December 2021 - Chimera-users - RBVI Mailing Lists

calculating radius of gyration
by Elaine Meng 14 Dec '21

14 Dec '21

> On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman(a)open.ac.uk> wrote: > > Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students. > > But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that? > > Best wishes Hi Simon, Thanks for introducing others to Chimera! I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does. RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates. There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Translate onto the X-axis
by Yasser Almeida 14 Dec '21

14 Dec '21

Hello, I have a complex of two proteins that I want to align to the X-axis. Specifically, I want to define a vector between the COMs of each protein, and then translate the whole system so that the vector is on the X-axis, where the COM of one protein is on the cartesian origin [0, 0, 0] and the other COM is in [+X, 0, 0]. How can I achieve this with Chimera? Thanks in advance, Yasser

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Save multiple fitted maps in Chimera
by Huabin Zhou 13 Dec '21

13 Dec '21

Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Help please: extracting distances from each frame of a short MD
by Anne-Frances Miller 11 Dec '21

11 Dec '21

Dear Chimera support, I want to extract a set of distances and one angle from each snapshot of an MD trajectory (there are 11 of them). My plan was to have all my distances appear in one of the MD-movie analysis>plot distances windows and use ‘Dump Values’ to get my numbers out in a way I could use for other plots. I realize angles cannot appear in the same plot, but hope I can measure an angle in the same script. I have a ‘per-frame’ script that runs fine on the first frame, however it returns ‘Problem in per-frame script: Distance monitor already exists’ when I step forward to a second frame. Nothing appears in a 'MD plots' window (such a window does not open on its own either). Reply Log shows the correct distances for the first frame but then only repeats the error after that. Problem in per-frame script: Distance monitor already exists My work-flow: Open MD/movie, load my trajectory open analysis, Per-Frame copy my script into the window (chimera commands) click ‘apply' in the script window, click ‘play’ or step forward one frame in the MD GUI (looping disabled) My script: ~disp ~ribbon disp :718,720,721,722,730,740,741,1058 distance :1058@O2 :741@ND1 distance :730@OH :741@NE2 distance :721@OG1 :1058@N5 distance :718@O :1058@N3 distance :721@N :1058@O4 distance :722@N :1058@O4 distance :720@N :1058@O4 distance :740@O :720@N angle :1058@C2 :1058@O2 :741@HD1 :741@ND1 Reply Log output: Distance between FDM 1058 O2 and HID 741 ND1: 2.8 Distance between TYR 730 OH and HID 741 NE2: 2.8 Distance between THR 721 OG1 and FDM 1058 N5: 3.4 Distance between ILE 718 O and FDM 1058 N3: 3.2 Distance between THR 721 N and FDM 1058 O4: 2.9 Distance between GLY 722 N and FDM 1058 O4: 3.2 Distance between GLN 720 N and FDM 1058 O4: 3.2 Distance between GLN 740 O and GLN 720 N: 3.0 Dihedral #0:1058@C2 #0:1058@O2 #0:741@HD1 #0:741@ND1: -51.0515 Problem in per-frame script: Distance monitor already exists Thank you for any assistance, Anne-Frances - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Questions about Matchmaker and GDT
by Ralph Loring 10 Dec '21

10 Dec '21

Hi, I don't know if there's a special user group for Matchmaker but this also involves other aspects of Chimera. 1) I'm looking at AlphaFold structures of RIC-3, a chaperone for nicotinic receptors that is also an intrinsically disordered protein. There are pdbs for six species in the AlphaFold database: Human, mouse rat, fish, fly and worm. These differ tremendously in terms of sequence, size and predicted secondary structures but they all have a putative signal sequence and a transmembrane domain. I used Matchmaker to align the human pdb to each of the others. The results of combining all 6 looks like a bowl of spaghetti until the parts before the putative signal sequence and the C-terminal tails are deleted. Then I can see that the putative signal sequences and the transmembrane domains are in the same plane as if they are in a membrane. I just want to confirm that this is merely a lucky coincidence and that Matchmaker has no preference for aligning hydrophobic alpha helices into a planar space corresponding to a membrane. The coincidence, if it is one, is striking and I just want to make sure. Note that I have a similar question for AlphaFold, the source of the pdbs. 2) Does Chimera do Global Distance Testing (GDT)? For that matter, does ChimeraX (I've been thinking about switching and if it does, this may be what it takes to get over the activation energy barrier)? I can't find GDT in any of the directions. When Matchmaker runs, for instance comparing human and fly RIC-3, the sequence alignment score is only 270 but the RMSD is 1.6 angstroms (but only for 7 pruned atom pairs and when all 233 atom pairs are considered, the RMSD is 55 angstroms, so clearly not much overlap). I've heard that GDT corrects somewhat better than RMSD for not having precise superimposition. However, I don't know that it would make a lot of difference in this case but I'd like to find out. The mystery is that drosophila RIC-3 works almost as well as human RIC-3 in helping assemble human pentameric nicotinic receptors even though the structures are so different. Thanks for your help, Ralph Loring

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re-sampled map (volume resample #X onGrid #Y) difference with general mrc map
by Dmitry Semchonok 10 Dec '21

10 Dec '21

Dear colleagues, I have an issue with the output map re-sampled from the resampling step protocol. Could you please explain how different the re-sampled map is compared to the general mrc map (without rotation manipulations)? Because it seems that some important information is missing or/changed in the re-sampled.mrc Kind regards, Dmitry

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Questions about IMOD files in Chimera software.
by 박시훈 09 Dec '21

09 Dec '21

Dear chimera-users community, I have questions about opening IMOD files in Chimera software. Can I open the IMOD files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover, the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera? Best regards Si Hoon Park

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Selecting residues from one chain
by Joao M.C. Teixeira 09 Dec '21

09 Dec '21

Hi, I am a bit confused on how to select residues from a chain. This is the command I am trying:

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Chimera error at start-up
by Hernando J Sosa 09 Dec '21

09 Dec '21

Dear Chimera, I cannot open Chimer anymore in a computer (Windos10 64) where it was running until yesterday. I tried with no success reinstalling the program and installing the latestChimera daily release. The error that I get at startup says: [cid:cfb0a3aa-9306-42f0-bfd0-328d433ceb1e] If I start in debug mode I get the following error in a command window: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 How can I resolve this issue? Thanks Hernando ___________________________________

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Mismatch between display and saved image
by Visvaldas K. 09 Dec '21

09 Dec '21

Dear all, I get a very odd mismatch between what is displayed and what is saved as a png image. I am attaching two figures, and you can probably guess what I want. Of course I will try this in ChimeraX if I am not able to fix the figure, but the image took quite some work, so I'd hate redoing it... Or I could use screenshot I guess... But certainly this is some sort of bug. I'm using Chimera 1.15 on MacOS 12.0.1. Thank you, Vis

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Chimera-users December 2021