December 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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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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WebGL viewer
by Thomas Hrabe 05 Jan '15

05 Jan '15

Hi everyone, I am trying to implement a EM density viewer in a HTML page based on the chimera webgl & html export feature. The original page chimera exports when you save a webgl / html scene has been modified to load multiple JSON objects with densities as they come from chimera. The bar at the bottom of the page essentially performs a coarse density sliding similar to chimera. Almost all works great but what I am missing is how to connect the rotation that was applied to one model and to propagate it to all other models. What is happening now is that when one rotates one model and slides the bar, the next model will not be rotated but will be in it’s original position. Here’s my page I am currently working on http://localize.pytom.org/php/displayWebGL.php?jobID=tutorial I tried catching the mouse event with a loop, but it seems it fails to propagate the rotation to the other models. Check the block at line 916 in the code try { var rotMat = vsphere(mouse_position, new_position); var camera = this.camera; var matrix = new Mat4; matrix.$translate(camera.target[0], camera.target[1], camera.target[2]); matrix.$mulMat4(rotMat); matrix.$translate(-camera.target[0], -camera.target[1], -camera.target[2]); for (var i = 0, models = this.scene.models, l = models.length; i < l; ++i) { var elem = models[i]; elem.matrix = matrix.mulMat4(elem.matrix); } } Thank you in advance for your help, Thomas

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mmaker usage with md-movie perframe
by Bala subramanian 02 Jan '15

02 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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Add reasonable bonds from command line
by Enrico Ronca 29 Dec '14

29 Dec '14

Dear Sir. I'm Enrico Ronca a post-doc researcher at the National Research Council of Italy in Perugia. I'm contacting you because I often work with metal atoms and not always chimera show me bonds. I solved the problem removing all bonds and pseudo bonds and adding "reasonable bond between selected atoms" in the adjust bonds menu of chimera. Is there a way to run the same procedure from the command line so that I could automate it by a script? Thank you in advance for your reply. I'm looking forward to hearing from you Enrico

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Re: [Chimera-users] Customizing Chimera
by Eric Pettersen 25 Dec '14

25 Dec '14

On Dec 22, 2014, at 1:08 AM, Michał Kadlof wrote: > Hello, > > I'm currently work on proteins with disulfide bonds. I'm very often do the same sequence of tasks in Chimera: > > 1. open structure > 2. Select -> chemistry -> functional group -> disulfide > 3. extend selection to have selected all atoms of Cys-Cys bridge > 4. Show selected atoms > > Is there any way to wrap it into one-click button on toolbar? Hi Michał, While it is literally possible to put what you want on the toolbar, it's a bit easier to make a menu item instead. To do that, you create a command alias for the actions, and put that in a file that Chimera reads at startup so that it is always available. Details: The alias would be alias ^showbridge sel disulfide; sel up; disp sel This creates an alias named "showbridge" which is only expanded if typed at the beginning of a line -- that's what the ^ indicates. Such beginning-of-line aliases are also placed in an Aliases menu that appears after the Favorites menu (if you have any such aliases). To get the alias read by Chimera at startup you would put it in any of the files listed in the "Files to read at startup" section of the Command Line preferences (Favorites->Preferences). This is also described in more detail here: Command Line. Finally, if you really want it on the toolbar instead, that will involve making your own (simple) plug-in in Python. I can provide more detail about that if you like. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Can't open the CASTp site
by Lei Jinmin 18 Dec '14

18 Dec '14

Hi, I have to use CASTp tool for research sake, but I can't open the site anymore( http://sts-fw.bioengr.uic.edu/castp/index.php ). I remember it worked a couple of weeks ago. Does anyboday know when it begins working again? Thank you in advance! Best, Jinmin Lei Researh assitant Aalto University, Finland

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constrain measurement of rotation to a particular axis?
by Elaine Meng 18 Dec '14

18 Dec '14

Begin forwarded message: > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] constrain measurement of rotation to a particular axis? > Date: December 18, 2014 11:07:57 AM PST > > I think the sensible thing is to report the hinge angles without trying to use a common rotation axis. I can think of different ways to define the common rotation axis (you have to align all the structure in some way, then say how much the observed rotation about the axis for a particular structure translates into a rotation about a slightly different common axis), all of them arbitrary and hard to explain, and even harder to compute, so I wouldn’t go that way. > > Tom > >> From: Oliver Clarke <olibclarke(a)gmail.com> >> Subject: [Chimera-users] constrain measurement of rotation to a particular axis? >> Date: December 17, 2014 2:36:45 PM PST >> To: Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> Hi all, >> >> When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? >> >> I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. >> >> Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... >> >> Best, >> Oliver. >>

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Chimera-users December 2014