- Chimera-users - RBVI Mailing Lists

SASA calculation per residue
by Andrew Macrae 25 Jun '18

25 Jun '18

Hello Chimera developers, I'm trying to calculate sasa scores for a list of individual residues in chimera and cant quite get it. Ive tried commands and the define attribute menu. The command ive been using is 0.23:23/areaSAS I've used similar things but I don't know what Im missing. Thanks for any help. Cheers, Andrew MacRae UCSC

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Exporting STL/COLLADA/OBJ with textures
by Healey, Joe 25 Jun '18

25 Jun '18

Hi, Is it possible for Chimera to somehow export the textures/colour mappings of the models when saving the scene as a .dea/.obj/.stl? At the moment I can export the models, including surfaces (with correct transparency) but I haven't found an option for texturing/colouring? Cheers Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Structure measurements
by Healey, Joe 23 Jun '18

23 Jun '18

Hi Chimera Team, Is there a quick/automatic way to determine the largest dimensions of a model (maybe its minimal bounding box or similar?) without having to select 2 atoms specifically to draw the distance between? Thanks Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Movie render issue
by BuddySphinx 23 Jun '18

23 Jun '18

Dear Chimera developer, I tried to use the animation to make movies. However, after recoding the output movie could not be seen (Can play but nothing shown). I was wondering what could be the issue? Thank you, Yangqi Sent from Mail for Windows 10

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different docking scores with SDFs and SMILES
by Kerr, Kelly E (HSC) 22 Jun '18

22 Jun '18

Hello, I have really enjoyed using your incredibly comprehensive and user-friendly program. I cannot overstate how much I appreciate it. I'm encountering a discrepancy though that I can't explain. It probably shows a lack of basic understanding on my part, but I would be grateful if you could help me figure this out. I have not been able to find 3D structure files for all of the ligands I'd like to run, so I have been using Chimera to build structures from the canonical SMILES presented on PubChem. I have also been using Chimera to minimize these structures. In order to be sure that the structures are completely minimized I've used the following... Steepest descent steps 1000 Steepest descent step size 0.02 Conjugate gradient steps 10000 Conjugate gradient step size 0.002 I ran this minimization and then AutoDock Vina for both the SDF and SMILES-built versions of several ligands. Both versions came from the same page (I was using PubChem) and both versions seemed to get minimized completely (the minimization outputs ended with many rows of RMSDs of zero). I'm confused that I'm getting different energy values (both initial and after minimization) for the two versions and I'm getting slightly different docking results as well. * Is it expected that SMILES and SDF files of the same chemical should have different energy values even after minimization? * Would you recommend using Zinc (aromatic) SMILES to build structures instead of the canonical smiles on PubChem? OR would you recommend using PubChem CIDs instead of SMILES? Thank you so much in advance for your time and guidance. Best regards, Kelly Kerr

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ChimeraX won't start on Ubuntu 16.04
by Petr Leiman 21 Jun '18

21 Jun '18

Dear ChimeraX users and Developers, ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows: This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Reinstalling the application may fix this problem. Fatal Python error: Aborted Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)? Thanks, Petr

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来自pengweiyucas的邮件
by pengweiyucas 21 Jun '18

21 Jun '18

Dear sir: I want to know how to show the disulfide bond ? Thank you !

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extract parts of a map based on 'volume data gradient norm'
by Dieter Blaas 18 Jun '18

18 Jun '18

Hi, I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume! Thanks for hints, bw, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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one more suggestion in chimera
by GLY 15 Jun '18

15 Jun '18

dear Eric I sorry to trouble you. Could you just give a more function in Distances of structure analysis, please? When count the distance, we must select 2 atoms exactly. For example, use the command 'select #0:2@CA #1:3@CA' and then click create button, so that we will get the distance between the CA of residue 2 in model 0 and the CA of residue 3 in model 1. HOWEVER, if we type 'select #0:@CA #1:@CA', we can't get all the distances between all CA in model 0 and all CA in model 1! :( So, how about just adding one function, so that the Create button could count serial distance? Maybe it will just be 2 buttons, one for 'select #0:@CA' and the other for 'select #1:@CA'. I am sorry to trouble you, and many thanks. best wishes! Guo NOTE: Maybe you recommend me multiple distance! But I try a lot, such as 'measure distance #0:@CA #1:@CA multiple true'. This command just result the minimum distances between all CA in model 0 and CA in model 1, not all distances! In addition, I see the site 'http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html', <http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html',> too. I am sorry, it doesn't work for we don't know how small the overlap should be. (the smaller overlap, the more contacts would be detected)

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Nucleotide Mutagenesis in Chimera
by Elhajjajy, Shaimae Imane 14 Jun '18

14 Jun '18

Hello, I am trying to mutate nucleotide residues in RNA using Chimera, and I've seen previous posts about using the "swapna" command. However, Chimera is giving the error message "Unrecognized command: swapna". Is there a way for me to enable swapna for Chimera to recognize so that I may use it? Thank you, Shaimae

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Showing/Hiding/Fading
by Gustaf Olsson 14 Jun '18

14 Jun '18

Hello Chimera users and developers, I’m back again. So my movie rendering is progressing though I have of course run into more problems. I have one PDB file open, I need to create a surface around one molecule that is close to other molecules so running the surface command directly does not work as intended. I therefore have to split the PDB file and calculate a surface around a single molecule. All is well, however after this I run into some problems trying to clean up the script. I assume that I am defining the modelID incorrectly though I cannot figure out how. The following works: split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 This splits the model putting one residue (17) in a separate model, I calculate the surface without issue, color it by coulombic charges. I then have to combine the models (the single residue (17) and the rest of the residues) and close the old “residue 17” model. I then need to hide the newly created surface to display it at a later point in the movie. The script above works, however this does not seem very neat. I have experimented with different other commands, including transparency transp 100,s #0.1 Which also works well, as long as I split and combined the models. However, I have to combine the model for this to work! split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 Everything but hiding the surface works. transp 100,s #0.1 This does not work either in this case. I am assuming that I am not defining the model ID correctly for the surface and this is why I cannot hide it? I also tried using surfcat: surfcat templ :17.het surf probeRadius 0.5 vertexDensity 20.0 templ coulombic -5 red 0 white 5 blue templ wait surftransparency 100 templ or any of the following: surftransparency 100 #0 surftransparency 100 :17.het surftransparency 100 #0:17.het transp 100,s #0 Hides the created surface, what am I doing wrong in defining the surface to hide it and show it again? Thank you for any input and best regards // Gustaf

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select a specified residue
by 张征锋 13 Jun '18

13 Jun '18

Dear Sir, It is nice to use the amaizing software of UCSF Chimera. I can select a kind of residue such as all 'SER's and label them, while I am able to select a specified number of residue, such as the 200th residue 'Ser'. Could you please show me how to do with this? Thanks a lot. Best, zhengfeng ------------------ Zhengfeng Zhang School of Life Science Central China Normal University. NO.152 Luoyu Road, Wuhan,Hubei, P.R.China 430079

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Symmetry operation calculations for multimeric fibrillar assemblies
by Einav Tayeb-Fligelman 13 Jun '18

13 Jun '18

Dear Chimera support team, I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt. Thank you in advance, Einav -- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <+972%2077-887-1964>

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make helical filament model using command sym
by Yaowang Li 13 Jun '18

13 Jun '18

Dear all, I have built a model from cryo-em density map, now I am going to create a model of a filament (have a length of the pitch, over 1000 A) from it. I think the command 'sym' can do it, but not easy for me. I have tried many times. sym #0 group h,rise,twist,100 or sym #0 group c2*h,rise,twist,100 coord #1 or sym #0 group h,2.292,179.6,100 coord #1 the model is wrong I also try to measure the symmetry first and sym #0 group #1 it is almost right, but I need much longer, how set it? using the 'n' parameter? and how? and if I want to set rise and twist myself, how to do it? Best wishes, Yaowang

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FindHBond tool not finding H-bonds with sulfur?
by Gustavo Seabra 12 Jun '18

12 Jun '18

Hi there, I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system. I’ve put together a simple example system here to show what I mean. After opening the files, I do: 1. Select the ligand (Select > Residue > LIG) 2. Tools > Surface/Binding Analysis > FindHBonds 3. Find These Bonds: Both 4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change) 5. Select “Only find H-bonds with at least one end selected” 6. Hit Apply. Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom. So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem. Thank you very much, -- Gustavo Seabra

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Fading structures/surfaces in/out
by Gustaf Olsson 12 Jun '18

12 Jun '18

Making a movie using a CMD script I am using something like the following to fade structures in/out transparency 95 :17.het; wait 8 transparency 90 :17.het; wait 8 transparency 85 :17.het; wait 8 transparency 80 :17.het; wait 8 transparency 75 :17.het; wait 8 transparency 70 :17.het; wait 8 transparency 65 :17.het; wait 8 transparency 60 :17.het; wait 8 transparency 55 :17.het; wait 8 transparency 50 :17.het; wait 8 transparency 45 :17.het; wait 8 transparency 40 :17.het; wait 8 transparency 35 :17.het; wait 8 transparency 30 :17.het; wait 8 transparency 25 :17.het; wait 8 transparency 20 :17.het; wait 8 transparency 15 :17.het; wait 8 transparency 10 :17.het; wait 8 transparency 5 :17.het; wait 8 transparency 0 :17.het; wait 8 Is it possible to use the “frames” function in transparency to achieve the same? Assuming that transparency is set to 100% and I want to fade in of course. transp 0,a :17.het frames 160 Best regards // Gustaf

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making a movie of sliding through contours
by Pranav Shah 10 Jun '18

10 Jun '18

Dear Developers, Would it be possible to make movie clips of electron density map at different density thresholds in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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scolor filament (geometry cylindrical)
by René Frank 08 Jun '18

08 Jun '18

Hello People, I would like to surface colour a filament within an EM map using cylindrical geometry (scolor geometry cylindrical). However, the electron density of the filament does not lie perfectly on the x, y or z axis. Is there a way of using two marker points placed at each end (on the longitudinal axis) of the filament to define the orientation of the cylindrical geometry and scolor the filament accordingly? My attempts to do this whilst executing the following command didn’t seem to work: scolor #0 geometry cylindrical axis sel cmap 5,gold:10,red:15,blue Many thanks for any suggestions/help, R. ====================== Dr René Frank ======================

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Re: [Chimera-users] Question Regarding on Finding Distances
by Tom Goddard 05 Jun '18

05 Jun '18

Hi Padua, Search online to find how to update your Windows graphics driver. Unfortunately for old laptops, there may not be any new graphics driver. Tom > On Jun 5, 2018, at 1:01 PM, Xiong, Padua L wrote: > > Hi Tom, > > After following what you have said, under the Gathered Information provided from the Bug Report Dialog I have found: > > OpenGL Vendor: Microscoft Corporation > OpenGL Renderer: GDI Generic > OpenGL Version: 1.1.0 > > Because everything is listed as you have said, I can see that this problem is occurring because of the graphics driver. > > Thank you so much for your fast response. > > Padua > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, June 5, 2018 1:48:07 PM > To: Xiong, Padua L > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question Regarding on Finding Distances > > Probably your graphics driver is not adequate. You can check what driver Chimera is using with Chimera menu Help / Report a Bug under “Gathered information” it will list OpenGL Renderer and Version. If it says Microsoft GDI 1.1 then you are using 1990s graphics and Chimera won’t do selection. You would need to update your driver. > > Tom > > >> On Jun 5, 2018, at 12:26 PM, Xiong, Padua L wrote: >> >> Hi there, >> >> My name is Padua and I'm an undergraduate research assistant working on pharmacogenomics. To do this, I have been using your program UCSF Chimera. >> >> I've been trying to find the distances between a protein and a drug but keep running into problems with selecting an atom in the graphics. When I try doing Ctrl-click or Shift-Ctrl-click to select an atom, I don't select anything at all (nothing is highlighted green as its supposed to when something is selected). >> >> My professor I'm working under has tried changing the mouse settings as well. Is there something I'm missing that's not listed in the User's Guide and tutorials? >> >> Much thanks, >> >> Padua >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Question Regarding on Finding Distances
by Xiong, Padua L 05 Jun '18

05 Jun '18

Hi there, My name is Padua and I'm an undergraduate research assistant working on pharmacogenomics. To do this, I have been using your program UCSF Chimera. I've been trying to find the distances between a protein and a drug but keep running into problems with selecting an atom in the graphics. When I try doing Ctrl-click or Shift-Ctrl-click to select an atom, I don't select anything at all (nothing is highlighted green as its supposed to when something is selected). My professor I'm working under has tried changing the mouse settings as well. Is there something I'm missing that's not listed in the User's Guide and tutorials? Much thanks, Padua

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Atom Specification not working in exported PDB
by Gustaf Olsson 03 Jun '18

03 Jun '18

Hello again Chimera Users So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number. PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like show :17 ~show @536-593 Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the show :XXX works as intended though this affects all residues XXX and I only want to affect residue 17. Am I doing something wrong or can I solve this in a simple way? Best regards // Gustaf

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Place marker at centre of volume box python command
by Kyle Morris 01 Jun '18

01 Jun '18

Hi Chimera dev, Is there a python command to place a marker at the precise centre of a volume’s box, regardless of the centre of mass of the volume in the box? I have played with creating dummy volumes and measuring their centres but it’s clunky and got a bit stuck with doing this. A single command would be cleaner, if it’s possible. As always thanks for your help! Best wishes, Kyle

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Command line syntax questions
by Divita Mathur, Contractor Code 6910, FN 01 Jun '18

01 Jun '18

Hi I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): 1. Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B. 2. Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18. 3. Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule. Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise! Best, -- Divita Mathur Postdoctoral Research Fellow Center for Bio/Molecular Science and Engineering Naval Research Laboratory Washington DC 20375 (202) 767-0687 (Office) divita.mathur.ctr.in(a)nrl.navy.mil

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Recording a movie of an MD simulation
by Gustaf Olsson 30 May '18

30 May '18

Hello everyone First time posting, looking for some advice. I have an MD simulation that was produced with the AMBER software package and I want to record a movie (MP4) file of the simulation. I wanted to use a CMD file and not go through the GUI since this would be a step in a series of steps and I was also hoping to perform some “in movie” modifications to the structure though I quickly ran into a huge issue, the frame rate. So basically i tried something like this: movie record size 3840,2160 format png supersample 3 coordset #0 1,-1 wait 10 movie stop movie encode output /Users/guolaa/Desktop/Arbete/Konferenser/MIP2018/Presentation/myMovieFolder/mdSimulationBox.mp4 format mp4 quality highest >From this I received what looked like a single frame of “movie”. This seemed very strange to me since I assumed that this would be 500 PNG images resulting in a 20 second movie at 25 fps. It seems I’m missing something in the process since MD iterations, frames and frame-rates does not seem to match up. I’ve gone through the documentation regarding maxFramerate, movie, coordset and so forth and I can’t work out a decent strategy. I have 500 iterations (MD-frames) loaded, I want to record a smooth 10 seconds (-ish) long MP4 movie file covering the entire range of MD-iterations (first frame to last frame though not necessarily every frame in between) and I want to do this in a CMD script and not using the GUI menu system since I plan to do more things while recording at some point (manipulating representations). Thank you in advance for any input, best regards // Gustaf

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chimera clear selection
by Brian Ondek 29 May '18

29 May '18

Hi chimera help,I have been using chimera and find it extremely useful. I was finding particular protein sequences within my structures and hit clear selection under the select tab.Now whenever I try and find a seq, it wdoes not show up and "selection cleared" appears in the bottom right corner of the window. I tried to reboot and the issue persists.Interestingly I can still see amino acid and chain selections just fine.How can I undo this "clear selection" issue I inadvertently caused? Thank you in advance for your help.Brian Ondek

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Interface residues in domain-domain contacts
by IDIGO Nwamaka 29 May '18

29 May '18

Hi, I am quite new to chimera. I was wondering how I can locate interface residues in different domains within the same protein model. For example, my protein has 3 domains and I want to find out the interface residues for the different domains. Thanks! Amaka Idigo PhD Student www.ed.ac.uk/centre-genomic-medicine<http://www.ed.ac.uk/centre-genomic-medicine> Centre for Genomic & Experimental Medicine<http://www.ed.ac.uk/centre-genomic-medicine> www.ed.ac.uk University of Edinburgh Centre for Genomic & Experimental Medicine The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Surface mesh and coloring queries
by Bala subramanian 29 May '18

29 May '18

Dear Chimera friends, Good day. Please enlighten on the following queries, a) I would like to know if I can write the surface mesh calculated within chimera to a file. From the documentation of the surface command, it seems that it is not possible. My idea is to have the vertices and faces as outputs to be fed to a plotting tool aimed for webpage display. Please guide me if this is possible or the related source code I can modify to have the output. b) How does chimera color surfaces, for instance, coulombic surface. What I am not understanding is the way the surface colors are interpolated to atomic charges. I would like to adopt the method for my plotting purpose. Thanks in advance, Bala -- C. Balasubramanian

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display vectors
by Michał Kadlof 24 May '18

24 May '18

Hi, I'm running MD simulation and I would like to display forces vectors "live". My strategy is to run: MD Movie -> PerFrame Script -> In this script create a shape (cone), and update it every frame. I transformed my vectors into ration axis and angle, and run it. However it works extreamly slow, and even lowering quality of cone didn't help. Do you have any clues? Here is how my script looks like: #1: close #1; shape cone radius 0.2 height 3.051701874476991 center :47 divisions 10 color red rotation 1.003198923120698,-0.8433298543660601,-0.5373867542336597,180 #2: close #1; shape cone radius 0.2 height 3.054021942152826 center :47 divisions 10 color red rotation 1.0022878678774028,-0.8433406134841704,-0.5373745205242975,180 #3 ... -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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coot/chimera model-map misalignment
by Gabriel Brandt 23 May '18

23 May '18

Hi. I've always been able to work around this problem, but I do often have to work around it, so I was wondering whether there's an easier way. Let's say I open a PDB file in Coot and export the map that it generates from the mtz file. If I attempt to open this ccp4-formatted map in Chimera, the coordinates appear to transformed so that the model and map are wildly misaligned in space. Normally, I work around this problem by using the map-generating feature in Phenix, which generates a model and map that align in Chimera. However, in this case, I'm trying to compare the maps that Coot generates on the fly to the those produced by Phenix, so it would be nice to be able to export a map from Coot and open it in Chimera. Thanks very much. gsb ………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846 shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...

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volume viewer ranges
by Tamas Hegedus 22 May '18

22 May '18

Hi, I have a .map file. If I open it in chimera, volume viewer indicates a range (-0.133 - 0.235 Level: 0.018 (in a textbox)), which range is different from the min and max values of data in the map file (read by python mrcfile). The chimera's range is narrower. - why is that? - I can imagine that chimera apply some cutoff; if this is the case, how can I display the full range of the .map file? Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

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Fitting structures in biological assembly surfaces
by Ahmad Abdelzaher 22 May '18

22 May '18

Hello, I have a structure that generates a surface of the biological assembly. How can I fit this surface with my structures? Regards.

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Re: [Chimera-users] [chimera-dev] Visualize 3D structure of Peptide
by Elaine Meng 22 May '18

22 May '18

Dear Reza, This is not really a Chimera question. You would need to go to the Protein DataBank website and search there. Their searching is powerful and has many options, which you can explore: <https://www.rcsb.org/#Category-search> Another way is to search for your protein of interest at UniProt, then see if there are PDB IDs given in the structures section for that protein. UniProt: <http://www.uniprot.org/> If there isn’t a known structure in the Protein DataBank, other possibilities are to: (A) look in databases of comparative models, e.g. ModBase, from which you can download a PDB file to open in Chimera <https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi> (B) build comparative model yourself if the structure of a similar protein/peptide is known <https://en.wikipedia.org/wiki/Homology_modeling> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> (C) if it’s a pretty small peptide, build from scratch, but still difficult to know if the conformation is realistic without more work (dynamics etc.). For example, Chimera allows you to build peptides (Tools… Structure Editing,... Build Structure; the Start Structure section includes a “peptide” option). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Finally, the chimera-dev e-mail address is for programming questions. If you have user questions, for future reference the better address is chimera-users(a)cgl.ucsf.edu (CC’d on this message). Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 21, 2018, at 10:25 PM, Mohammadreza Behi <m.behi(a)sydney.edu.au> wrote: > > Dear Sir/Madam, > I am trying to visualize a peptide and a protein using Chimera, yet I am not sure if the peptides may have an ID to fetch the structure by ID. > Even I could not find the ID for my protein. > Can you please let me know how I may find the ID for these items? Or if there is not any ID how to visualize them for further studies? > Kind regards, > Reza\

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Hidden capability to compute all bonds on a per-frame basis
by benjamin.horsman＠alumni.ubc.ca 20 May '18

20 May '18

Hello, A 2014 message to chimera-users mentioned that "There is also a hidden capability in Chimera to compute all bonds on a per-frame basis." (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009759.html) Could someone please elaborate on this? Does this functionality still exist is recent versions of Chimera, and has it been documented anywhere? My requirements are just that - to catalogue all (hydrogen) bonds over every frame in a trajectory. Thank you, BGSH

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chimera options opening in tabs and not windows
by Pranav Shah 17 May '18

17 May '18

Dear Developers, I have somewhat of a strange problem with chimera where, different options of the program open into tabs in the same window as opposed to having their own windows. While this is mildly irritating especially when I am using the volume viewer to change the contour level of the map and not being able to visualise the changes in the map as they appear, what gets my goat is that the options/prgorams become unavailable to access when i pull the tab out into its own window. I know this isnt a chimera problem as i have the same issue with other python based programs such as imod and eman. Would you know where i can tweak the preferences so that the programs do not open in tabs but their own independent windows? I appreciate your assistance. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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Calculating screw transformation between two protein subunits
by Nikita Chopra 17 May '18

17 May '18

Hi I have two protein subunits, which I have aligned along the z-axis. I am considering both the subunits as rigid bodies. Is there a way I could find the screw transformation (rotation along z-axis and displacement along xy plane) between them in chimera ? Thank you for your help.

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Volume viewer levels question
by Markus Heller 15 May '18

15 May '18

Hi all, I have an issue displaying a map file that I opened using the insightgrid.py script. When displaying the grid at the highest level I can get, the levels are still too low, but when I set the levels higher by typing something into the level field (e.g. 1.2e+03 instead of the 1e+03), the levels disappear altogether as shown in the second screenshot. As soon as I adjust the slider, the levels reset to 1e+03. What am I doing wrong? Thanks Markus [cid:image001.png@01D3EC35.74E6A210] [cid:image004.png@01D3EC35.9B86A230]

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insightgrid.py
by Markus Heller 14 May '18

14 May '18

Hi all, I'm looking for a copy of Tom's insightgrid.py script, referenced here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009651.html If somebody could let me know how to get hold of a copy, that'd be great! Thanks and Cheers Markus

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query about splitting volumes using local resolution criterion
by Banavali, Nilesh K (HEALTH) 14 May '18

14 May '18

ResMap, a program that calculates local resolutions for cryoEM maps, also provides a chimera script to visualize the local resolution. This script opens Volume #0 (cryoEM map), and colors its regions using the values from Volume #1 (ResMap-generated file) as follows: open #0 example_map.mrc open #1 example_map_resmap.mrc volume #1 hide scolor #0 volume #1 cmap 3.00,blue:5.00,cyan:7.00,green:9.00,yellow:11.00,orange:13.00,red I was wondering if there is a way to generate split maps based on the resolutions stored in Volume #1 instead of just coloring the original map. Alternatively, is there way to play with the transparency of the regions with specific resolutions stored in Volume #1. The goal is to separate low resolution regions from the higher resolution regions in the original map to be able to better understand/annotate the accuracy of atomic models that are generated based on the map. I tried to look for ways to do this using 'volume', 'scolor zone', and 'vop' options, but was unable to make any progress. Any help would be greatly appreciated. Thanks, Nilesh

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Regarding saving image in chimera nogui
by NAGARAJAN 14 May '18

14 May '18

Hi all, I have to use chimera --nogui and do the following 1. load a structure 2. make Surface representation 3. Color surface of selected residues with a selected color 4. save image Any idea how to do the 4 steps in chimera --nogui? Thank you

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tiling multiple chain structures
by Healey, Joe 11 May '18

11 May '18

Hi chimera team, Sorry for pestering you again so soon! Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups? e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other. The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first). Is there any way to do this without the hassle of saving and reloading? Many thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Re: [Chimera-users] saving new position of the model (map saving)
by Elaine Meng 10 May '18

10 May '18

Hi Dmitry, You need to specify two maps, the one you are sampling and the one whose grid you are sampling on, e.g. vop resample #0 onGrid #1 This means map #1 with the desired grid must already exist. As mentioned in that link, you could create it with “vop new” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> You can show outline boxes indicating axis orientation with the data display options in Volume Viewer or “volume” command, and move models separately by specifying model to move with the “models” option of “turn” (or “roll”) or with the mouse after freezing some models by unchecking their “A”ctive buttons in the Model Panel. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2018, at 11:56 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > > Thank you for your answer. > > I read the last link > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting > > but I still can not save the map > > <F8EED359A67845868DD4F80A9DAF3499.png> > > If I put onGrid I get this > > <B7696E2A55B04A298BEB09E32A85BDF2.png> > > Could you please briefly tell how to make it work? > > Thank you. > > > Sincerely, > Dmitry > > > Sent from Mail for Windows 10 > > From: Elaine Meng > Sent: Thursday, May 10, 2018 5:59 PM > To: Dmitry Semchonok > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] saving new position of the model > > Dear Dmitry, > For atomic models, of course: you can just specify saving transformed coordinates in the Save PDB or Save Mol2 dialog (or “write” command). > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> > > The rotating could be done by hand with the mouse or with commands “turn” or “roll." > > However, I’m guessing you probably mean a map since that is more complicated. As explained in the “Saving Maps After Fitting” link below, you would generally have to resample the map onto a different grid that has the axes oriented how you want: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 10, 2018, at 8:34 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > > > Dear colleagues, > > Is there a way to rotate the model and than save it with a new x y z? > > Thank you > > Sincerely, > > Dmitry > > > <F8EED359A67845868DD4F80A9DAF3499.png><B7696E2A55B04A298BEB09E32A85BDF2.png>

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saving new position of the model
by Dmitry Semchonok 10 May '18

10 May '18

Dear colleagues, Is there a way to rotate the model and than save it with a new x y z? Thank you Sincerely, Dmitry Sent from Mail for Windows 10

2 1

Setting map origin index to 0 while keeping fitted structures
by Ahmad Abdelzaher 08 May '18

08 May '18

Hello, I have spent some time fitting structures to my map. I want to set the origin to 0, however, that will lose me all the work I did. Any suggestions? Regards.

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Help
by Kimberley Perry 08 May '18

08 May '18

Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong? Kim

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join models
by VALENTINA BRANDI 08 May '18

08 May '18

Hi, I’m a Phd student and I need to join different domains of a protein. I have used the tool “join models” of Chimera, but unfortunately after the union there is a partial superimposition between the two models. How can I solve this problem? Thank you so much, Valentina Brandi Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

2 1

movie recording
by Michał Kadlof 04 May '18

04 May '18

Hello, I would like to make a movie using Chimera. I need to interpolate between key frames. I know how to do it using Animation tool, but I would like to do it for thousands of frames and clicking it all by hand is not doable. Is there any magic command for making timeline automatic way? -- best regards, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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trying to use per-frame pdb 'CONECT' information in movie maker
by Black, Kersey 04 May '18

04 May '18

Hi, Just recently back to using Chimera after a long time, so a bit rusty on this. I am reading in a trajectory of a small hydrocarbon for a single pdb file, and with each fram I include the geometry and the connectivity I want with ‘CONECT’ lines. But, when I use the Movie Maker tool to read it in, it seems to using one or more frames (perhaps the last one? to detect connectivity to auto detect connectivity and then applying it to all geometries, and this is putting bonds in places where I do not want them. Does movie maker honor CONECT information for each step? Is there a way to have it do so? Or is connectivity set once for the entire trajectory? Thanks much for any help on this, Kersey

2 1

Coloring ensemble atoms by distance from mean structure
by Tom Goddard 03 May '18

03 May '18

Hi David, I’ve attached a Python script mean_distance.py that can compute the distance of each atom in an ensemble from the mean structure. Then you can color using that distance. Here’s an example set of Chimera commands. open 1mtx show open mean_distance.py rangecolor distance_from_mean 0 blue 3 white 6 red The script uses all open molecules as the ensemble. The coloring can also be done with menu Tools / Depiction / Render by Attribute. Tom > On May 3, 2018, at 10:10 AM, Morgan, David Gene wrote: > > Tom, > > Hope you are doing well. Jim Powers and I here at IU keep thinking we need to invite you and/or the team back for another chimera workshop, but we haven't done the ground work to see how possible that would really be. But I keep hoping! > > In the meantime, I have a question about whether chimera can do something, and if not, I have a feature request... I was watching a grad student give a talk showing lots of superposed atomic structures. The structures included some molecular dynamics simulations and some crystal structures of the same protein in subtly different conformations (packing into a viral capsid, where the different subunits in the asymmetric unit have slightly different conformations). It occurred to me that _after_ showing the mess of spaghetti he had, the points he needed to make would be better served with a different visual: If he were to average the ensemble of MD atomic positions to a single chain (and color-code by the ensemble RMS difference from the average) and do the same for all his ensemble of X-ray structures, it would be much easier to talk about and show the consistencies and inconsistencies in the atomic co-ordinates from all the data. This same sort of averaging an ensemble of atomic co-ordinates is sometimes done with NMR structure ensembles (but I don't know about the color coding with the RMS). > > I have looked at lots of packages that manipulate atomic co-ordinates, but haven't found anything that seems to actually do what I want to do. For example, gromacs is supposed to do the averaging but it really wants to work with MD data and at a minimum, I'm not smart enough to make it work with a series of standard PDB files. My NMR colleague suggested molmol for the averaging, and I need to explore that more. But there doesn't seem to be a recent linux version nor does it seem to be "scriptable" (i.e., if I wanted to do this for a dozen different ensembles, I would have to painfully mouse click my way through the process). On top of all that, I ran into numerous on-line discussions about how averaging was "the wrong thing to do." All those people had valid reasons for saying so, but right now, I'm really talking about a more simple visual that conveys some of the information contained in any sort of ensemble of atomic co-ordinates. > > So my first question is: does chimera have a utility that would do this sort of thing? I looked at various commands but did not see anything that looked like it would do this. If not, can I put a feature request into the queue? > > Looking forward to hearing from you and chatting some more. > > -- > politics is more difficult than physics. > A. Einstein > > David Gene Morgan > Electron Microscopy Center > 047D Simon Hall > IU Bloomington > 812 856 1457 (office) > 812 856 3221 (3200) > http://iubemcenter.indiana.edu >

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Question regarding rotating dihedrals
by Rodrigo Galindo-Murillo 02 May '18

02 May '18

Hello! I need to do a dihedral scan around the phi/psi angles of alanine dipeptide and to create the input files to later do single point calculations I am using the cmd script: open ../scan.pdb rotation 0 @/serialNumber=7 @/serialNumber=9 rotation 0 180 write format pdb #0 test.pdb I need to use atom serial numbers since the idea is later do the scan with non-canonical peptides that will not work with the native phi/psi descriptions. The script is not modifying any angle but I can see that is generating test.pdb correctly. Could you please orient me if this is the correct set of instructions? Thank you! Rodrigo.

2 1

Changing depth cue to side to side from front to back
by Trevor Harris 02 May '18

02 May '18

Hello, I would like to know if it is possible to change the depth cue to side to side rather than front to back. I don’t want to change the position of the molecule. Is it possible? Thanks, Trevor

2 1