 nvidia card on windows 7.0 thanks Director Structural Biology, Biocryst Pharmaceuticals.

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rainbow color scheme
by Shreeramesh 09 May '16

09 May '16

Dear Sir, I guess blue represents N-terminal of protein in rainbow coloring and would like know the indication of other colors in rainbow scheme of chimera for protein structure. Thanks & regards *Ramesh M* Email: shreeramesh(a)gmail.com Mobile: (91) + 9646469938 (27) + (0) 844556164

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I get this when i tried to start chimera 1.11rc on windows 7. any suggestions?
by Krishnan, Raman 09 May '16

09 May '16

[cid:image001.jpg@01D1A55D.8C415B10] krish Biocryst Pharmaceuticals.

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Re: [Chimera-users] [chimera-dev] suggestions for better STL export - remove internal, reduce atom vertices
by Tom Goddard 09 May '16

09 May '16

Hi Jakob, We discussed the excessive STL vertices in atoms and bonds last week and I put a fix into the daily build and release candidate. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html Apparently you are not using those versions since your images show the high vertex density. I’ve attached an image using the current Chimera release candidate that shows reasonable vertex density. Unfortunately eliminating internal structures and stitching together meshes for atoms, bonds and ribbons at the seams is very difficult. Yes $10000 CAD software packages can do it but we don’t have the resources to solve that problem. Since every 3d printer has to deal with this problem I expect the printer software to be able to handle it, but perhaps it is too hard a problem for the 3d printer companies as well. Perhaps there is free software that can eliminate internal structures and stitch mesh intersecting edges together, I have not researched it — I’d start looking at MeshLab. Tom > On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote: > > Dear Chimera developers, > > Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. > > > 1 - Remove invisible internal and therefore unnecessary structures. > > Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). > <Screen Shot 2016-04-15 at 13.24.44.png> > as well as copious amounts of invisible internal surfaces for wire and ball and stick models. > <Screen Shot 2016-04-15 at 13.27.36.png> > If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. > > > 2 - Reduce the number of vertices for atom models. > > Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. > > Best regards, > > > Jakob Suckale, PhD > Lecturer in Biochemistry > University of Tübingen > +49-7071-29-73363 > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Alter both clipping planes at same time?
by Oliver Clarke 05 May '16

05 May '16

Hi, is there any way to alter both global clipping planes at the same time? This is handy to move the current viewable section, without altering its thickness. At the moment I use an alias for this: # move both clip planes hither or yon. # Usage: zslab x # Move hither and yon clip planes towards (positive) or away (negative) alias ^zslab clip hither $1; clip yon $1 This works fine, except when the clip planes are close together - in that case, I get an error stating that I'm trying to move the near clip plane behind the far clip plane. It would be nice to have an option to move both planes at once - e.g. maybe changing the syntax of clip so either hither, yon, or both can be specified in the same command would be possible? Cheers, Oliver.

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ImportError: No module named Chimera
by Eiros Zamora, Juan 04 May '16

04 May '16

Hi, I’m running a per-frame script to display the time in a MD movie. I used to run it without problems until I downloaded the new Mac OS X 64-bit 1.11 version. (I erased the old app, also tried to re-download the old version with no success). More specifically, I load the MD movie, and in the command line I write: 2dlabels create timer text "0 ns" color white ypos .9 xpos .9 size 50 then I open a per-frame script with the following commands: from Chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame']*0.02)) and get the error: Problem in per-frame script: ImportError: No module named Chimera I’ve googled it and found this reply: [Chimera-users] How to install chimera as a python module http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010120.html I’ve tried setting the $CHIMERA_PATH environment variable to /Applications/Chimera.app/Contents/Resources/share but I still run into the same problem. Now, I don’t want to run the script directly from the command line, as it’s a per-frame script I have to run after I load the MD movie and create the 2dlabel object. Anything obvious I’m missing here? Cheers Juan

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how to move the model and save as mrc
by rongjian li 04 May '16

04 May '16

Hi, I am trying to move the model/protein in some MRC file and save it as a new MRC file. I know how to do it in Windows by clicking the mouse, but I have lots of such operations expected. So I am wondering how could I realize this in Linux such that it can be done automatically. Thank you very much. Best, Rongjian

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Multiple Docking Using Chimera
by SOBAHY, TURKI MOHAMMED 02 May '16

02 May '16

Hello, I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000). The protein is in PDB file format, while ligands are in a SDF file format. Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest. This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score. So, basically I have scoring tables without any key IDs!! Kindly, I want to know if you have encountered the same problem and what approach you took to solve this. Thanks,? ______________________________ Turki Sobahy Research Associate Research Center (J-04) King Faisal Specialist Hospital & Research Center (Gen.Org.)-Jeddah Branch PO Box 40047, Jeddah 21499, Saudi Arabia Tel# +966 667 7777 ext. 66736| MCD# 40716 Mobile# +966 505837027 email tsobahy(a)kfshrc.edu.sa<mailto:ESan-Diego@kfshrc.edu.sa>

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