- Chimera-users - RBVI Mailing Lists

matchmaker command
by Haas, Ryan Matthew 10 Jul '06

10 Jul '06

Dear Chimera Users, How does the matchmaker command perform its superposition? Is it a C-alpha superposition, or just backbone atoms, or all atoms? Is it appropriate to use these RMSD values obtained from "mmaker" in a manuscript? Help is greatly appreciated. Matthew Haas

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Re: [Chimera-users] script for residues w\in zone
by Eric Pettersen 06 Jul '06

06 Jul '06

On Jul 6, 2006, at 1:54 PM, Sorani, Marco wrote: > Thanks. I'm running Chimera and Python\IDLE on Windows XP. > > a) Can I still use the "script.com" you suggested? You could, by getting a UNIX-shell-like environment such as Cygwin (www.cygwin.com) or possibly just from the DOS prompt. If you don't care if Chimera's interface shows as the script runs, you could just run Chimera and then use File...Open to run the script. > b) When I try "script.py", I can't find the module "chimera" or > "chimera.py". Where should I look? script.py will only work if Chimera is the interpreter, rather than a stand-alone Python interpreter. So you need to either run "chimera -- nogui script.py" using methods like in the previous answer, or open the script using Chimera's main File...Open dialog. --Eric

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script for residues w\in zone
by Sorani, Marco 06 Jul '06

06 Jul '06

Hi, A question: For a given PDB structure (say, 1J4N) and a given point mutation (say, C104K), I want to find all residues within 5 angstroms. Manually, this is easy to do with 'Select' --> 'Zone...', but if I have 1000 mutations, is there a way to automate the process and send results to a file? ****************** soranim(a)pharmacy.ucsf.edu Marco Sorani Program in Biological & Medical Informatics University of California, San Francisco

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calculating charges for Dock
by Joshua D Campbell 28 Jun '06

28 Jun '06

Hello, My name is Josh Campbell and I'm trying to prepare a ligand for docking that is made up of non-standard residues using Chimera. The Dock Prep tool of course does not assign charges to non-standard atoms. I looked at your UserGuide and it said that there were other places to calculate non-standard residues using the Antechamber module, but I could not find any of these tools anywhere in the Chimera program. If you could give me some clarification as to adding charges on non-standard residues, I would be very greatful. I am working with "beta version 1 build 2199 2006/01/24". Thanks. Sincerely, Josh Campbell Harvard Medical School Laboratory of Structural Cell Biology

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select certain transformants of multiscale models.
by Jonathan Hilmer 27 Jun '06

27 Jun '06

Actually, it is possible to use the command line to select portions of a multiscale-models generated volume set: it's just not really efficient. Open your structure and apply the BIOMT with multiscale models. Then select all the surfaces of the multiscale structure. Hide the surface representation and then show a ribbon representation. You might have to wait awhile for this to finish on a large structure. This will generate a new model for each subunit that can be selected manually, via command line, or with the model panel. You can then use the multiscale models panel to make color adjustments, show surfaces etc using selections defined in the command line. However, I can say from experience that learning the Python code is worth the effort in the long run. Jonathan > Hi, > > I'm wondering if it is possible to select specific volumes generated > via the multiscale model tool via the command line? E.g., for a set > of 60 biomt matrices I'm interested in coloring the chains generated > with matrices 1-20 in one color, matrices 21-40 in another color, and > matrices 41-60 in yet another color. Any suggestions on how to > accomplish this would be appreciated. > > thanks! > > Cathy Lawson > > > > *****************************************************************' > Catherine Lawson > Laboratory for Structural Biology and Bioinformatics > Department of Chemistry and Chemical Biology > 610 Taylor Road > Piscataway, NJ 08854 USA > http://roma.rutgers.edu > http://rutchem.rutgers.edu/~lawson > ***************************************************************** > > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Jun 2006 18:18:57 -0700 (PDT) > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] selecting multiscale model volumes > To: cathy.lawson(a)rutgers.edu > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <200606270118.k5R1IvGE1909532(a)guanine.cgl.ucsf.edu> > > Hi Cathy, > > Unfortunately no Chimera commands allow selecting or coloring > multiscale surfaces. The multiscale tool in general is not well > integrated with the other Chimera capabilities -- like the Actions > Color menu won't color chain surfaces that you select with the mouse. > We plan on fixing this in the future but it may take a while (6 months > or more). > > Everything is possible using Python code, although this can be quite > difficult to figure out. It is not documented and the best approach is > to ask for examples from us that you can then modify. Below is code > to color multiscale surfaces with specific matrix subunits and chain IDs. > If you open that file in Chimera (with File / Open..., or with the "open" > command) it will do the type of coloring you requested. When you modify > the code be careful not to change the indentation since this is important > in Python. > > We could easily do a little better and add a Chimera command so that > you would not have to edit a Python script to specify what residue > ranges and colors to use. > > I am going on vacation tomorrow until July 18 but can make that > command for you when I return. It just requires some additional > Python code that Chimera will load at startup. > > Tom > > ---- > Python file mmcolor.py follows: > > # ---------------------------------------------------------------------------- > # Color certain matrix subunits and chains of a multiscale model. > # > def color_multiscale(rgba, model_num, matrix_nums, chain_ids = None): > > import MultiScale > d = MultiScale.multiscale_model_dialog(True) > for cp in d.chain_pieces(): > g = cp.surface_group > if g.model().id == model_num: > mnum, chain_id = g.oslName.split('.') > if chain_ids == None or chain_id in chain_ids: > if int(mnum) in matrix_nums: > cp.set_color(rgba) > > # ---------------------------------------------------------------------------- > # > red = (1,0,0,1) # Red, green, blue, opacity > green = (0,1,0,1) > blue = (0,0,1,1) > cyan = (0,1,1,1) > > color_multiscale(blue, 1, range(1,21)) # Color matrix subunits 1-20 > color_multiscale(cyan, 1, range(21,41)) # Color matrix subunits 21-40 > color_multiscale(green, 1, range(41,61)) # Color matrix subunits 41-60 > > # Example coloring subunits 1-20, only chains 'A' and 'B'. > #color_multiscale(red, 1, range(1,21), ['A', 'B'])

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new snapshot release
by Eric Pettersen 27 Jun '06

27 Jun '06

We just put out another snapshot release (1.2255), principally to improve Antechamber reliability (particularly on Windows), but it nonetheless has a few other significant improvements: If you have Modeller installed, the Model Loops extension (very much under development) can fill in missing sections of structure. The defaults for Movie Recorder have been changed to improve playback performance and the ability to produce .avi files has been added. Multalign Viewer can add plain-text sequences to an existing alignment. Volume Viewer can display meshes as squares instead of just triangles. The "reset" command can interpolate between saved positions (i.e. positions in "savepos" commands) to ease creation of scripts involving motion. A new "Alignments" tutorial covers MatchMaker and Match->Align capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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selecting multiscale model volumes
by Cathy Lawson 27 Jun '06

27 Jun '06

Hi, I'm wondering if it is possible to select specific volumes generated via the multiscale model tool via the command line? E.g., for a set of 60 biomt matrices I'm interested in coloring the chains generated with matrices 1-20 in one color, matrices 21-40 in another color, and matrices 41-60 in yet another color. Any suggestions on how to accomplish this would be appreciated. thanks! Cathy Lawson *****************************************************************' Catherine Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology 610 Taylor Road Piscataway, NJ 08854 USA http://roma.rutgers.edu http://rutchem.rutgers.edu/~lawson *****************************************************************

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Making aliases persist
by Jeramia J Ory 26 Jun '06

26 Jun '06

I have some students this summer who are using Chimera to check out ligand anomalies in the PDB, and have fallen in love with the 'alias' command, no surprise. Is there a way to have them persist between sessions, or save them in the preference file somewhere? I imagine piling them all into a file and then having them 'read' it each session would work, but I thought I would see if there is a better way. Thanks, Jeramia Ory

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question
by Jaya Bhatnagar 26 Jun '06

26 Jun '06

Hi, Is it possible in chimera to define a new amino acid residue? Also, what algorithms does it support involving docking of two proteins? And is there a limit on number of amino acids present in the protein? thanks a lot, Jaya

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Selecting from a surface area
by Miguel Ortiz-Lombardia 26 Jun '06

26 Jun '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'd like to pick an area of a (msms) surface (like with a "lasso" tool) and from that area, select the atoms/residues from which it is built. I haven't found anything like this in the documentation, so I'm afraid it's not possible. Or is it? Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFElFsPF6oOrDvhbQIRAiLYAJ9NHoF7sHbXJnZijo9Gfv8z9HJatQCfb9XQ 9q3hYNVjsZjVslF3Hv9+8ZU= =5dnB -----END PGP SIGNATURE-----

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