- Chimera-users - RBVI Mailing Lists

Chimera and DelphiController
by Nihshanka Debroy 31 Jul '06

31 Jul '06

Hi, My name is Nihshanka Debroy, and I am a graduate student at Duke University. I recently joined this mailing list. I was wondering if I could ask a couple of questions about the software. The first one is more related to Delphi. I have been using the Delphi Controller tool in Chimera, and I have been getting warnings that certain radii records are missing from my .siz file, and some residues have a net positive charge. I used the default files provided when installing Delphi. I was wondering if anyone has faced this problem before. Is there an online database where I could get the missing radii and charge values for atoms and residues ? Secondly, I am trying to generate the Connolly surface for certain proteins. What I have been doing so far is running Delphi Controller and assigning a probe radius of 1.4 Angstroms in the Parameter section. I just wanted to make sure that this is different from the molecular surface (MS) that is generated when simply choosing Actions->Surface->Show. Thank you for your time. Sincerely, Nihshanka

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Segmentation Fault
by Donglu Xie 24 Jul '06

24 Jul '06

Hi All, Anybody has met this issue. When running chimera, it only shows "Segmentaion Fault", or " Segmentaion Fault (core dump)". No interface is shown. If you need more information about the system, please let me know. Any help is appreciated. Donglu Xie

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Surface color key
by Alexander Rusnak 20 Jul '06

20 Jul '06

Hey Folks, I'm using Chimera to create a surface colored representation of a virus based on radius. That was not the hard part, my question is how do you make a key to show the scale of coloring. I cannot find that in the documentation, faq nor the server list. If it's there and I missed it sorry but you point it out to me and if it's not an option any suggestions on how to create one. Thanks. Alex

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write out adjusted EM map?
by jbrown 20 Jul '06

20 Jul '06

Hi, I've recently used Chimera to manually fit several PDB subunits into my EM map. I am trying to figure out a way to write out the EM map in CCP4 format with the adjusted rotation/translations that I performed during my fit. Is there anyway to do this in Chimera (or are there any other programs you would suggest)? Also, any plans to include a means for writing out EM maps from Chimera in future versions? Thanks a lot, Jesse --------------------------- Jesse Brown Research Technician TSRI, Dept. of Cell Biology 858.784.8598 jbrown(a)scripps.edu

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chimera on linux ia64 (sgi prism)
by Sabuj Pattanayek 14 Jul '06

14 Jul '06

Hi, I was wondering if there is a port for chimera to run on Linux IA64 (sgi prism)? The x86 version runs in emulation mode on the system, thus the graphics defaults to Mesa indirect glx (really slow). Would a dev be willing to port it for this system if given access to the system? I'm also working on getting pymol compiled for it. vmd already has a native port with good performance. Thanks, Sabuj Pattanayek

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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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