April 2015 - Chimera-users - RBVI Mailing Lists

Autodock vine problem
by Tunc Morova 04 Apr '15

04 Apr '15

Hello, I was trying to use built-in auto dock vina tool of chimera. I came a cross with an error saying service local`c:\”program filex(x86)”\”the scripps research Institute\Vina\Vina.exe` is unavailable. I have been checking forums for a longtime. Unfortunately, i couldn’t run the docking. couple days ago, I think i accidentally ran the docking locally but i am not sure. Is my pathing correct? how can my local auto dock vina be unavaible ? Please help me for finishing my thesis :D Thank you for your support -Tunc

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Opening Gromacs .trr: error with "bham_lr"
by Alan Manning 03 Apr '15

03 Apr '15

Hi I want to import a Gromacs trajectory (a .trr file) in order to create an animation. I'm using the "MD Movie" tool, and I specify the input .tpr and .trr files. However, I get the following error when I try and make the movie: Don't know correct parameters for 'bham_lr' function Does anyone know what this is from? I'm using Gromacs 5.0.4. The complete Reply Log is as follows: using memory mapping VERSION 5.0.4 using floats version 100, generation 26 2613 atoms box o water Don't know correct parameters for 'bham_lr' function Thanks! Regards, Alan Manning

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drawing ribbon
by Hartzell Jr., Criss 03 Apr '15

03 Apr '15

I have a protein with 10 transmembrane domains and would like to make a movie in which the ribbon is drawn in time from the N- to the C- terminus. I wrote a script that does that. But, the 10 transmembrane domains become hard see because they overlap one another. To solve this problem, I wanted to make the first 600 amino acids become 70% transparent after they had been drawn. Then the drawing would continue with the second half of the protein with no transparency. The problem is that the script that I have written to do this draws the first 600 amino acids 70% transparent immediately as they are drawn. Then the second half of the protein is drawn with 0 transparency. I set the wait time to 600 because I want to execute the transparecny command after the first 600 amino acids were drawn. But, instead, the drawing of the first 600 amino acids is tremendously slowed down by this command as if a wait of some duration occurs after each amino acid rather than after all 600 amino acids. I would appreciate your help. Thanks. movie record supersample 4; perframe "ribbon #2:$1" range 1,600; wait 600; transparency 70,r #2:1-600; perframe "ribbon #2:$1" range 601,959; movie stop; movie encode “d:\Dropbox\Chimera_files\movie1.mp4”; Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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New molecule from selection?
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, This may already be implemented, but I couldn’t find it - the nearest equivalent feature I know of is copy/combine, but that only works on whole models, not taking into account selections. I was wondering if it would be possible to implement a feature creating a new model comprised of all atoms in the current selection? This would be particularly helpful when combining many parts of multiple models, or when creating a separate model consisting of a subselection of the current model. This can be done at present using a combination of copy/combine and selecting and deleting those parts of the copied molecules that are not in the selection, but this gets messy for complicated selections. Best, Oliver.

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select by color (or other display attributes)
by Oliver Clarke 02 Apr '15

02 Apr '15

Hi, one feature I would love to see in a future version of chimera is the capacity to select residues/atoms by color - this would be magic for modifying figures. Example use case: I’ve made a figure in which some complicated selection or set of selections is colored medium blue, and another selection is colored red. I’ve saved the session for the figure, but I (stupidly)didn’t save the corresponding selections, and now I have to remember exactly what selections I used. If there was a “select by color” function, I could simply select all the atoms that are colored medium blue (or some other color ID), and change them to another color, without having to know which residues were in the original selection. Analagously, it would also be handy, although less frequently useful, to be able to select on the basis of whether a residue is displayed, or represented in a particular manner - in particular, being able to restrict selection to displayed atoms/residues would be useful to avoid inadvertent modification of undisplayed models or parts thereof. Cheers, Oliver.

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Smoothly change level of density map in animation?
by Oliver Clarke 02 Apr '15

02 Apr '15

Is there any way to alter the density level in a gradual fashion during an animation? I would like to first show the overall envelope of a cryoEM map, and then smoothly change to a higher contour level where I can see helices etc. Many other parameters, such as the presence of a MSMS surface or the position of a clipping plane, seem to automatically gradually transition between two key frames of an animation, but density level doesn’t seem to do so. Oliver.

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mclip suggestion - match to arbitrary plane
by Oliver Clarke 01 Apr '15

01 Apr '15

Hi, Currently the mclip command can be used to match a model specific clipping plane to the global near/far clipping planes, or the per model clipping plane of another model. I think it would be a handy addition to a future chimera version to be able to match the per model clipping plane to an arbitrary plane, pre-defined in axes/planes/centroids - e.g. “mclip #1 match p2” would match the per model clipping plane of model #1 to the plane named “p2”. This would be useful because it allows one to easily generate a per-model clipping plane that intersects a certain set of atoms, which also facilitates precise description of a figure. Cheers, Oliver.

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