June 2015 - 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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Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 21 Nov '15

21 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

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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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Center of rotation cross-hair
by Tom Goddard 28 Jul '15

28 Jul '15

Hi Oliver, I added display of a cross hair (plus sign) at the center of rotation in the graphics window. You turn it on with command set showCofR and turn it off with ~set showCofR The crosshair is white on black (and dark) backgrounds and black on white (or light) backgrounds. This will be in tonight’s daily build. Tom

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Using Chimera to read Maestro files
by CG Deer 30 Jun '15

30 Jun '15

Hello Chimera Developers and Users, My name is Christopher Deer, and I am trying to use Chimera as part of a workflow for getting a maestro file (.mae) ready for presentation in a CAVE environment. The .mae file contains color references and specifics defined by a researcher. However, these details are not appearing when I open the file in Chimera. So is there any way to open this file type without having to redefine all the specific features the researcher originally made? Here is a screenshot of what I am seeing in Chimera, and I have attached what the researcher originally wanted it to look like (minus white background).[image: Inline image 1] Thank you for your help, --Chris Deer University of Arizona Research Computing, Data Visualization Specialist

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animation error
by Hartzell Jr., Criss 30 Jun '15

30 Jun '15

I am at a meeting making an animation for a talk using my MacAir. When I play it back from the animation panel, about half way through the animation, I receive this error and the animation crashes. Can you help debug? Thanks. File "/Volumes/ChimeraInstaller 1/Chimera.app/Contents/Resources/share/Animate/SceneState.py", line 1031, in _msmsSameColors return false NameError: global name 'false' is not defined Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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morph volumes after alignment
by Haselbach, David 30 Jun '15

30 Jun '15

Dear all, I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the "fit in map" functionality. This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command: vop morph #0-19 playstep 0.003 constantVolume true frames 1000 the maps are morphed in their original position so the morph is quite jumpy. Is there a way to morph through them in the aligned coordinate system directly? Kind regards David ----------------------------------------------------------------------------------- Dr. David Haselbach Max-Planck-Institut für biophysikalische Chemie AG Stark Am Fassberg 11 D-37077 Goettingen dhaselb(a)gwdg.de<mailto:dhaselb@gwdg.de> +49-551-2011302

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Linux and stereo in the vizvault
by Greg Couch 29 Jun '15

29 Jun '15

So it works with some caveats -- iff the projector is the primary and only display and you use reverse sequential stereo. Getting there was difficult, you have to disable the LCD monitor with the system display settings instead of the amdcccle interface that appears to do the same thing. But you need to use the amdcccle interface to turn on quad-buffered stereo. Once quad-buffered stereo is setup (after several reboots), you can turn on and off the LCD monitor, but the stereo-sync signal is only generated only if the LCD monitor is turned off. The driver also got confused occasionally and wouldn't display a stereo image -- that was fixed by reenabling the LCD monitor and disabling it again. -- Greg

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on chimera saved PDB file
by Smith Liu 29 Jun '15

29 Jun '15

Dear All, By chimera I have saved a PDB file, but at the end of the saved PDB there are following sentences which I do not understand: CONECT 3 2 4 17 CONECT14560145591456114574 CONECT29117291162911829131 Will you please explain it to me the meaning of "CONECT 3 2 4 17" and the other 2 sentences? And why there is no space in "CONECT14560145591456114574"? Smith

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Chimera-users June 2015