- Chimera-users - RBVI Mailing Lists

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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RMSD
by Valerio Chiarini 17 Jul '15

17 Jul '15

Hi everyone, I am dealing with an NMR structure and I noticed in literature that among the parameters required for presentation is included "RMSD from the ideal geometry". Does anyone know if is possible to calculate such value from chimera and how? Currently I just know how to calculate RMSD to the mean coordinate... thank you all in advance Val

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question
by leila karami 16 Jul '15

16 Jul '15

Dear chimera users, 1) I want to have electrostatic surface of my protein in chimera. To this, I used *Tools... Surface/Binding Analysis... Coulombic surface coloring* A new window is opened, but apply bottom is inactive. 2) There are ray command in pymol to obtain better image of molecular structures. Is there a similar command or utility in chimera? Any help will highly appreciated. Best wishes, Leila

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adjusting threshold values on volume rendering
by Dougherty, Matthew T 15 Jul '15

15 Jul '15

Hi, I can access threshold values from solid/volume rendering. eg: from VolumeViewer import active_volume v = active_volume() if v==None: return levels = getattr(v, "solid_levels") t,a=levels[0] How can I change a threshold value? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Error opening file
by Sneha Poondru 10 Jul '15

10 Jul '15

Hello! I’m trying to prepare a receptor for dock6, so I downloaded a file (1tvb_.all.sph) from our cluster onto my desktop. However, when I click to open it, I keep getting this error message from Chimera: non-standard sph header Error while processing /Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph: cannot open file "/Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph": syntax error, line 1832 Any help is appreciated! Thanks! ~Sneha

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Structureviz Cytoscope plugin problem
by Ahmed Ezat 10 Jul '15

10 Jul '15

Dear Sir, I am trying to use structureviz Cytoscope plugin to launch Chimera, but it does not work. I installed Chimera and Cytoscope properly and set the path to Chimera in structureviz settings but it is not working. What can I do? I am using windows 7. I have also a problem to install chimera on Linux. if possible,c Can you send me detailed procedure for the installation process. Best Ahmed A Ezat

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swapaa: choosing rotamers
by roz orchidea 09 Jul '15

09 Jul '15

Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex

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How to display two EM map and a PBD simultaneously
by 师扬 08 Jul '15

08 Jul '15

Dear all, Recently, I have a task to display two EM density map ('A' and 'B') and one PDB ('C') at the same time. B and C fit in map to A. So, I need to make A and B transparent to observe them simultaneously. However, one strange thing happened when I made A and B transparent. I can only see the density which A is lager than B or B is larger than A, and I could not see the buried density. In another words, when I make both A and B transparent, the map can be changed in to the 'A+B' map, and I could not see any 'A-B' or 'B-A' information. Have anyone met this problem? Do change something in setting can solve this problem? Best regards Yang

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on the movie command “turn y 3 120”
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, For movie command "turn y 3 120", the molecule will turn counter-clockwise. Will you lease tell me the movie command which makes the molecule turn clockwise？ Best regards. Smith

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Measure translation of two domains?
by Oliver Clarke 07 Jul '15

07 Jul '15

Hi all, I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation. I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output? Cheers, Oliver.

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question
by A G Szabo 07 Jul '15

07 Jul '15

I am pleased to inform you that I have been using aspects of Chimera that permit me to prepare images of proteins deposited in the pdb. It was a pleasant surprise to find that the learning curve was not as steep as I thought it might be. Mind you, there are many aspects of Chimera that I have not yet attempted to use. Now I wish to do something that may not be possible to do with Chimera. And I am not sure where to look in the tutorials. I have a ribbon diagram of a protein-RNA complex, PDB 4p3e, two proteins, SRP 19 and SRP68, bound to a segment of 7SL RNA. I can also obtain the structure of another protein SRP54 which also bind to this complex. However, the structure of pdb 4p3e with SRP54 is not available. I know where SRP54 should bind to the RNA, and I know which domain of SRP54 binds to the RNA. How can I somehow combine the two files, one for SRP54 and the other 4p3e and locate SRP54 onto the 4p3e structure? (not sure it is possible) Of course crystallographers know how to achieve this structural combination. I don't have a clue. I checked the tutorial list and the closest I seemed to come was the Merge command. However, the tutorial did not seem to deal with what I wanted to do. Thank you in advance for your assistance. Arthur G. Szabo Ph.D. Professor Emeritus, Chemistry Wilfrid Laurier University Waterloo, Canada.

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Question
by Damjanovic Marko 07 Jul '15

07 Jul '15

To whom it may concern, I am trying to solve a problem that is more of mathematical nature, and I would be very grateful if I could get any advice or pointers on how it may be possible to do this (in Chimera or some other program I am not aware of). I have a molecule that is more or less of cylindrical shape (quite simple shape). I would need a way to surround this molecule with a certain number of layers of solvent molecules that fit around the surface of a cylinder (preferably 1 layer and then going up gradually). The solvent molecules should be packed around the central molecule efficiently (closest packing). An alternative way to approach this would be to take a sphere made out of solvent molecules, put in the centre of the sphere the one cylindrical molecule what is of interest, and let the big sphere accommodate the new molecule. Also, for the sake of simplicity, the solvent molecules can be approximated as small spheres as well (their exact shape is not that relevant). When this is done, all I would need is to get this file in a format like cif, mol or gjf. I underline here that I am looking for a relatively crude model. Could anyone please advise me on how to do something like this? Thanks in advance and best wishes, Damjanovic Marko

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chimera extensions & dialog location
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

1) How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? 2) How can I position the location of IDLE using python? I have IDLE on autostart. In a user extension I have a button, when pressed it organizes the various dialogs, placing them in specific locations. When I try to do something with IDLE, running dialogs.activeDialogs() does not show IDLE in the list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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change B factor
by McCafferty, Caitlyn (NIH/NEI) [F] 06 Jul '15

06 Jul '15

Hi, Is there a feature in Chimera that allows you to change the B-factor of the Amino Acids. I have a txt file with the values that I would like to replace the current B-factors with. Thank you, Caitie

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Undisplay pseudo bonds (missing segments) in pipes-and-planks representation?
by Oliver Clarke 03 Jul '15

03 Jul '15

Hi all, just wondering if there is an option I am missing to undisplay pseudobonds when using pipes-and-planks? At present chimera seems to represent missing segments in pipes-and-planks as a continuation of the chain rather than a break, which is a little confusing, e.g. check the following pair of snapshots (chain break in green section corresponds to missing 10aa loop): https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5… <https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5…> https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0… <https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0…> Also in general it would be nice if cylindrical representations of helices were more integrated into chimera, perhaps with their own style adjustments (e.g. allowing for curved cylinders), as for large structures they provide much less visual clutter, but I guess that is probably something for Chimera 2. Cheers, Oliver.

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