October 2014 - Chimera-users - RBVI Mailing Lists

Remove shapes programmatically
by jiserte＠unq.edu.ar 08 Oct '14

08 Oct '14

Hello. I'm having a problem working with shapes in chimera. I'm adding shapes with a script using commands like: shape tube #:1@CA#:100@CA radius 0.1 I want to remove some of the shapes later in the script, however i can not find the proper way to do it. I know is posible to do it using the GUI (picking the shape with control key and then "Actions>Surfce>Hide" in the menu bar), but i dont know how to do the same with the command line. Also, i can not find the way to manipulate existing shapes (increase radius, change color, etc). There is a way to delele, hide or manipualte shapes? Thank you all. Javier Iserte PhD Fundación Instituto Leloir Buenos Aires, Argentina.

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. Tom open 2xyz rainbow chain sym #0 surf true # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 molmap #0 10 sym i,n25r On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: > Dear Tom, > > I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? > I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html > > All the best, > -Reggie > > -- > Reginald McNulty, Ph.D. > Postdoctoral Research Associate > The Scripps Research Institute > Johnson Lab > Department of Integrative Structural and Computational Biology > 10550, N. Torrey Pines Road, MB-31 > La Jolla, California 92037 > > > > > >

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help
by JESSE JAYNES 06 Oct '14

06 Oct '14

I am a long time user of Chimra and greatly appreciate the software. I am also a professor at Tuskegee university and I use it in the classroom. I am Mac user. I have a question. How can I model an all D-form of a 10 amino acid peptide and generate its pdb? Thank you! Jesse M. Jaynes

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delete water residues: mangled atom specifier
by George Tzotzos 06 Oct '14

06 Oct '14

I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one. If I do del :WAT !1355.water I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated Regards George

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Question about RMSD calculation of MatchMaker
by Matthias Fellner 03 Oct '14

03 Oct '14

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. In addition a small question which I guess wont be possible - is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? Thank you Matthias [cid:image001.png@01CFDE66.FDAB5BD0] Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 191 atom pairs is 0.506 angstroms Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 188 atom pairs is 0.551 angstroms Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 193 atom pairs is 0.336 angstroms

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Chimera-users October 2014