June 2018 - Chimera-users - RBVI Mailing Lists

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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Chimera-users June 2018