- Chimera-dev - RBVI Mailing Lists

(no subject)
by David Baker 18 Jun '13

18 Jun '13

hello, we are interested in having a rosetta-cryoEM plugin to chimera that would allow users to refine models into maps with Rosetta through a button on chimera (or other simple interface). who would be good to discuss this with? thanks, David and Frank

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developing my own trajectory parser
by Dennis N Bromley 03 Jun '13

03 Jun '13

Hi, I apologize if this is a newbie question - I've searched for material but didn't seem to find any answers. I would like to write a plugin that allows chimera to parse up my own trajectory format. I would like it to be seekable rather than loading the whole shebang into memory at once. Is there an example trajectory parser out there or maybe someone could point me in the right direction? I saw charmm.py, which might be a good place to start, but I am not sure of which bits I need to replicate. Any pointers on a good place to begin looking would be very appreciated. thank you! -denny-

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Installing Biopython using Chimera's Python copy
by Mateusz Dobrychłop 29 May '13

29 May '13

Hello, In response to one of my older e-mails, I was instructed to install Biopython using the Python copy that comes with Chimera's installation, in order to be able to import Biopython libraries inside my Chimera plugin. Can you please explain briefly how to do that on Windows and on Ubuntu? Cheers, Mateusz

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Importing modules causes crashes
by Mateusz Dobrychłop 23 May '13

23 May '13

Hello, I'm writing a Chimera extension that uses modules that it imports an external module. To do this, I append the sys.path with a path to the directory where the module is placed and then I just import it. And then Chimera crashes. The line with the import is the one that directly causes the crash. I'm attaching a screenshot of the error that Chimera throws when I run it with --debug option. I have no idea what might be wrong. Thank you for your time, Mateusz

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Trajectory and MD Movie GUI
by Alex 18 Apr '13

18 Apr '13

Dear all, I'm developing a plugin and would like to add frames to a model on the fly and being able to use the trajectory (MD Movie) GUI to navigate among the frames. Unfortunately, I can't find a way to instanciate the dialog MovieDialog (Movie/gui.py) with a model already opened. It seems that I have to use an Ensemble object (Trajectory/__init.py__) but its constructor requires another ensemble, and the Ensemble objects seem to be created inside MovieDialog's constructor. I'm rather confused right now and would appreciate some help on the matter. Thank you in advance, Best regards, Alex Tek --------- Alex Tek, Phd Department of Cell and Molecular Biology BMC Box 596 SE-751 24 Uppsala Sweden

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ligand
by Muhammad Ali 16 Apr '13

16 Apr '13

sir When I retrieve a ligand structure in SDF files from PDB site, it contains many ligand, how to get a single ligand ??? also ligand files are why not available in PDB files ?? I have to covert them in Chimera.....

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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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Pseudobonds and gap detection
by Ibai Gazpio 10 Apr '13

10 Apr '13

Dear, We are developing a chimera extension and I would like to know if there is a way to detect or select those models which have an internal sequence gap, represented by the program as a pseudobond in order to distinguish them from those who haven't. Is there a function to do that? Thank you very much and congratulations for the program. Sincerely Ibai

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3dconnexion
by Dougherty, Matthew T 03 Apr '13

03 Apr '13

Hi, I am starting to build a matrix of USB HID devices using controllermate on a mac. I am planning to use two 3dconnexion devices. one to handle 6D translation/rotation, and the other to manage color/lighting; or maybe left hand for trans and right for rotation, etc. . The current driver in chimera only sees one device. If I touch the first USB 3dconnexion device plugged in, it behaves as expected. Touching the second device, chimera acts as though it is the first device. So the driver is not keeping track of the number of devices. In controllermate I can see both devices and can program them independently. For example, I will be able to remap these signals to my choosing and pass it on to a chimera extension I am developing. The second problem I am having is when chimera starts up it exclusively grabs the low level driver, ignoring the the high level driver which incorporates context management. Consequently controllermate is unable to intercept and modify the signal before passing it on. A good reason to do this would be creating deadband zones, or a user defined response curve, or integration with multibutton panel like the logitech g13 so that I can modulate the response (eg, 0.1x,1x,10x,100x, etc). How do I disable 3dConnexion so that it will not load in chimera? I could wipe out the code, but would prefer minimally screwing with chimera base code which is a headache for daily builds and has a risk factor of unforeseen consequences. Something in preferences would be helpful. In a related question on preferences, the scroll wheel is tied to camera zoom. I would like to remap that as a movement in z. Generally I like to keep my scale factor at 1; I find heavy or casual use tends to get me into camera problems. Is this possible? at the moment I disable the scroll wheel. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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changing position for a residue using python
by Jean-Didier Maréchal 27 Mar '13

27 Mar '13

Hi all, I have a problem with a prot and it seems that renumbering could help. I'd like to automatically add 230 to the residue number of the aa of my second chain. As I feared, when looping other residue to change res.id.position, my script fails as position can not be modified. How could I do this? Should I delete position and re-create it? Best JD

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