July 2015 - Chimera-users - RBVI Mailing Lists

Volume level rms option
by Oliver Clarke 31 Jul '15

31 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.

3 6

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.

1 0

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

2 8

"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.

2 1

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

1 0

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

2 1

DNA ladder different color than backbone
by Belle Lin 26 Jul '15

26 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]

3 3

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

1 0

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.

2 1

PB lines visualization
by Sana Saeed 22 Jul '15

22 Jul '15

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

2 1