December 2010 - Chimera-users - RBVI Mailing Lists

Chimera Error
by יוכבד 13 Dec '10

13 Dec '10

---------- Forwarded message ---------- From: יוכבד <ybaime(a)gmail.com> Date: Mon, Dec 13, 2010 at 11:44 AM Subject: Chimera Error To: chimera-users(a)cgl.ucsf.edu Hi I'm trying to open a density map file using chimera and for some reason the file won't open. The opening is followed by an error message regarding the file size being too small for the grid size. The same error appears also in the old version (1.4.1) and also in the newest version. How can I solve this problem? How can I change the grid size? The same file opens successfully on a friends computer with the 1.4.1 version and so I assume the file is not corrupted. Attached is an image of the error message. I'd appreciate your response. Thank you Yocheved Baime Bar-Ilan univ.

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Calculating Solvent Accessible Surface of individual residue in a model
by Sumitro Harjanto 10 Dec '10

10 Dec '10

Hi Meng, I would like to find out if I can use Chimera to calculate the solvent accessible surface(SAS) of each residue in a model..? I would like to find out, basically, if I show the surface of the molecule, which are the residues buried (SAS = 0) and which are the ones contributing to the surface contour (SAS > 0). Thanks! =] Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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Measuring the volume enclosed by a complex
by Anindito Sen 10 Dec '10

10 Dec '10

Dear All This question may have been answered before but will be helpful if you can let me know - How can I measure the volume enclosed by a protein complex. Thanks Andy Dr. Anindito Sen (Ph.D) School of Biological Sciences University of Auckland 3A Symonds Street Room 420 Auckland City. New Zealand. Tel: +64 -9- 373-7599 ext: 87593

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Recommended HW for Chimera 3D
by Marek Basler 07 Dec '10

07 Dec '10

Hi, what would be recommended HW and OS for trouble free 3D using glasses with new 120Hz LCDs? Linux or Win? What is the best graphics card? I don't care about money but nothing crazy either. Any suggestions? Thanks a lot! Marek

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Re: [Chimera-users] Query regarding Fit in Map
by Tom Goddard 07 Dec '10

07 Dec '10

Hi Arun, So you just want to measure the correlation for a selected atoms in a map, no fit optimization. This can be done without Python. Make a simulated map with the Chimera "molmap" command, and report the correlation with "measure correlation". molmap sel 12.5 modelId #5 measure correlation #5 #0 Here the map is #0, selected atoms are referred to using "sel" and a simulated map for those atoms is created as model #5. Results with be in Chimera reply log (menu Favorites / Reply Log). I don't think you want to turn off the "use only data above contour level". If you do it will measure the correlation of the entire box of simulated data including all the zeros far from the atom, which probably will not match the non-zeros in your map. If you really want that use option "aboveThreshold false" with the measure correlation command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Tom > Hi Tom, > > Thank you very much for your kind reply. It is quite helpful to know. > I am able to run the script and fit a map on to a map. But the problem > at had is slightly different. I have got the fits done already with > Flex-EM and I am actually trying to measure (ideally automate it with > the Chimera script) the correlation for the currently selected atoms > in the given map using the 'Update' option available in the Fit in Map > dialog. I would also like to specify the following option in the script. > > Real-time correlation / average update (turn off within the script) > Use map simulated from atoms, resolution = value > use only date above contour level from the first map (turn off within > the script) > optimize correlation > correlation calculates about mean data value (turn off within the script) > rotation (turn off within the script) > shitf (turn off within the script) > Move whole molecule (turn off within the script) > > I am not sure how to put all this options in a script and calculate > the correlation for the currently selected atoms with the Update > option. I would greatly appreciate if you could provide me with some > more insight on how to change the code specifically. Thanking you. > > with kind regards, > Arun Prasad > > > Tom Goddard wrote: >> Hi Arun, >> >> Yes you can use Fit in Map in a script. I've attached an example >> Python script. This script comes from the Chimera Python scripts web >> page but that web site is down right now. It is necessary to use >> Python rather than a simpler Chimera command script because there is >> no Chimera command to use Fit in Map. There probably should be, but >> since Fit in Map only does a local optimization you need some way to >> initially position the molecule or map you are fitting. That is the >> hard part and so there hasn't been much demand for the fitting command. >> >> The Python code for the Fit in Map dialog is included in all >> Chimera distributions in the directory >> >> chimera/share/FitMap >> >> You could look at the __init__.py and gui.py to learn what the >> available functions are. The gui.py (graphical user interface) file >> shows how those functions are called by the dialog. >> >> Tom >> >>> Hi all, >>> >>> I would like to know whether its possible to automate the operations >>> available with 'Fit in Map' tool and its options within a script. >>> Actually I would like to calculate the correlation for certain segments >>> of the atomic structure and it would be help if I could do it with a >>> script rather that the GUI. Any suggestion is greatly appreciated. >>> >>> Thank you, >>> Arun Prasad >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> >

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problem in showing disulfide bonds
by Pardeep kumar 06 Dec '10

06 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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"Surface calculation failed, mscalc returned code 5"
by Sumitro Harjanto 06 Dec '10

06 Dec '10

Hi Meng, I've run into this problem a few times when I wanted to calculate and show the surface of a pdb model. I got the following on my reply log: C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed. Falling back to single-component calculation. C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn't work. Any suggestions? One particular file that gives me the problem is 1IGT from PDB. I've tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D. but still the problem persists. Thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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Query regarding Fit in Map
by Arun Prasad Pandurangan 03 Dec '10

03 Dec '10

Hi all, I would like to know whether its possible to automate the operations available with 'Fit in Map' tool and its options within a script. Actually I would like to calculate the correlation for certain segments of the atomic structure and it would be help if I could do it with a script rather that the GUI. Any suggestion is greatly appreciated. Thank you, Arun Prasad

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need examples of Chimera crash on Mac OS X 10.6.5
by Greg Couch 03 Dec '10

03 Dec '10

There have been occasional reports of Chimera crashing in the graphics driver on Mac OS X 10.6.5. However, the reports have not included enough information to allow us to reproduce the problem and debug it. If you observe this crash, please report it to Apple (a dialog to do this will appear when the crash happens). The next time you start Chimera after the crash, another dialog will appear with the option to send us a bug report too. Please go ahead and do that, including a description of what you were doing before the crash, and your email address in case we need to request further details. Thank you, Greg

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how to product a color scale bar
by C.J. 03 Dec '10

03 Dec '10

Dear all, I am writing to ask how to product a scale bar to indicating different radius with different color when I visualizing a spheric structure with Chimera. Thanks. Regards! C.J.

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Chimera-users December 2010