- Chimera-users - RBVI Mailing Lists

Worm representation / command line
by Xavier ROBERT 01 Jul '15

01 Jul '15

Dear all, I am wondering if there is a way to call "Render by Attribute" at the command line in order to render a worm representation? If not, is this feature planned for the near future and is there any workaround for this? Thank you very much in advance. Kind regards, Xavier R.

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generating symmetry mates of a surface model created with shape command
by Carmen San Martin 01 Jul '15

01 Jul '15

Dear all, is it possible to generate symmetry-related copies of a surface model created by the shape command? I am interested in masking out certain map regions related by symmetry. I got the right shape at the right place but now cannot figure out how to create the shape symmetry mates. The sym command followed by the model number of my shape complaints that no molecules are specified. Thanks, Carmen ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 http://www.cnb.csic.es/ http://tinyurl.com/carmensanmartinlab http://orcid.org/0000-0001-9799-175X ------------------------------------------------------------

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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 So is there any way to open this file type without having to redefine all the specific features the researcher originally made?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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Morph volumes after alignment
by Haselbach, David 28 Jun '15

28 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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ViewDock
by leila karami 27 Jun '15

27 Jun '15

Dear all Now, I want to save 1 pdb file containing target + one of poses of ligand for example, number 3. For this aim, what to do? I did following steps, but I did not succeed: file ---> save pdb ... In save models section, I selected both of target.pdb (#0) and (#1.3) In file name section, I wrote complex.pdb and then save. I encountered with error (see the below link): https://www.dropbox.com/s/bdkq1x1db96amhi/chimera%20error.png?dl=0 I tested other names such as $target.pdb and $1.3.pdb. Unfortunately, I encountered with the same error. Best regards,

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drawing shapes
by Bala subramanian 25 Jun '15

25 Jun '15

Friends, I have used HOLE program ( http://www.sciencedirect.com/science/article/pii/S026378559700009X) to find the pore radius of a channel as a function of z-axis. As output, the program gives the location of capsules (that were filled inside the channel), capsule length and radius etc, as a function of z-axis. Capsule graph option***** Data: cenxyz.cvec eff.rad area CAP.LEN cap.rad angle.X-axi cen.line.di integ.s/(ar point sourc *-14.00000* *2.23465* 15.68804 *1.72142* 1.39301 73.21487 0.00000 0.03187 (sampled) -14.50000 2.40709 18.20262 1.96609 1.46141 58.41143 -0.54015 0.05934 (sampled) -15.00000 2.51292 19.83844 1.37866 1.78410 73.19154 -1.11224 0.08454 (sampled) -15.50000 2.69525 22.82171 1.34834 1.97026 87.40431 -1.71545 0.10645 (sampled) I was wondering if i can use the shape command to draw the capsules in Chimera. I thought to create 'tube' with 'shape' command but i was not lucky. For instance, the following command didnt work (i opened channel as model #0) shape tube #0 radius *2.23* bandLength *1.72* center 0, 0, *-14.00 * Pls help to know some way to do this. Thanks, Bala -- C. Balasubramanian

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