April 2016 - Chimera-users - RBVI Mailing Lists

Other Tools button not present in the Segment Map Dialog
by silvia desanctis 13 Apr '16

13 Apr '16

Dear all, I have performed a segmentation on my map but if I click the Shortcuts button in the Segment Map dialog I cannot see the Other Tools section where I would select the Fit, Extract, rSeg or SegLoop tools. Why not? I updated to the daily built version of Chimera just yesterday so I have no idea why this complete line of tools is missing. Greeetings Silvia

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Mirrored density artefact
by Morris, Kyle 13 Apr '16

13 Apr '16

Dear Chimera dev and community, I am using "vop cover” to extract a box of density around a PDB and making the box quite large with the following: $ vop cover #0 atomBox #1 pad 55 I have noticed in the extracted density that as I increase the pad size the true density gets duplicated and mirrored on the opposite edge of the cell containing the volume. This seems like strange behaviour to me, is there something wrong or that I am doing wrong? Many thanks for your help. Best, Kyle

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using standard OS keyboard shortcuts with Chimera?
by Jakob Suckale 12 Apr '16

12 Apr '16

Dear all, It's perplexing for newbie users that Chimera does not react to the basic keyboard shortcuts that are used across all OS applications like Cmd+S, Cmd+O, Cmd+W. Is it possible with Chimera to use those? If not, it should be enabled. I'm aware that there are special 2-letter Chimera shortcuts (http://bit.ly/1Xr5uA4) but they are more confusing for beginners and therefore also disabled by default. We see a lot of user errors like saving the session with Cmd+S, then quitting Chimera with Cmd+Q (the only standard shortcut available, I believe) and then asking why their session info has not been saved. Included standard shortcuts as a feature in one of the next releases seems like a small thing with a lot of benefit. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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fivefold rotate command
by Cheng-Chen Xu 11 Apr '16

11 Apr '16

Hi Chimera, Is there anyway to rotate each pentamer around its own fivefold axis separately and simultaneously when dealing with a T=1 icosahedral virus capsid? Many thanks, Chen

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Color holes in mesh?
by Oliver Clarke 08 Apr '16

08 Apr '16

Hi, When I want to show electron density around, for example, a single alpha helix in a structure, there are a couple of options in chimera - one would be to use vop zone, which I don't like for this purpose, because it creates a new map that can be recontoured (so one can't see where the original map has been cut). The sop analog of this, sop zone, works quite well for the purpose, but there is no easy way that I can find to cap the holes that are created in the mesh - I want to do this so that I can make it obvious where "carving" the map has affected the shape of the resultant map, or has truncated connected regions that are not displayed. Would it be possible to add such an option in ChimeraX? Or having an option to represent the inside of a surface differently from the outside would do the trick also. For the moment I have a work around (used in the attached pic): 1. Create a mesh. 2. Duplicate the mesh, change to surface rep and set transparency to 0.001. 3. Create a copy of this surface, change the transparency to 0.99 and increase the volume level by 0.001. Cheers, Oli.

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Re: [Chimera-users] how to generate good STL code for atoms display
by Jakob Suckale 08 Apr '16

08 Apr '16

Hi David, Yep, you recalled that well despite the convoluted name. It does help with overall simplification but it does that for all structures proportionally and ribbons are well converted. It's just the atom models that are excessive. What I cannot do yet in Meshlab is get rid of all these pointless internal structures. The 5-membered ring in the attachment for example is full of invisible vertices inside that inflate the file size. There are ways to partially remove internal structures with Meshlab (http://bit.ly/1Tyzz1u) but they don't do a very good job because they typically remove some of the outer ribbon surfaces as well creating hole that need to be filled. All the best, Jakob On 7 April 2016 at 23:01, David Bhella <David.Bhella(a)glasgow.ac.uk> wrote: > I use meshlab for this I am not in front of my mac just now but from memory the filter is quadratic edge collapse decimation (or something like that). It works well to reduce the poly count. > E-mail me if you want help trying it. > Another useful tool is netfabb to repair stl files by removing unwanted shells and fixing non-manifold maps. Lately I have found surfaces from chimera don't suffer from this as much as they used to.... > > Sent from my iPad > >> On 7 Apr 2016, at 21:17, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: >> >> Hi Jakob, >> >> One way to reduce the number of STL triangles generated is to lower the subdivision amount in the graphics quality section of the Effects dialog in Chimera. >> >> Another way is to load the STL output into the open-source MeshLab program, http://meshlab.sourceforge.net/, and use its tools to simplify the mesh. I have not that, so if someone has done that, please chime in, and describe which MeshLab filters to use. >> >> You may need to use both techniques to make 3D printer software work. If your 3D printer takes VRML input, I would recommend using Chimera's VRML output instead. >> >> HTH, >> >> Greg >> >>> On 04/04/2016 05:13 AM, Jakob Suckale wrote: >>> Sorry, the message was truncated. This is the missing part. >>> >>> A netfabb repair of the chromophore STL does significantly simplify >>> the model and reduce the file size from 13.7 to 5.7 MB indicating that >>> there's a lot of room for improvement in the STL export esp. of atom >>> models. >>> >>>> On 4 April 2016 at 11:54, Jakob Suckale <jakob.suckale(a)uni-tuebingen.de> wrote: >>>> Dear chimeras, >>>> >>>> Does anybody know of a good way to generate lean STL code for atom/bond display? >>>> >>>> Take this example. I'm generating STLs to 3D print GFP. Exporting the >>>> ribbon of the beta barrel generates an ok STL of 6.8MB. However, >>>> exporting the wire atom display of the chromophore generates a >>>> horribly inflated STL of 13.7MB - almost twice the ribbons file >>>> despite the tiny size (see screenshot attached). Printing the >>>> chromophore is problematic since it contains a lot of weird internal >>>> structures instead of being a clean surface model of the wireframe. A >>>> netfabb repair of the chromophore STL >>>> >>>> Looking forward to your expert ideas. >>>> >>>> All the best, >>>> >>>> Jakob >>>> >>>> >>>> >>>> Jakob Suckale, PhD >>>> Lecturer in Biochemistry >>>> University of Tübingen >>>> +49-7071-29-73363 >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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how to generate good STL code for atoms display
by Jakob Suckale 07 Apr '16

07 Apr '16

Dear chimeras, Does anybody know of a good way to generate lean STL code for atom/bond display? Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL Looking forward to your expert ideas. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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3D viewing
by Mohamed Noor 07 Apr '16

07 Apr '16

Dear all Where can I find information on the hardware required for 3D viewing with Chimera? I am building my Linux system, so I would appreciate useful pointers. 1. IIUC, I need a Quadro card as this does not work with GeForce. What should I look for when selecting a suitable card? 2. I want to also have a second monitor. Since this is not going to be used for 3D, can I just hook up any normal monitor? Or do both monitors have to be the same model etc.? 3. I have read that I need to have a card with 3-pin DIN port. Is this true? Thanks. Mohamed

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Advice on SASA
by George Tzotzos 07 Apr '16

07 Apr '16

I have a couple of questions on Chimera’s implementation of SASA. First, I’ll try to explain briefly my problem and then ask the questions. My protein is a homodimer. There exist 3 X-ray structures of the protein in complex with serendipitous ligand as well as in complex with biological ones. The ligands bind at the interface between the two chains of the homodimer. It is not clear whether dimer formation is a crystallographic artefact. Biochemical experiments are likewise inconclusive. It has been argued that the biological ligands may stabilise the formation of the dimer. Furthermore, it has been argued that upon ligand binding some of the interface residues become buried. I’ve conducted extensive MD simulations with and without the biological ligands. I would like to test whether ligand binding has an effect on the SASA of the interface residues. 1. Can I restrict measurement of SASA to selected residues only? In other words, can I use a mask specifying the residues of interest? 2. From the documentation, I understand that the Chimera implementation of SASA is applied on single pdb structures and not on trajectories. If I use representative structures from MD clusters, should I strip the ligand before measuring SASAs? Thank you in advance for your suggestions and apologies for the long-winded explanation. Best regards George

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save gaussian volume filter as a new map?
by H. Adam Steinberg 06 Apr '16

06 Apr '16

Hi All, How do I save a map that I applied a gaussian volume filter to? I opened a cryo EMD map and then applied a gaussian volume filter to it with a width of 1.5 to clean up some of the extra detail. I would now like to save that map out of Chimera to use elsewhere. When I save the Chimera file it says “EMD-6413.map gaussian was not saved with the session.To have them included in the session it must be saved in separate volume files before the session is saved.” How do I do that? <http://www.artforscience.com/> <http://www.artforscience.com/>H. Adam Steinberg Artist & Scientist 7904 Bowman Rd Lodi, WI 53555 608/729-5944 <http://www.artforscience.com/>artforscience <http://www.artforscience.com/> Facebook <http://facebook.com/artforscience1> Twitter <http://twitter.com/artforscience> McPherson Eye Research Institute <http://www.vision.wisc.edu/>

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Chimera-users April 2016