- 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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Reg: Peptide Dimer
by Amit Jaiswal 30 Sep '14

30 Sep '14

Hi, I would like to know if is it possible to prepare peptide dimer In Chimera. If yes, how and if no what are the possible ways to prepare it? Thanks in advance. With kind regards, Amit Jaiswal -- *Yours Sincerely,* *~~~~~~~~~~~~~~~~~~~~~~~~**~~~* *Amit Jaiswal,* *A.T. Road, Tarajan,* *Jorhat - 785001,* *Assam.-------------------------------------------* *Centre for Bioinformatics,Pondicherry Central University,* *Pondicherry - 605014,* *Pondicherry. * *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*

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Proposal to add ability to load CATH domains in Chimera
by Tony Lewis 30 Sep '14

30 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please may I propose an addition to allow users to access our CATH domains in the same way that they can currently access SCOP domains ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/scop.html )? PDBs for CATH domains can be loaded from URI's of the form: http://data.cathdb.info/latest_release/pdb/1cukA01 For information, CATH domain IDs contain 7 digits: - 1-4 : (eg 1cuk ) : PDB code - 5 : (eg A ) : chain code - 6-7 : (eg 01 ) : 2-digit domain number ( '00' for whole chain domains ) We here at CATH would be very happy to provide any other information required to implement this. Many thanks for your help. Kind regards, Tony Dr Tony Lewis Orengo Group UCL

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Regarding organic molecule minimization
by Satheesh G 29 Sep '14

29 Sep '14

Dear Sir, The azo compounds (organic molecule) minimization using Chimera software giving linear form (R-N=N-R to R-N=N-R (180 degrees bong angle between R-N=N instead R-N=N- 120 degrees). Which is not true. I have used the gasteiger and amber ff12sb force field. Please suggest me to solve this problem. Thanking you. Satheesh. [image: Inline image 1]

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Select next residue
by Tom Goddard 29 Sep '14

29 Sep '14

Hi Yanyan, I added three new keyboard shortcuts. “rn” selects the next residue after the currently selected one and the currently selected one gets unselected — basically it just moves the selection down by one residue. This applies even if a several residues are selected, the whole selection just gets moved down the chain by one position. “rp” selects the previous residue, and “ri” selects all residues between two currently selected residues. These should help you move the selection along in a quick way. Chimera keyboard shortcuts are not enabled by default. To enable them use the Chimera command “ac” (stands for accelerators) or use menu entry Tools / General Controls / Keyboard Shortcuts and click “Enable keyboard shortcuts”. If you use that menu entry then it will be remembered and shortcuts will be enabled when you start Chimera the next time. Shortcuts are all 2 letters and you don’t hit return after typing one. To get back to typing a command instead of a shortcut use the shortcut “cl” (command line). Here’s the list of shortcuts from the Chimera documentation. http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ali… The new ones will be in tomorrow’s daily build (dated Sept 27, 2014). Tom On Sep 26, 2014, at 7:10 AM, Zhao, Yanyan wrote: > Hi, Tom. > > Thank you so much for the chimera lecture yesterday. It is very helpful. > I'm Yanyan from Baylor college of Medicine and is a rotation student in Wah's lab now. I'm using this software now. But I have a problem finding the keyboard shortcuts for selecting residues. I want to select residue one by one along the whole chain. But Ctl+left mouse click is a pain when dealing wit so many residues. Is there any shortcuts that I don't need to click the mouse and still can flow through the chain? > > Thanks. > > Best regards, > Yanyan

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running chimera on FC20
by David Roberts 29 Sep '14

29 Sep '14

Hi all, I just did a clean install of FC20 on an AMD dual core system. I opted for the 32 bit version, as these workstations are used for multiple things (and I find that it’s just easier most of the time, though 64 bit may be where I need to go eventually). I installed Chimera Version 1.9, Build 39798 on Fedora FC20. When running chimera, my computer constantly freezes. Obviously I’m missing something. I’m not doing anything fancy - I use Zalman monitors connected to generic video cards. I can run coot fine - I don’t know about ccp4i (it seems to run, but I haven’t challenged it in any way). As long as Chimera is not running, my computer runs nicely. I have flash/etc… working fine. Any thoughts on where I should start here? This happens on 3 separate systems (that are essentially the same, but not identical clones). I’m assuming I missed something obvious in the install. Thanks Dave

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