- Chimera-users - RBVI Mailing Lists

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 26 Jun '06

26 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 26 Jun '06

26 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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Re: [Chimera-users] question
by Goel, Manisha 26 Jun '06

26 Jun '06

Hi Elaine, I too have been looking for a good protein-protein docking program, so I am jumping on the bandwagon .. Just small question regarding point 2 in the mail .. Does chimera do any minimization/optimization of the complex after we manually dock the two protein together ? Thanks a lot for your help.. Regards, -Manisha -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Monday, June 26, 2006 11:34 AM To: Jaya Bhatnagar Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] question Dear Jaya, (1) Chimera will display whatever coordinates and residue names are present in the input file. It does not matter if the residues or the atoms in them are standard or not. However, you cannot define new residues to be built by Chimera with the "swapaa" or "addaa" commands. We have recently added a Build Structure tool (Structure Editing category) that lets you add arbitrary atoms and bonds to structures interactively. It is in the early stages of development, however, and is likely to change in the future. If you use this, you may want to check the bond lengths and adjust them in the "Set Bond Length" section of the Build Structure tool. The man page for Build Structure: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html (2) Chimera does not do any automated docking. However, you can manually/interactively dock structures by moving one relative to the other (to freeze a structure and move only the others, you would uncheck its Active button in the Model Panel or its checkbox under the Command Line). The man page for the Model Panel: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html (3) I believe there is no limit on the number of amino acids present in the protein. There may be limitations due to the input file format (that is, the residue number column can only be a certain width in the input file format, usually PDB). However, in combination with use of different chain IDs this limit is quite high. For example, ribosome structures can be viewed in Chimera, although it may take a while for the structure to load. I hope this helps, Elaine On Jun 23, 2006, at 8:06 AM, Jaya Bhatnagar wrote: > 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 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Chimera-users Digest, Vol 38, Issue 12
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Thanks to all for the quick responses on interpolation. Here's a quick example showing what I was concerned about: arrows.bld ------------------ .color red .arrow 0 0 0 1 0 0 .color green .arrow 0 0 0 0 1 0 .color blue .arrow 0 0 0 0 0 1 ------------------ matrix2 ----------------- Model 0.0 0.505641 0.433743 -0.745785 -2.58211 -0.807506 0.542275 -0.232105 2.90884 0.303746 0.719587 0.624446 -0.194334 ----------------- matrix3 ---------------- Model 0.0 0.60158 -0.458982 0.653787 0.653219 0.190507 -0.712397 -0.675423 5.48737 0.775763 0.530872 -0.341124 0.0103466 ---------------- The first matrix is just unity. The 'reset'-based interpolation works great for going between 1 and 3 or 1 and 2 in both directions, as well as 3 to 2, but fails from 2 to 3. Since all this is new to me, I can't say for certain that this is due to gimbal lock, but that was my first guess. I haven't had the opportunity yet to try out Tom's axis-angle approach, but that should rule out any Euler problems. The other problem for me is that all my current methods are based upon a stepwise approach via commands (ungainly, but very functional when combined with shell scripts, imagemagick etc), and this is incompatible with the 'reset' interpolation. Perhaps it was misleading to mention the use of 'matrixset'. I appreciate that it is more trouble to deal with external files, but if it is not possible to easily implement the interpolation I'm looking for dynamically within Chimera's Python (due to required math libraries, etc) then I would have to hard-code the interpolation matrices into the .py script file anway, defeating the purpose. Thanks for the help: I'd love to hear about any future development in this area.

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Chimera paper virus models
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Ulrich, This week I made 5 paper virus models using the Chimera flatten icosahedron tool. You can have the images I created: http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/ The image files are named according to the Protein Data Bank (PDB) 4 letter id code. The page http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/vipergaller… shows images of the approximately 200 known virus capsids taken from the VIPER web site. http://viperdb.scripps.edu/ I added some comments to the flatten icosahedron documentation a few days ago describing "tiling" of the Chimera image to handle capsid proteins that are cut in half -- so they appear on both sides of the cut. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… I printed my images on standard photopaper. The images above will need to be scaled to fit on a piece of paper. I just asked my web browser to scale them to fit when I printed. One additional note about my images -- I turned on "silhouette edges" to give the black outlines around the proteins. This is done using Chimera menu entry Tools / Viewing Controls / Effects. Tom

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