- Chimera-users - RBVI Mailing Lists

Nucleotide Mutagenesis in Chimera
by Elhajjajy, Shaimae Imane 14 Jun '18

14 Jun '18

Hello, I am trying to mutate nucleotide residues in RNA using Chimera, and I've seen previous posts about using the "swapna" command. However, Chimera is giving the error message "Unrecognized command: swapna". Is there a way for me to enable swapna for Chimera to recognize so that I may use it? Thank you, Shaimae

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Showing/Hiding/Fading
by Gustaf Olsson 14 Jun '18

14 Jun '18

Hello Chimera users and developers, I’m back again. So my movie rendering is progressing though I have of course run into more problems. I have one PDB file open, I need to create a surface around one molecule that is close to other molecules so running the surface command directly does not work as intended. I therefore have to split the PDB file and calculate a surface around a single molecule. All is well, however after this I run into some problems trying to clean up the script. I assume that I am defining the modelID incorrectly though I cannot figure out how. The following works: split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 This splits the model putting one residue (17) in a separate model, I calculate the surface without issue, color it by coulombic charges. I then have to combine the models (the single residue (17) and the rest of the residues) and close the old “residue 17” model. I then need to hide the newly created surface to display it at a later point in the movie. The script above works, however this does not seem very neat. I have experimented with different other commands, including transparency transp 100,s #0.1 Which also works well, as long as I split and combined the models. However, I have to combine the model for this to work! split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 Everything but hiding the surface works. transp 100,s #0.1 This does not work either in this case. I am assuming that I am not defining the model ID correctly for the surface and this is why I cannot hide it? I also tried using surfcat: surfcat templ :17.het surf probeRadius 0.5 vertexDensity 20.0 templ coulombic -5 red 0 white 5 blue templ wait surftransparency 100 templ or any of the following: surftransparency 100 #0 surftransparency 100 :17.het surftransparency 100 #0:17.het transp 100,s #0 Hides the created surface, what am I doing wrong in defining the surface to hide it and show it again? Thank you for any input and best regards // Gustaf

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select a specified residue
by 张征锋 13 Jun '18

13 Jun '18

Dear Sir, It is nice to use the amaizing software of UCSF Chimera. I can select a kind of residue such as all 'SER's and label them, while I am able to select a specified number of residue, such as the 200th residue 'Ser'. Could you please show me how to do with this? Thanks a lot. Best, zhengfeng ------------------ Zhengfeng Zhang School of Life Science Central China Normal University. NO.152 Luoyu Road, Wuhan,Hubei, P.R.China 430079

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Symmetry operation calculations for multimeric fibrillar assemblies
by Einav Tayeb-Fligelman 13 Jun '18

13 Jun '18

Dear Chimera support team, I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt. Thank you in advance, Einav -- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <+972%2077-887-1964>

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make helical filament model using command sym
by Yaowang Li 13 Jun '18

13 Jun '18

Dear all, I have built a model from cryo-em density map, now I am going to create a model of a filament (have a length of the pitch, over 1000 A) from it. I think the command 'sym' can do it, but not easy for me. I have tried many times. sym #0 group h,rise,twist,100 or sym #0 group c2*h,rise,twist,100 coord #1 or sym #0 group h,2.292,179.6,100 coord #1 the model is wrong I also try to measure the symmetry first and sym #0 group #1 it is almost right, but I need much longer, how set it? using the 'n' parameter? and how? and if I want to set rise and twist myself, how to do it? Best wishes, Yaowang

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FindHBond tool not finding H-bonds with sulfur?
by Gustavo Seabra 12 Jun '18

12 Jun '18

Hi there, I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system. I’ve put together a simple example system here to show what I mean. After opening the files, I do: 1. Select the ligand (Select > Residue > LIG) 2. Tools > Surface/Binding Analysis > FindHBonds 3. Find These Bonds: Both 4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change) 5. Select “Only find H-bonds with at least one end selected” 6. Hit Apply. Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom. So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem. Thank you very much, -- Gustavo Seabra

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Fading structures/surfaces in/out
by Gustaf Olsson 12 Jun '18

12 Jun '18

Making a movie using a CMD script I am using something like the following to fade structures in/out transparency 95 :17.het; wait 8 transparency 90 :17.het; wait 8 transparency 85 :17.het; wait 8 transparency 80 :17.het; wait 8 transparency 75 :17.het; wait 8 transparency 70 :17.het; wait 8 transparency 65 :17.het; wait 8 transparency 60 :17.het; wait 8 transparency 55 :17.het; wait 8 transparency 50 :17.het; wait 8 transparency 45 :17.het; wait 8 transparency 40 :17.het; wait 8 transparency 35 :17.het; wait 8 transparency 30 :17.het; wait 8 transparency 25 :17.het; wait 8 transparency 20 :17.het; wait 8 transparency 15 :17.het; wait 8 transparency 10 :17.het; wait 8 transparency 5 :17.het; wait 8 transparency 0 :17.het; wait 8 Is it possible to use the “frames” function in transparency to achieve the same? Assuming that transparency is set to 100% and I want to fade in of course. transp 0,a :17.het frames 160 Best regards // Gustaf

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making a movie of sliding through contours
by Pranav Shah 10 Jun '18

10 Jun '18

Dear Developers, Would it be possible to make movie clips of electron density map at different density thresholds in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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scolor filament (geometry cylindrical)
by René Frank 08 Jun '18

08 Jun '18

Hello People, I would like to surface colour a filament within an EM map using cylindrical geometry (scolor geometry cylindrical). However, the electron density of the filament does not lie perfectly on the x, y or z axis. Is there a way of using two marker points placed at each end (on the longitudinal axis) of the filament to define the orientation of the cylindrical geometry and scolor the filament accordingly? My attempts to do this whilst executing the following command didn’t seem to work: scolor #0 geometry cylindrical axis sel cmap 5,gold:10,red:15,blue Many thanks for any suggestions/help, R. ====================== Dr René Frank ======================

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Re: [Chimera-users] Question Regarding on Finding Distances
by Tom Goddard 05 Jun '18

05 Jun '18

Hi Padua, Search online to find how to update your Windows graphics driver. Unfortunately for old laptops, there may not be any new graphics driver. Tom > On Jun 5, 2018, at 1:01 PM, Xiong, Padua L wrote: > > Hi Tom, > > After following what you have said, under the Gathered Information provided from the Bug Report Dialog I have found: > > OpenGL Vendor: Microscoft Corporation > OpenGL Renderer: GDI Generic > OpenGL Version: 1.1.0 > > Because everything is listed as you have said, I can see that this problem is occurring because of the graphics driver. > > Thank you so much for your fast response. > > Padua > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, June 5, 2018 1:48:07 PM > To: Xiong, Padua L > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question Regarding on Finding Distances > > Probably your graphics driver is not adequate. You can check what driver Chimera is using with Chimera menu Help / Report a Bug under “Gathered information” it will list OpenGL Renderer and Version. If it says Microsoft GDI 1.1 then you are using 1990s graphics and Chimera won’t do selection. You would need to update your driver. > > Tom > > >> On Jun 5, 2018, at 12:26 PM, Xiong, Padua L wrote: >> >> Hi there, >> >> My name is Padua and I'm an undergraduate research assistant working on pharmacogenomics. To do this, I have been using your program UCSF Chimera. >> >> I've been trying to find the distances between a protein and a drug but keep running into problems with selecting an atom in the graphics. When I try doing Ctrl-click or Shift-Ctrl-click to select an atom, I don't select anything at all (nothing is highlighted green as its supposed to when something is selected). >> >> My professor I'm working under has tried changing the mouse settings as well. Is there something I'm missing that's not listed in the User's Guide and tutorials? >> >> Much thanks, >> >> Padua >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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