- Chimera-users - RBVI Mailing Lists

3D environment
by Heymann, Bernard (NIH/NIAMS) [E] 11 Jul '18

11 Jul '18

Hi I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? Bernard

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Clustering algorithm
by David Adrian Saez San Martin 10 Jul '18

10 Jul '18

Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one? Regards. David-.

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Problem with netcdf trajectories
by David Sáez 09 Jul '18

09 Jul '18

Hello, I am using UCSF Chimera, candidate version 1.13 LInux64. When I load an MD Movie with prmtop and netcdf files (both created using Amber) the software crashes and gives segmentation fault error. In the trajectory dialog box the netcdf format is not shown as an option. With the previous version, I was able to open those files. Regards.

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Need your Kind help..
by Rajlakshmi Chetty 09 Jul '18

09 Jul '18

Dear Sir/Madam Greetings for the day!! Myself Rajlakshmi Chetty, is Doctoral student in field of Nanomaterials. I am self learning and using chimera since back few days with the help of website tutorials and am stuck with a problem which is described below: I have .pdb file format of docked complex (Hex software) in which their is H bond is missing between ligand and receptor when opened in chimera. I tried Tools>structure depiction>find H bond but in that parameters query when i apply I am getting H bond of the whole complex which I don't want. I want to visualize H bond or any bonding between ligand and receptor. Is their any other way or what parameters change i need to do? I have attached H bond parameters dialog box with this mail. This problem where I am stuck is need for the time for my research work. So your kind help will be a great blessings for me. Your help of gratitude will be highly appreciated. Thanking you and looking forward for your reply!! -- *Kind Regards* *Rajlakshmi Chetty* Doctoral Student School of Chemical Sciences Central University of Gujarat Gandhinagar 382030 India Mobile No :- * +91 9427178591* +91 8780155455 e_mail :- *rajlakshmi(a)cug.ac.in <rajlakshmi(a)cug.ac.in>* [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/07/18, 12:27:44 PM

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Interactions pairs
by Francesco Pappalardo 05 Jul '18

05 Jul '18

Dear All, We started to use Chimera since few time. I have, maybe, a very easy question. How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking. For the sake of clarity I attach a figure showing what we wish to get. Thank you. Francesco Pappalardo

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(no subject)
by Eslam Nofal 04 Jul '18

04 Jul '18

Hello Thanks a lot for your effort please help me to know how can I determine My Model for a certain mutated gene (like smn protein for normal sequences,type I,II,III,and IV Spinal muscular atrophy) How can I know the protein model for different seq is functional or non functional? I made models for different affected cases of SMA with A suitable template for pdb and Recorded The Qmean and GMQE number for each model with but till now I can not be able to determine this sequence produce good functional protein or not especially with gene have Frame shift mutation which produce new protein and also have a lot of stop codon in the sequence I hope you understand the meaning of my Question ? and hope to guide me to suitable tool or method Thanks

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What is exactly matchDist?
by Murpholino Peligro 04 Jul '18

04 Jul '18

Got 8 x-ray structures. Load them into Chimera and did Structure Comparison -> MatchMaker (with multiple sequence alignment). In the alignment I choose Structure-> Asses Match and it creates a residue attribute named matchDist. I guess is the Distance in angstroms for every alpha carbon in my ith structure (where i=1, 2, 3, ...7) to every matching alpha carbon in my reference structure? Thanks

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Horrible FPS Drop after Operation Chimera Update
by Bellamy Baron 04 Jul '18

04 Jul '18

Any of you got this problem? I had a Horrible FPS Drop after Operation Chimera Update. Thanks in advance for your assistance -------------------------------------------------------------------------------------------------------- Bellamy Specialist - iWYZE https://www.iwyze.co.za/products/car-insurance

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Please unbundle libRMF
by Yuri 02 Jul '18

02 Jul '18

Chimera installs lib/libRMF.so, and UCSF IMP also installs lib/libRMF.so, so that they can't be used together, despite the claim that "IMP can also be used from the Chimera <http://www.cgl.ucsf.edu/chimera/> molecular modeling system" (see https://integrativemodeling.org/) Please unbundle libRMF (https://github.com/salilab/rmf) and use an external package for it. Also imagine if some other software used libRMF too, how can they all be installed together? Bundling is a mess. Please never bundle software packages because this only causes problems down the road. I also asked IMP to unbundle libRMF.so: https://github.com/salilab/imp/issues/1005 Thanks, Yuri

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Chimera application questions
by Yanhe Zhao 02 Jul '18

02 Jul '18

To whom may concern, This is Yanhe Zhao from UT Southwestern Medical Center. I have to question when use Chimera as below, hopefully someone could do me a favor to answer it. 1, my crystal structure have four copies in one Asymmetrical structural unit. When I try to combine two of them by selection and combine command, always combine all of them. I pretty sure that I only select two of them; 2, I got one PDB from SASDB, how can I show it as a density map like CryoEM? When I open, it's shown as lines-like map so as to which couldn't be used for docking. I really appreciate it if someone could do me this favor. Thanks a lot. Best, Yanhe

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Chimera Through VirtualGL
by Logan Sweezy 28 Jun '18

28 Jun '18

Hello! I have been trying to get Chimera working through ssh, where the Chimera installation is located on a Red Hat based cluster, but the user is using a MacOS machine to access the cluster. Looking through the archives of the mailing list, I found a suggestion to use VirtualGL to run Chimera through ssh. VirtualGL seems to be running as intended, but isn't working entirely correctly with Chimera (it runs glxgears and other applications fine). It gets farther in start up than without VirtualGL, but crashes on the Initializing OpenGL step around 80% of the time. I have traced the point of failure to reside within a call to the makeGraphicsWindow function within the tkgui.py file. Specifically, it fails at the line within the makeGraphicsWindow function: graphics = Togl.Togl(parent, **kw) which is found somewhere around line 2690 within the try / except portion which is itself nested in the while 1 loop. I can't determine why exactly it is failing here, and trying to trace the problem to a specific line within the instantiation of the Togl object proved fruitless. I was wondering if anyone would be able to shed some light on what could be causing this issue, or know how to fix it? Alternatively, if anyone knows of another good solution for using Chimera through ssh on a Mac machine, that information would be greatly appreciated. Thanks for taking the time to read my inquiry! Best, Logan Sweezy Scientific Systems Admin Rockefeller University

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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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