- Chimera-users - RBVI Mailing Lists

DockPrep sometimes fails with altPos
by Visvaldas Kairys 24 Jun '17

24 Jun '17

Dear Chimera users and developers, I’d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens via DockPrep. If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused and puts “TER” between the residues, also reporting non-integer charges in the log. I think what is happening, the program picks “A” variant for one residue and “B” for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess). I resolve this by manually editing out one of the AltPos (say, “B”) out of the PDB file for the offending residues, but I guess the program should be able to do it automatically. A PDB example where this happens is 2r3i (or 2r3r). Best regards, Vis

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strand inside and edge color
by Kyle Morris 23 Jun '17

23 Jun '17

Dear Chimera dev, Sorry if I missed this in the documentation and online… Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white. Thanks for your help as always! Best wishes, Kyle

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suggestion: data mode
by Dougherty, Matthew T 23 Jun '17

23 Jun '17

would be helpful to display data mode (byte, float, etc) on the volume viewer panel, approximately in the same location as origin index, voxel size, etc. For mrc files I can dump the header and pick thru it, for other formats the method is not so clear. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Measuring Distances in the Reciprocal Space Transform
by Martin Lawrence 23 Jun '17

23 Jun '17

Dear Chimera Users, I would like to measure the reciprocal space distance between features in the fourier transform of my map. Can anyone give me a hint as to the easiest way to do this? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Please Help Me: Vina Tool Error in Chimera:
by Sarah Qassem Azzam 22 Jun '17

22 Jun '17

Dear Chimera help desk, Hope this email finds you well. I am facing a problem with Vina Tool in Chimera, while running molecular docking. I got the following error message: "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file. ---- Application stdout ----- [no output] I did install Vina, and I am trying to run it in Chimera using 'Local' option for executable location. Can you please advise on how to solve this issue? Your time is highly appreciated. Kind regards, Sarah Azzam

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Selecting only protein surfaces programmatically
by Ashton Omdahl 20 Jun '17

20 Jun '17

Chimera friends- I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line? Thanks! Ashton

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Installing Chimera and ChimeraX on a CentOS box without root
by Healey, Joe 20 Jun '17

20 Jun '17

Hi Chimera team, I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges. After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1" And when I close this dialogue box, I get this: "Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 717 Current serial number in output stream: 718 libxcb: WARNING! Program tries to lock an already locked connection, which indicates a programming error. There will be no further warnings about this issue." ----------- And when running ChimeraX for the first time, I get this: " ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) " Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries? Any advice/documentation you have to get the programs working would be much appreciated. Joe Healey M.Sc. B.Sc. (Hons) MSRB 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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alter to periodic box
by paul buscemi 17 Jun '17

17 Jun '17

I was experimenting with mixed solvents and found that if you create a box around a molecule say 10A on a side, then de-select "remove solvent" and then create a second box, say 2A on a side, that second box forms around the first. You can then constrain the second box which will for the most part retain the first and the parent molecule during a simulation. This allows visualization of the live trajectory as well. I used MON around water and he process is faster to create than selecting the six outside surfaces of a solvent box. Paul

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Question about Chimera
by Shabnam Nadjafi 17 Jun '17

17 Jun '17

Dear Manager I have a question about "Chimera". Is " "Chimera" free ? Can this program be used without license and complete freely? Thanks, Sincerely Yours, Shabnam Nadjafi

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Re: [Chimera-users] Run procedure
by Elaine Meng 16 Jun '17

16 Jun '17

Hi Paul, (1) please send questions to the chimera-users address, CC’d here. Questions sent just to me may fall through the cracks. (2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation. You can see it by clicking the Help button on the dialog or viewing the copy at our website: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html> See the sentence containing “clicking Run” about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run…” I am guessing that you chose the recording option in the MD Movie dialog. If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier. Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I’m no longer sure about whether it overwrites or just gets added to the end. However, you should be able to tell by the number of frames in the output trajectory. 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 16, 2017, at 12:03 PM, pbuscemi <pbuscemi(a)q.com> wrote: > > Elaine, > > In doing a simulation, does it matter which screen is used to select "RUN" ie, minimize, equilibrium,production, or other. > > i.e If I select equlibrium, is production also run ? When a movie is recorded, is it from equilibrium or production portion ? > > thanks > Paul > >

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