January 2015 - Chimera-users - RBVI Mailing Lists

Creating a cubic box for a density map
by Juan Luis Loredo Varela 18 Jan '15

18 Jan '15

Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan -- Juan Luis Loredo Varela PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York

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Scripting image writing in Mac OSX
by Mike Sivley 16 Jan '15

16 Jan '15

I have a Chimera script that takes a set of attribute files and generates a collection of scenes images. This script is usually run on Scientific Linux using the Headless Linux 64-bit distribution of Chimera. I'm now trying to run this script on Mac OSX Mavericks and hitting issues with the GUI. If I pass the --nogui flag to Chimera, then the script fails, stating that the GUI is necessary to save images. If I remove the flag, the GUI starts up correctly, but scripted control stops once the new attributes are defined. The user is prompted by the Render by Attribute window, and the script will not progress until the user confirms the changes and closes the GUI. How can I get the script to run start-to-finish without stalling for user-interaction, the way it does in linux? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

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Re: [Chimera-users] dotted lines
by Elaine Meng 16 Jan '15

16 Jan '15

On Jan 16, 2015, at 8:46 AM, Thomas Evangelidis <tevang3(a)gmail.com> wrote: > Hi Elaine, > I don't know why, but none of the 3 approached works, even with the latest Chimera version. > […] Hi Thomas, Your pseudobonds are in stick style. You would have to change the stick to wire before doing those other things; in Chimera there are no “dotted or dashed” sticks, only wires (lines). E.g. in Selection Inspector, inspect: Pseudobond, change bond style to wire. That only changes the specific pseudobond(s) you have selected; if you first select one distance pseudobond, you can press keyboard up arrow to expand the selection to all the distance pseudobonds. Can also be done with setattr command, e.g.: setattr p drawMode 0 Hard to see on white background. Can change color with setattr too: setattr p color black When you first create distances they are normally already in wire style, which is why I didn’t mention the stick/wire issue before. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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vop add
by Fco Javier Chichón 16 Jan '15

16 Jan '15

Dear all I would like to merge several volumes. Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. Anyone know how to do that? Thanks -- ======================================================= Francisco Javier Chichón García Centro.: Centro Nacional de Biotecnología Dept.: Macromolecular Structure Lab.: S1-S0.1 Tel.: (+34) 91585-5497:4690 =======================================================

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dotted lines
by Thomas Evangelidis 15 Jan '15

15 Jan '15

Greetings, I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed? thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ =============================================================== *Physics is the only real science. The rest are just stamp collecting.* *- Ernest Rutherford*

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Distance measurement in density map
by Maarten Schledorn 14 Jan '15

14 Jan '15

Dear reader, I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at? With my sincere thanks in advance, Maarten

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shown/hidden state of axes/planes not saved with scene
by Oliver Clarke 14 Jan '15

14 Jan '15

Hi all, Planes seem to be shown by default when I load a scene, regardless of whether they were displayed when I saved the scene. This is not normally an issue, but it is a little problematic when preparing animations using many different scenes - I will often have a plane defined at the start so I can use it to align the x/y/z axes to the normal of that plane (e.g. aligning the fourfold axis of an ion channel), but I do not want the plane displayed during the animation, and I don’t want to have to delete it from each scene and re-arrange the animation timeline if I can avoid doing so. Would it be possible to alter this behavior such that chimera knows the displayed/undisplayed states of axes/planes/centroids when saving a scene or session? Best, Oliver Clarke.

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New to Chimera
by Mike 12 Jan '15

12 Jan '15

This is my first day with Chimera. I'm trying to find how to draw a small molecule, minimize the structure of the small molecule and then have it interact with my protein of interest. However, I don't see any way for me to draw a small molecule (potential drug). Can you provide any direction ? Thanks, Mike

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need guidence
by Maria Saqib 08 Jan '15

08 Jan '15

Dear user i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? Waiting for your reply Maria

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VR in Chimera?
by Andrey Malyutin 07 Jan '15

07 Jan '15

Good morning, With recent resurgence in virtual reality technology, such as Oculus Rift and Samsung Gear VR, is it possible that we'll see support for VR headsets in future releases of Chimera? Thank you, Andrey

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Chimera-users January 2015