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Average structure
by George Tzotzos 03 Aug '15

03 Aug '15

Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC. Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 6
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 5
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Morphing a residue through MD trajectories
by George Tzotzos 02 Aug '15

02 Aug '15

Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 4
by feisun＠ibp.ac.cn 02 Aug '15

02 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 3
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 2
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 1
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Open model from pdb with designated model id?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.

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Option to not record duplicates in the command history?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I like the command history in chimera a lot - it makes it very quick to repeat previous commands. One minor alteration that might make it a little bit better would be to have an option (maybe in the Command Line section of the preferences?) to not record sequential duplicate commands in the history (like the “ignoredups” option for the bash history). I will often repeat the same command a bunch of times (for example “turn x 5” or one of the various aliases I use for navigation and recentering), and so not having all these duplicates recorded in the history would make it a lot faster to find recently used commands. Cheers, Oliver.

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Addh function and fake N, C-terminii
by gaelle garet 31 Jul '15

31 Jul '15

Hi, I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not. For example, for the structure 3L4F, I obtain the following log : Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C Chain-initial residues that are not actual N terminii: GLY 652.D Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii, can you explain me why and how the algorithm detect that ? Thank you in advance for your answer. -- Gaëlle

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How to explore two protein structures on the same screen?
by Jing Tang 31 Jul '15

31 Jul '15

Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing

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Recent problems with linux x64 version
by Peter L. 30 Jul '15

30 Jul '15

Hello, Recently I used Chimera for a internship/volunteer work with my older brother, and it did not start up due to some seemingly graphics drivers problems. I'm running Ubuntu 15.04 on a AMD radion 5450M on this machine and NVidea gtx 760 on another. Both would not start up due to having libGL error: unable to load driver: nouveau_dri.so etc etc, as so documented here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015February/010734.html (Error from the NvIdia machine) and would not load r600. However both had the same fix, that seemigly works by removing the file /Chimera64-1.10.2/lib/libstdc++.so.6, I renamed it to libstdc++.so.6.bak in case I might need it, but it works on both machines now. It seems as some older libs are colliding with mesa drivers, and casung them to break, and removing this fixes the problem. Its been documented before with other programs here, where the fix is simular. http://askubuntu.com/questions/614422/problem-with-installing-steam-on-ubun… I also found that in the chimera mail I found, it was recommend to update some drivers, or Nvidia drivers, however, nvidia drivers for linux tend to break the system a lot or cause other problems. Hope this helps!, Peter

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Volume level rms option
by Oliver Clarke 30 Jul '15

30 Jul '15

Hi all, Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD? E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to. Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function. Cheers, Oliver.

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Useful aliases
by Oliver Clarke 30 Jul '15

30 Jul '15

Attached are a bunch of aliases that I find very useful in Chimera. Usage and intended purpose of the alias is described in the #comments immediately preceding the alias. Some of these will only work in the latest nightly build because they take advantage of command options that were only added recently. Hopefully someone else finds these useful too! If any other chimera users have aliases or shortcuts they find particularly handy maybe we could exchange ideas/code snippets in this thread? Oliver.

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Center of rotation cross-hair
by Tom Goddard 28 Jul '15

28 Jul '15

Hi Oliver, I added display of a cross hair (plus sign) at the center of rotation in the graphics window. You turn it on with command set showCofR and turn it off with ~set showCofR The crosshair is white on black (and dark) backgrounds and black on white (or light) backgrounds. This will be in tonight’s daily build. Tom

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"newmap" command? (Or other way to resample on arbitrary grid?)
by Oliver Clarke 28 Jul '15

28 Jul '15

Hi all, Is there any way to use vop to resample on an arbitrary grid, that is, not the grid of an existing map? This would be useful, for example, when one wants to interpolate to finer grid spacing than is present in the input map (but otherwise keeping the original dimensions and origin). I note in the old chimera documentation that there used to be a command called “newmap” (http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html) which allowed for the generation of an arbitrary map which one could use for exactly this purpose, but this command does not seem to be recognized by modern Chimera builds. Does this command still exist somewhere under a different name? Or is there another way to accomplish this? Cheers, Oliver.

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Hydrogen Bond Criteria
by jjeon＠caltech.edu 28 Jul '15

28 Jul '15

Hello, I would like to learn more about the distance/angle settings that Chimera uses for hydrogen bonds. I have read that the criteria are outlined in the paper Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. I have been waiting to be granted access to the full version since I can only seem to find the abstract on other sites. Is there a website that offers access to the full paper for free? Thank you, Janice

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hbonds
by leila karami 27 Jul '15

27 Jul '15

Dear chimera users I have 2 models in my system (#0 for protein and #1 for ligand). I want to use hbonds command for showing the hydrogen bonds between #0 and #1 models? (I know how to do this using FindHBond, but I want to know related command). What is the best options for hbonds command to get above state? Best, Leila

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DNA ladder different color than backbone
by Belle Lin 25 Jul '15

25 Jul '15

Dear Chimera users/developers, Is there a way to make the DNA ladders a different color than the backbone? I am able to do so when the side (sugar/base) is shown in the "tube/slab" mode, but when I change it to the "ladder" mode I am unable to change the color of the rungs. I have included photos below which hopefully make my question more clear. Thank you in advance for your help!! Thanks, Belle Lin _____________________________________________________________ Able to create: [image: Inline image 3] [image: Inline image 2] Trying to create: [image: Inline image 1]

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Announcing the 2015 EMDataBank Map Challenge
by Cathy Lawson 23 Jul '15

23 Jul '15

Dear Chimera User List Members, EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single 3D electron microscopy single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. Challengers are sought to create single particle reconstructions from the targets, and then to upload their results with associated details. Assessors are sought to participate in evaluating submitted reconstructions. Registration is now open for all interested participants. Challengers may submit maps between August and December. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in early 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MAP CHALLENGE" in the menu bar. The map challenge is the first of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The second challenge, focused on creating coordinate models from 3DEM maps, will be announced later this year. Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Map Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Mac-Book Pro
by Bobby Barnett 22 Jul '15

22 Jul '15

I have some students who have mac's, so I tried to download and install chimera on my Mac-Book Pro 17" . I get the following message. I downloaded chimera-1.10.1-mac64.dmg from your site. I am the only user on my computer. Any suggestions? Should I try and downloading it again? Bobby Barnett “Chimera” can’t be opened because the identity of the developer cannot be confirmed.

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PB lines visualization
by Sana Saeed 22 Jul '15

22 Jul '15

is it possible to visualize periodic boundary lines (solvated box) in chimera.

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On the fly map sharpening?
by Oliver Clarke 21 Jul '15

21 Jul '15

Hi, just a request for a future chimera version (probably Chimera 2 I guess) - would it be possible to integrate on the fly map sharpening into chimera, perhaps as an option for vop? It would be great to be able to play with different negative B-factors within chimera and thereby get instant feedback on map contrast and detail in different regions. Alternatively, would it be possible to call an external program that does the same thing from within chimera, perhaps bfactor from the Grigorieff lab or similar? Cheers, Oliver,

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Electrostatic Potential based on Poisson-Boltzmann using APBS
by leila karami 18 Jul '15

18 Jul '15

Dear chimera users, I am using chimera 1.10.1. I did following steps to obtain Electrostatic Potential based on Poisson-Boltzmann using APBS: open... pr.pdb action... surface... show to obtain *.dx file, I typed APBS in command line, after minutes, *.dx file was created and surface color window was opened, I pressed color tab. Please see the figure in following link: https://www.dropbox.com/s/99gjecypqu910hu/apbs.png?dl=0 Why are the colors black and white in the surface, instead of blue and red? Any help will highly appreciated.

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