- Chimera-users - RBVI Mailing Lists

help please
by Sezer Akgöl 22 Jun '15

22 Jun '15

how can I associate 2 protein with each other from their C and N terminals respectively

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Feature request - lock center of rotation to center of view ("pseudo-Coot mode")
by Oliver Clarke 22 Jun '15

22 Jun '15

Hi, I have a request for a future version of Chimera - would it be possible to add a command or menu item that (reversibly) locks the center of rotation to the center of view, such that when the view is translated, the cofr is updated automatically also? This is the way structure navigation works in Coot, and I find it is a much more intuitive and precise way to travel when examining the finer details of a structure (as one would expect given that the main purpose of Coot is model building while Chimera is exceptionally good for structural analysis and visualization). This would make navigation of large structures much easier, particularly when one is just browsing around the structure. In addition, it would be nice to have a dynamically updated pseudoatom to indicate the current center of rotation - this is implemented in Coot as the “pink pointer”, and I find it very helpful for getting my bearings. Cheers, Oliver.

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Chimera in Virtual machine
by Milo Westler 18 Jun '15

18 Jun '15

Well I thought I had this figured out, but then my VM broke and I can't get chimera to run in my VM again. I am running Vritualbox with a guest system of ubuntu-mate 15.04. I want to be able to use chimera in the VM for a workshop that we are presenting. I have installed the 64 bit version for linux. I get: ~> chimera pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 751 Current serial number in output stream: 752 ~> And when I run: /opt/UCSF/Chimera64-1.10.1/share> python __main__.py Chimera is misconfigured. Please reinstall chimera. Thanks, -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Query on GPI-anchor proteins
by Aditya Padhi 17 Jun '15

17 Jun '15

Dear Chimera Users, I am working on a protein, which is known to cleave few GPI-anchor proteins (Glycosylphosphatidylinisotol). Also, I know that there are several other candidate GPI-anchor proteins which may or may not be cleaved by my protein of interest. I was wondering, if there is any tool/method in Chimera using which I can atleast get some preliminary information on which of the proteins that could be probably cleaved by my protein of interest. The 3D structure of my protein of interest and most of the GPI-anchor proteins is not available. I was therefore wondering if there is any such tools/methods available that I am missing using which I can find out which of the GPI-anchor proteins are being cleaved. Any suggestion/guidance would be highly appreciated. Thank you so much, Aditya

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What happened to my model?
by Sara Cuellar 17 Jun '15

17 Jun '15

So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.

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Scripted registration of a perframe python script
by Kersey Black 17 Jun '15

17 Jun '15

Hi, I have been 'opening' a python script file from within Chimera to start a session and in that script I open the MovieDialog manager (mdm) and read in a pdb with a series of models to be viewed as a trajectory. That part is working thanks to help from other responses in chimera-users. To modify the molecule (color, etc) it seems like the mdm.ensemble.molecule is giving me the access, though that may not be the right approach for my needs, because it seems to act on all frames. What I would like to do, from within this same initial python script, is to apply/register a perframe (also in python) script to control things like color on a frame by frame basis. I would like to do this as a way of keeping all of the setup in a single script file such that then I just need to record the movie manually, or perhaps there is a way to do this also from the script. Thanks much for any help and/or direction to documentation on the python api to the MovieDialog that allows control of these functions. Kersey

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ImportError: no module named chimera
by 陈雷 16 Jun '15

16 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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ImportError: no module named chimera
by ryanch＠mail.ecust.edu.cn 15 Jun '15

15 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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restoring sessions with python & triggers
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

Normally a save session by a python extension is invoked by a trigger SAVE_SESSION. For restoring a session, several related chimera APIs are available that are typically not used. 1) post model restore: SimpleSession.registerAfterModelsCB(afterModelsRestoredCB, arg) 2) BEGIN_RESTORE_SESSION and END_RESTORE_SESSION triggers. I need to reset extension gui values based on midas positions. I presume a normal restore in the session file does not guarantee that these midas positions will be loaded at that time, so I need to delay the gui updates until the restore process has ended or possibly when the models are loaded loaded. What is the distinction between END_RESTORE_SESSION and registerAfterModelsCB? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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setting viewing pref using python
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

the viewing dialog sets the Camera:Stereo parameters:units to inches, and Side View:Side to right. using python how can I reset them to mm & top? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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