- Chimera-users - RBVI Mailing Lists

adding measurement to Angles/Torsions via command line
by Ryan Pavlovicz 28 Jun '18

28 Jun '18

Hi, Is there a way to add a torsion measurement to the Angles/Torsions table via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session? The best workaround I can think of is to just use the 'angle' command followed by 'start Reply Log'. Thanks, ryan

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Re: [Chimera-users] Display errors
by Elaine Meng 28 Jun '18

28 Jun '18

Hi Ahmad, To summarize for the others: this is not a display error but missing secondary structure information. The reason is that the multiple-model single-PDB format is technically only for multiple coordinate sets of the same set of atoms (like an NMR ensemble), and there is only one set of helix/strand information at the top of the file that is used for each of the models. Chimera includes only the information from the first model when writing the file. In your case, although the two models look like copies of each other, they actually have some different chain IDs. In the new single file, your second model is mostly lacking this information. As I mentioned before, you can simply calculate helix and strand after opening the file: ksdssp However (and you might not care about this anyway), the assignments might be slightly different than in the original files. If you want to keep exactly the original secondary structure assignments , the better way to make a single PDB file is to combine the two models into one model before saving. You can combine models using the Model Panel (open from Favorites menu): choose both models on the left, then click “copy/combine” on the right, or with the “combine” command, for example: combine #0,1 model #2 close true and then save only the new combined model (#2) to a PDB file. I hope this helps, Elaine > On Jun 28, 2018, at 11:01 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Thanks a lot Elaine. I would appreciate you taking a look at my structures. Please find it in the attachments. > > Kind regards. > > On Thu, Jun 28, 2018 at 12:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ahmad, > I do not have this problem when I just open two structures and save them as a single PDB. When I reopen the saved PDB it shows all the secondary structure of both structures. > > When you save make sure you are saving all of the atoms (do not use options “Save displayed atoms only” or “Save selected atoms only”). Other than that, I don’t have any idea what happened with your file, without seeing that file. You could send (attach) it to e-mail. You could send to just me if you don’t want to put it on the list. > Regards, > Elaine > > > > On Jun 27, 2018, at 5:30 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > I open the structures in the first image, which have the secondary structures displayed correctly. I click file save pdb as single file.That's the process I follow to save the file. How can I fix it? > > > > On Wed, Jun 27, 2018 at 4:54 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Ahmad, > > I don’t what process you used to save the structures in a single file, so I don’t know what went wrong. All I can tell from your images is that in the bottom image, some of the copies do not have secondary structure assignments, and that is why they show up as thin “coil” ribbon instead of the wider helix and strand ribbon. It might be that something is wrong about the format of your single file, or that some of the backbone atoms are missing. If you don’t think there are missing backbone atoms, you could try command “ksdssp” to reassign helix and strand, but the assignments probably won’t be exactly the same as from the original PDB file. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jun 27, 2018, at 8:24 AM, Ahmad Abdelzaher <underoath006(a)gmail.com> wrote: > > > > > > Hello, > > > > > > After saving the two side by side structures in a single file, I get the weird display errors in the picture shown below. How can I fix that? > > > > > > Regards. > > > <before_saving.png><after_Saving.png> > > > > > <A9_padded.pdb><A10_padded.pdb>

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Display errors
by Ahmad Abdelzaher 28 Jun '18

28 Jun '18

Hello, After saving the two side by side structures in a single file, I get the weird display errors in the picture shown below. How can I fix that? Regards.

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(no subject)
by Ahir Pushpanath 27 Jun '18

27 Jun '18

Dear Chimera Team/Users, I wanted to write a python script within chimera that aims to essentially print out a contact map of a selected chunk of residues on an open structure. However, before doing so, I wondered if there is any programmatic way to generate the rotamer library at every position (i.e when you open up the rotamer tool, you get an option of 5-6 conformations you can pick for a residue), I wanted to generate that for every residue in the protein programmatically (and save every rotamer possibility) (as an altlocation?) in the crystal structure. Only after that do I want to calculate the contact map, in essence, I am trying to be as expansive as possible for each residue's "possible" contacts with any other, taking into account the full rotamer ensemble. Any tips on how to manage this programmatically? -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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Chimera bug report submission
by Bharat Reddy 27 Jun '18

27 Jun '18

Is it possible to view more than three volumes in the volume viewer window? Whenever I open more than three, the least recent density contouring disappears. I can always go to the data tool bar and select it, but it gets teadious when you are juggling 4+ volumes classes and trying to observe the difference between them. Cheers, BR File attachment: volume_viewer.png

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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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