April 2013 - Chimera-users - RBVI Mailing Lists

Radial density plots
by Pranav Shah 15 Apr '13

15 Apr '13

Hi Tom, I am trying to plot a graph of average density as a function of radius in Chimera v1.7. I tried the code that you wrote for Padma in an earlier post. However, Chimera spits up this error "Accelerators file C:\Program Files\Chimera 1.7\share\Accelerators\radial_density.py has no register_accelerators() function." when I try to load the radial_density.py in the keyboard shortcuts menu. Could you tell me how this bug can be fixed? Awaiting your assistance, Warm regards, Pranav Shah Postgraduate student (Infection and Immunobiology), College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK.

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IDLE : code completion under MAC OS X
by Benjamin SCHWARZ 12 Apr '13

12 Apr '13

Hello, I started to develop simple python/chimera scripts. The manual is rather poor on these aspects (btw, is there a doxygen somewhere ?), and therefore the code completion in the chimera IDLE shell is particularly useful… Unfortunately, on my MAC (OS X), it appears to be messy : the TAB key triggers the usual "completion scrollable list window" on both my windows and linux (debian) machines, but not on my MAC. Note that I am still able to scroll through the "invisible" choices by pressing TAB and then using the up and down arrows, it is just that I cannot see the list, which is a bit annoying to have a clear view at once. I guess this has more something to do with the IDLE configuration than with chimera itself, but I don't know how to dig that up, so if you have any idea how to solve this I'd be pleased to read from it. --Ben

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Very similar structures
by Rebecca Swett 11 Apr '13

11 Apr '13

Hi guys, I have a question, I have two structures that are different by just a few atoms. Is there any way I could use the selection tools in chimera to find them and display them? -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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Re: [Chimera-users] Three suggestions
by Antoine Maillard 10 Apr '13

10 Apr '13

Dear Eric, Thank you for your replies and your quick implementation of an automated refresh for named selections! Concerning suggestion #1: changing Chain ID of a portion of a chain was meant to assist matchmaker in targeting the right domain and not let it take adventice (meaningless) pieces into account. I realize now that this could be quiet a challenge for Chimera to interpret in all the procedures already available... and will stick to the cut-into-domains-of-interest approach. About suggestion #2: the ~namesel command that you proposed would allow to edit the listing, which is sometimes useful, i.e. when you happen to get more and more named selections, sometimes similar in different models, and realize the names given were not specific enough. That would be nice! Suggestion #3: if this is a problem then leave it where it stands! (In case it is not: would it sound more reasonable to offer the window-size memorization as a tickable option? Could the window-location memorization and the tiling be combined when the "same" window is to be opened more than once?) All in all, suggestion #2 might make it: that's a big thank you already! Cheers, Antoine Antoine Maillard wrote: >> Dear Chimera developpers, >> >> Thank you so much for your work and your dedication! >> Having used Chimera quiet intensively recently, I have listed a few suggestions for your consideration. >> >> Suggestion #1: >> Tools > Structure Editing > Change Chain IDs: lacks a "restrict to current selection" button (would allow to name various domains of a single protein) > Are these domains disconnected from one another? Because I don't think there are many programs (including Chimera) that will like connected polypeptide chains that change chain IDs in the middle. If we're talking about disconnected domains then I can see the usefulness. Otherwise I would think that a named selection or and alias would be more appropriate -- and more descriptive. > >> Suggestion #2: >> Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability). >> - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened... > In the current daily build if a named selection becomes empty (which will happen during session close for example) it will delete itself. Does this meet the need you're describing? Otherwise I could implement ~namesel for deleting them even when they're not empty... > >> Suggestion #3: >> The 'window-size memory' feature that was devised by Eric for the File>Open window would be of interest to most windows: model panel / matchmaker / match / etc... Could you make it a general feature of the various windows in the GUI? > Well, due to the way the windowing library we use (Tk) works, it is quite a headache to impose an overall size on a window a priori. The File->Open thing works by imposing a size on the browser widget inside the window and the window adjusts to compensate. I wouldn't want to try to do this on a generic window basis. Nonetheless, for certain dialogs where it would be high value (i.e. that get a lot of use and that are resized initially a lot) I could see implementing it. The Model Panel comes to mind as you suggested. I'd listen to other suggestions... > >> (It would also be a plus if the preferred location of any of these windows could be memorized as well.) > This has been suggested and I have thought about it. The are several problems. One is that it doesn't work well with tiling. Say you bring up some dialogs that get tiled. Then you bring up a dialog whose placement is remembered, and it is right on top of the tiled dialogs. Or say you make the main Chimera window larger today that you did yesterday -- there's an excellent chance that the memorized positions will be on top of the larger window. Or you put the Chimera window on the right side of your display instead of the left side. Or you put it on a second monitor. I think you get the idea. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >> I trust your expert appreciation whether these suggestions are to be implemented sooner or later... or never :-( >> Thank you for your consideration and for your help! >> >> Antoine >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] Select incomplete sidechains
by Huang, Shengyou 10 Apr '13

10 Apr '13

Dear Chimera developers, Thank you for developing such a great and convenient software package. Is there a way to use commands to select/identify those incomplete sidechains of a protein? In addition, is it possible to do the DockPrep job using commands instead of menu? Thank you very much for your help! Shengyou Shengyou Huang, PhD Research Support Computing Division of Information Technology University of Missouri Email: huangshe(a)missouri.edu Phone: (573)882-3281

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Three suggestions
by Antoine Maillard 09 Apr '13

09 Apr '13

Dear Chimera developpers, Thank you so much for your work and your dedication! Having used Chimera quiet intensively recently, I have listed a few suggestions for your consideration. Suggestion #1: Tools > Structure Editing > Change Chain IDs: lacks a "restrict to current selection" button (would allow to name various domains of a single protein) Suggestion #2: Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability). - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened... Suggestion #3: The 'window-size memory' feature that was devised by Eric for the File>Open window would be of interest to most windows: model panel / matchmaker / match / etc... Could you make it a general feature of the various windows in the GUI? (It would also be a plus if the preferred location of any of these windows could be memorized as well.) I trust your expert appreciation whether these suggestions are to be implemented sooner or later... or never :-( Thank you for your consideration and for your help! Antoine

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Create custom macros / commands
by Thomas Hrabe 09 Apr '13

09 Apr '13

Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas ---------------------------------- Thomas Hrabe (Ph.D.) Sanford-Burnham Medical Research Institute 10901 Torrey Pines Road 92037, La Jolla, CA, USA

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Suggestion regarding
by Jean-Didier Maréchal 09 Apr '13

09 Apr '13

Dear all, in the fast access window, the last structure files and session are listed. Would it be possible to organize those files under a project name? I think that would be an interesting feature. Cheers, JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://g <http://asklipio.qf.uab.es>ent.uab.cat/jdidier<http://ent.uab.es/jdidier>

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computing dihedrals difference along simulation
by Ignacio Faustino 08 Apr '13

08 Apr '13

Dear Chimera users, I would like to know if there is a easy way to compute the difference between a couple of dihedrals a color a residue depending on the result. I guess I have to do some python scripting but just in case I want to ask. Regards, ************************************************************* Ignacio Faustino Plo, PhD student Institute for Research in Biomedicine (IRB Barcelona) Parc Cientific de Barcelona (PCB) C/ Baldiri i Reixac 10 08028 Barcelona - Spain email: ignacio.faustino(a)irbbarcelona.org *************************************************************

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Thumbnail images
by George Tzotzos 08 Apr '13

08 Apr '13

Is it possible to depict in Chimera a protein and/or ligand (any) in a water box. The reason I'm asking is because I want to show the thermodynamic cycle for calculating a binding free energy. The image should be high resolution for publication purposes. Many thanks in advance for any suggestions Regards George

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Chimera-users April 2013