December 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

4 6

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

5 7

Identify hinges and rigid groups using Morph Conformations?
by Oliver Clarke 04 Jan '16

04 Jan '16

Hi, I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long) Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes. Cheers, Oliver.

3 3

Include "perframe" command as action in Animation panel?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi, I really like the animation panel of chimera because it makes it incredibly easy to create a nice looking movie, but transitions are still a bit limited compared to what one can do in a script - e.g. smoothly transitioning from one contour level to another, moving along a chain and highlighting specific residues, etc. On the command line, it is easy to do this and a bunch of other iterative processes using the “perframe” command. Perhaps it might be worth considering inclusion (in ChimeraX presumably) of an equivalent of the “perframe" command as an action in the animation GUI (One could call it “Custom” or “Script” to avoid confusion), to enable mixing in code snippets into the animation GUI? It would only need to have a couple of parameters - the frame range, variable range, interval, and command to execute (with a checker to catch invalid syntax prior to execution). Alternatively/additionally, it would be nice to have the option to export the current animation setup as an editable script, to provide a starting point for a more complex movie, although I am not sure whether this is feasible given the way the animation tool incorporates scenes. Cheers, Oliver.

2 1

HLS color adjustments?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi all, Suggestion for ChimeraX: Allow tweaking (not replacing) color of selection, to adjust hue, lightness or saturation of selection (which could contain multiple colors). This would be handy when creating duotone images, where one selection is one color and another selection is a lighter (or darker) version of the same color; Or for creating Goodsell-style images where carbons are one color and heavier elements are a darker version of the same color. In general this would also be useful in cases where you want to edit a color that is close to but not quite the desired one - currently, launching the color editor defaults the selection to black, and it can sometimes be difficult to locate the exact color one had previously, so a way to edit colors in place would be useful for this purpose. Another suggestion to consider - would it be possible to allow exporting to a format (perhaps SVG?) where both vector and bitmap information can be edited separately? Specifically, I’m envisioning a three-layer file, with a bitmap + text and lineart, where lineart would include pseudobonds and potentially silhouettes. This would allow easy adjustment of the thickness, style etc of silhouettes and pseudo bonds post-Chimera, and editing/reformatting of text labels. I am not sure how practical this is, but if it is feasible to implement eventually it would certainly be useful. Cheers, Oliver.

2 2

Can Chimera specifically superimpose renamed atoms of a ligand ?
by Yogendra Ramtirtha 29 Dec '15

29 Dec '15

I have to detect the presence of a ligand in many PDB files. So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand. Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ? In general, can Chimera superimpose ligands in 2 PDB files ? Thank you

2 1

SaveScene Error
by Alvaro Rossan De Brandão Prieto Da Silva 28 Dec '15

28 Dec '15

I can't save UCSF Chimera sessions with saved scenes. What should I do in order to circumscribe this error? My ReplyLog Error in after-models callback: KeyError: (-1, 0) File "C:\Program Files\Chimera 1.10.2\share\Animate\SceneState.py", line 1252, in modelsLookup mList = [ m for m in SimpleSession.modelMap[ref] See reply log for Python traceback. -- Dr. Álvaro Prieto, D.Sci PqC-IV *Biologia Molecular de Toxinas Animais* Laboratório de Genética Tel +55 11 26279721 Mob. +55 11 982227144 email alvaro.prieto(a)butantan.gov.br

2 1

Fwd: Fit to segments
by Elaine Meng 24 Dec '15

24 Dec '15

Begin forwarded message: > From: Greg Pintilie <gregdp(a)gmail.com> > Subject: Re: [Chimera-users] Fit to segments > Date: December 24, 2015 at 9:38:59 AM PST > > […] that’s a good question… some comments below. > >> Begin forwarded message: >> >> From: Luca Pellegrini <lp212(a)cam.ac.uk> >> Subject: [Chimera-users] Fit to segments >> Date: December 18, 2015 at 4:07:08 AM PST >> To: chimera-users(a)cgl.ucsf.edu >> >> Hi, >> I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. >> >> After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. >> > > This can happen quite often especially at lower resolutions, so I’m not too surprised. Try looking at the Z-score as well. For more details see the “Docking Scores” section at http://ncmi.bcm.edu/ncmi/software/segger/docs. It like won’t be too high either in this case though. In such cases it’s often useful to argue that this is the correct fit using other experimental evidence. >> Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. >> > > Yes, it is true the scores are calculated using the whole map. One way to use only the selected segment is to extract the densities for that segment first and then do the fitting procedure using that segment only.

1 0

2dlab problem
by jrb53 24 Dec '15

24 Dec '15

Hello all, I am making a movie in Chimera and labelling the various proteins as they appear. For some reason I am having trouble with 2dlab If I write 2dlab create kvlab4 text “Voltage-gated potassium channel” size 48 style bold color blue xpos .04 ypos .9 I get the error Keyword 'potassium' doesn't match any known keywords Its like it doesn’t get that the quotes are even there and it sees the label as multiple command line arguments. I get the same error with single quotes. If I use one word labels, it works fine. Any idea? Or am I missing something simple? John

2 2

Chimera User's guide for command ine usage
by Yogendra Ramtirtha 22 Dec '15

22 Dec '15

I would be prefer me a PDF version of the user's guide to run commands through the command line Is the Chimera home page down ? Thank you, Yogendra

2 3