June 2018 - Chimera-users - RBVI Mailing Lists

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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Question Regarding on Finding Distances
by Xiong, Padua L 05 Jun '18

05 Jun '18

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

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Atom Specification not working in exported PDB
by Gustaf Olsson 04 Jun '18

04 Jun '18

Hello again Chimera Users So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number. PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like show :17 ~show @536-593 Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the show :XXX works as intended though this affects all residues XXX and I only want to affect residue 17. Am I doing something wrong or can I solve this in a simple way? Best regards // Gustaf

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Place marker at centre of volume box python command
by Kyle Morris 01 Jun '18

01 Jun '18

Hi Chimera dev, Is there a python command to place a marker at the precise centre of a volume’s box, regardless of the centre of mass of the volume in the box? I have played with creating dummy volumes and measuring their centres but it’s clunky and got a bit stuck with doing this. A single command would be cleaner, if it’s possible. As always thanks for your help! Best wishes, Kyle

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Command line syntax questions
by Divita Mathur, Contractor Code 6910, FN 01 Jun '18

01 Jun '18

Hi I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): 1. Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B. 2. Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18. 3. Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule. Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise! Best, -- Divita Mathur Postdoctoral Research Fellow Center for Bio/Molecular Science and Engineering Naval Research Laboratory Washington DC 20375 (202) 767-0687 (Office) divita.mathur.ctr.in(a)nrl.navy.mil

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Chimera-users June 2018