- Chimera-users - RBVI Mailing Lists

NAMD trajectory and AMBER topology
by Francesco Musiani 02 Mar '10

02 Mar '10

Hi all, I would like to visualize in Chimera a trajectory obtained with the program NAMD, but I have a .prmtop topology file generated using AMBER instead of a .psf topology file. I have these files beacuse in NAMD is possible to use AMBER format topology. Is it possible to implement an additional feature in Chimera which allows to visualize NAMD trajectory using AMBER topology? Thanks in advance, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin 40, I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it Web: http://bioinorg.agrsci.unibo.it

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load pdb files from local PDB mirror
by Mark Moll 02 Mar '10

02 Mar '10

I have a local mirror of all PDB structures (as pdb files). It’d be nice if Chimera could use this, but it seems that Chimera expects a “flat” directory structure rather than the hierarchical directory structure of the PDB. For example, on my machine the pdb file for 1ady is stored in ${HOME}/pdb/ad/pdb1ady.ent.gz, but when I fetch by ID, the file will not be found. Instead, Chimera will download the file and save it in ${HOME}/pdb/PDB/1ADY.pdb. Is there some way to handle both cases (flat & hierarchical directory structure)? -- Mark

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multi-threading
by Jean-Paul Armache 02 Mar '10

02 Mar '10

Hello, I know that this topic might've emerged earlier, but I was curious whether there were any plans to implement multi-threading into Chimera ? Best regards, Jean-Paul Armache

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Re: [Chimera-users] How are chains paired in morphing?
by Eric Pettersen 01 Mar '10

01 Mar '10

The sequences are in input order unless you ask for the return value to be a dictionary (with the 'asDict' keyword). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 22, 2010, at 11:25 AM, Conrad Huang wrote: > There's a comment in Segment.py: > > # Get the chains from each model. If they do not have the > # same number of chains, we give up. Otherwise, we assume > # that the chains should be matched in the same order > > It uses molecule.sequences() to get the chains. Eric, does > sequences() return the chains in input order, or is it random (eg > hash order)? > > Conrad > > On 2/22/2010 10:26 AM, Thomas Goddard wrote: >> Bobby Laird showed me a homo-tetramer with chains A, B, C, D that >> when >> morphed between two states with the Chimera morph conformations tool >> swapped two of the monomers. In other words the 4 chains from one >> state >> weren't correctly paired with the 4 chains from the other state so >> two >> monomers exchanged positions during the morph. The tetramers were >> built >> from dimers 1pfk and 2pfk by using the symmetry of the unit cell with >> other software (coot?). >> >> How does morph conformations decide which chains to pair? >> >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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saving moved maps
by Erika Mancini 26 Feb '10

26 Feb '10

Dear Chimera users, is it possible, after moving maps around, to save them into their new positions? I tried save map from volume viewer, but maps are saved in their original positions. Thanks! erika

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question
by Huang, Xinlei 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei

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variable surface visualization
by Zambonelli, Carlo 25 Feb '10

25 Feb '10

Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo

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quesitons
by Xinlei Huang 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei Chemistry Department Indiana University-Bloomington

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Re: [Chimera-users] [chimera-dev] run chimera's IDLE in terminal on mac os x
by Eric Pettersen 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 5:34 PM, Yang wrote: > Hi Eric > > I want to manipulate with electron density maps, and just use > chimera functions for reading pdb files and density maps. However, > for high-resolution maps, it takes too long to run the my program on > my mac book. So I want to remotely use the server of our department, > which has much larger memory, to complete this task by typing > commands in terminal. Before that, I had everything done in > chimera's IDLE. So I prefer using chimera functions somehow in > terminal assuming chimera is installed first. > > Thanks for your advice. I think you just want to take whatever commands you were using in IDLE and put them in a Python script (file ending: .py). You can then execute them with "chimera --nogui myscript.py". If you need to supply arguments to the script then instead run it like this: "chimera --nogui --script myscript.py -- arg1 arg2 ...". This is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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version 1.3
by n.prahl＠freenet.de 24 Feb '10

24 Feb '10

Hi everybody, I don`t find a link on your homepage to download the chimera version 1.3. I only find version before or after chimera 1.3. How can I download the version 1.3? I need this version for my studies. Thank you, Nicole Heute schon ge"freeMail"t? Jetzt kostenlose E-Mail-Adresse sichern! http://email.freenet.de/dienste/emailoffice/produktuebersicht/basic/mail/in…

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