- Chimera-users - RBVI Mailing Lists

Select residue by array index, not residue id
by Thomas Hrabe 03 Mar '15

03 Mar '15

Hi everyone, is there a way to select a residue by it’s array index, starting at 0 -> sequence length rather than using the residue id? Thank you in advance for your help, Thomas

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Re: [Chimera-users] rmsd calculation for pre aligned structures
by Elaine Meng 02 Mar '15

02 Mar '15

Hi Oliver, In that case, you can just show the sequence of one protein, then use the sequence window menu: Structure… Associations to associate both structures with that one sequence, then sequence window Headers menu to show the RMSD of interest, etc. This would work even if the sequences of the structures were slightly different, as long as they were both similar enough to the sequence in Multalign Viewer that Chimera could figure out the association accurately. Elaine On Mar 2, 2015, at 3:12 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Elaine, thanks for the reply! This sounds like exactly the right solution. However, when I try to add a sequence in the sequence dialog, Chimera hangs on “running Needleman-Wunsch”. > > I suspect this is because my sequences are so long (~5000 residues). > > But I don’t actually need to align them - they are already aligned as they are actually the same sequence, because I am looking at different conformations of the same protein. > > I guess I can create a dummy sequence alignment, with two identical sequences, but it would be nice to have some way of telling chimera not to align the sequences, or to allow for manual alignment in cases such as these - perhaps a “Do not align” or “align manually” checkbox in the add sequence dialog would do the trick. > > Thanks again, > Oliver.

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rmsd calculation for pre aligned structures
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi, I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. Is there any way to do this at present? The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular “rmsd” command. Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed? Best, Oliver.

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explicit parentheses in atom selections
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi all, Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent” could be “ligand z<5 &~(ligand | solvent)”). Is there a reason why this kind of syntax is not used at the moment? Also, just a random thought for a future version - it would be really handy to have something like the “Macro recorder” function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner. Cheers, Oliver.

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Embed chimera into my gui code
by hy liao 26 Feb '15

26 Feb '15

Hi, I am creating a GUI using tkinter, and I would like to embed chimera into it. Specifically, I would like to display a 3D molecule density map using chimera and inside my GUI. Chimera would be activated while the GUI is on. Is there documentation to accomplish this? Thanks! Stu

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Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Dear Chimera users, Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if I want to keep the density within the eraser while getting rid of other parts? Many thanks Kai

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Re: [Chimera-users] Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Thanks! This is a good solution. But I wonder if there's an interactive way just like the eraser, but doing the opposite thing. It might help on difficult cases when you want a real time feedback what you are erasing and keeping just in Chimera without external command. Kai > difference ma p > <kzhang(a)mrc-lmb.cam.ac.uk>于2015年2月25日星期三写道： >> Dear Chimera users, >> Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if >> I want to keep the density within the eraser while getting rid of other parts? >> Many thanks >> Kai >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <javascript:;> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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about model coordinates
by Tat Cheung Cheng 20 Feb '15

20 Feb '15

Hi, I recently got a ~4.4A EM map and built a improved model using MDFF. The map and model is well aligned when loaded in Chimera. But it is off when I hit "center" in the volume viewer, as the origin is shifted. As I try to improve the model in Coot, the map and model isn't aligned at all in Coot, seemingly by the same offset when "center" button was hit. And also the values in the original index in the volume viewer is different from the values in the header in the density map. So I wonder what determines the origin index? and is it possible to find the shift and transform the coordinates in the model so as to align the model with the map in coot? Thanks a lot. Tc

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problem installation on linux 64 bit
by Chiara Parravicini 20 Feb '15

20 Feb '15

<chimera-users(a)cgl.ucsf.edu>Dear Chimera Users, After installing Chimera from the precompiled version chimera-1.10.1-linux_x86_64.bin (the installation completed without any error), I get the following error when I run the binary: libGL error: unable to load driver: nouveau_dri.so libGL error: driver pointer missing libGL error: failed to load driver: nouveau libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 156 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1455 Current serial number in output stream: 1455 I would appreciate any help or suggestion! Many Thanks in advance Chiara

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Restricting "select by conservation" to a subset of sequences in a multiple alignment
by Oliver Clarke 18 Feb '15

18 Feb '15

Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don’t know about them!): 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. Cheers, Oliver Clarke.

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