March 2020 - Chimera-users - RBVI Mailing Lists

Changing cryo-em density map x=voxel size in Chimera
by Ouadou, Anes (MU-Student) 16 Mar '20

16 Mar '20

Hello, I am using cryo-em density maps to create a deep learning model that detects C-alpha atoms. the model I trained uses maps with voxel size of 1x1x1 A. Experimental maps come in different voxel sizes. I found that I can change the voxel size using the option "model-spec". However, I looked everywhere in Chimera menu bar but could not find "model-spec". can you please show me where to find it. I am also open to any other suggestion to change voxel size. Regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

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question about specific protein display
by Galotto, Giulia 13 Mar '20

13 Mar '20

Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute

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Re: [Chimera-users] Getting the analysis of the side chains that are not in the density map
by Dmitry A. Semchonok 13 Mar '20

13 Mar '20

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Getting the analysis of the side chains that are not in the density map
by Dmitry Semchonok 13 Mar '20

13 Mar '20

Dear colleagues, I have a map with the fitted model inside. Some of the side chains are out for the density map. I want to have a get a file where the side chains that are not in the density map are listed. Does anyone know how to do that? Thank you! Sincerely, Dmitry

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Help please
by Dr Musa Said 11 Mar '20

11 Mar '20

Dear there I am training myself in Chrimera software. The first example shows the ligand is on one side and 1HOM is on another side. Where did I g wrong, please. Please see the attachment. Regards Musa

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Re: [Chimera-users] how to create a sphere in Chimera
by Elaine Meng 11 Mar '20

11 Mar '20

Hi Sc Ke, Chimera doesn't do that projection calculation; you would have to do it yourself. I think you could select all the nitrogens within the sphere and then write out their coordinates, but any other steps after that would require your own processing. You don't even need the sphere (it may just be for display purposes) since you already have an atom at the center of it to define the radius for finding nitrogens. I think you could select the nitrogens, for example, by just selecting the center atom (Ctrl-click on it, you may need to hide the sphere first if it's covering the atom), and then using a command something like: select N & sel za<8.5 ... where instead of 8.5 you would put the radius of the sphere. It means select element N and also within 8.5 angstroms of current selection, which is the center atom you selected first. You can hide the sphere by un-checking its S (Shown) checkbox in the Model Panel (show by choosing Model Panel from the Favorites menu). Then you could get the coordinates of the selected nitrogens, for example with command getcrd sel ... and then look in the Reply Log for the list of coordinates (show by choosing Reply Log from the Favorites menu). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 10, 2020, at 6:05 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > > Hi, Elaine, > Thank you for the detailed instruction. I got the sphere. > > May I ask one more question: > How do I define an equator plane of that sphere and project all nitrogen atoms within that sphere onto the equator plane; i.e. the polar coordinates of the nitrogen atoms within a sphere are what I would like to have? > Thank you very much. > sc > > -----Original Message----- > From: Elaine Meng [mailto:meng@cgl.ucsf.edu] > Sent: Thursday, March 05, 2020 12:46 AM > To: Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] how to create a sphere in Chimera > > Hi Sc Ke, > There is more than one way. Say you have already selected the single atom. Then, > > (A) to put a marker (essentially a fake atom) at that position, command “measure center”, for example: > > measure center sel mark true radius 4.0 color pink model #8 transparency 50 #8 > > see manual for command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> > > (B) to put a spherical surface model at that position, command “shape sphere”, for example: > > shape sphere radius 8.5 center sel color orange modelid #8 transparency 60 #8 > > see command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Mar 4, 2020, at 2:40 AM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: >> >> Hi, >> I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. >> Thank you. >> Sc Ke >> Professor >> Department of Physics >> National Dong Hua University >> Hualien, Taiwan > > > -- > 此電子郵件已由 AVG 檢查病毒。 > http://www.avg.com > >

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Change default pseudobond color?
by Oliver Clarke 10 Mar '20

10 Mar '20

Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli

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Numbers(markers) inside/on the map
by Dmitry A. Semchonok 10 Mar '20

10 Mar '20

Dear colleagues, I would like to place the numbers (markers) inside/on our map. Could you please prompt how to do that ? Thank you. Sincerely, Dmitry

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Regarding Structure minimize
by Yash Bahl 08 Mar '20

08 Mar '20

To do structure minmization, what is the adequate values? Steepest descent should be changed to 75 from 100. What else? Should intervals be also changed to 25? Thanks

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visualizing potential with volume data
by Christos Deligkaris 06 Mar '20

06 Mar '20

dear all, I have obtained a cube file from NWChem with the electrostatic potential around a molecule. I visualized the molecular surface using Actions->Surface->Show and then colored it using the volume data (followed instructions https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in tools->surface color (electrostatic surface coloring)) . Since I do not have my data stored in a potential file, can I still do the surface offset? The chimera tool webpage discusses why that is preferred than showing the potential on the solvent excluded surface and it seems to me that option to not be available with volume data. Also, my surface does not look like the electrostatic potential surface shown here: https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html . The molecular surface we get with Action->Surface->Show seems to be constructed with greater atomic radii than the one shown in that image. I am not sure how important that is though. Is there a way to ask Chimera to visualize the electrostatic potential volume data with the same options Chimera would use if it was reading a Delphi, PBS file? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics

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