- Chimera-users - RBVI Mailing Lists

Animating a C-alpha chain trace
by Tom Goddard 13 Feb '09

13 Feb '09

Hi Matt, A Python script can make a chain trace movie with density display that adds one residue at a time. I've attached an example script and movie. I used the today's Chimera daily build that has a nice 1-layer transparency option. That won't work in earlier Chimera versions. Tom Matthew Dougherty wrote: > Hi Tom, > > Over the last couple years I have moved my animation off the > SGI/IrisExplorer to Chimera/Amira. > > I have one piece of code on Explorer that I have not moved; attached > is a typical animation. > > what is being accomplished is a demonstration of the folding of a > protein based on c-alpha backbone and related density. > starting at the first residue, it proceeds by adding one residue at a > time. > > How would you suggest to move this to chimera? > > Matt > > > > > > > > > > > > > > > # ----------------------------------------------------------------------------- # Trace C-alpha backbone adding one residue at a time and show simulated map. # pdb_path = '/usr/local/src/staff/goddard/pdb/pdb1fav.ent' resolution = 5.0 # Simulated density resolution, Angstroms map_color = (.6,.7,.8,.3) # red,green,blue,opacity. from chimera import runCommand # Open model from chimera import openModels as om m = om.open(pdb_path, 'PDB')[0] # Orient molecule runCommand('turn y 90') runCommand('turn x 30') # Color molecule and background runCommand('rainbow') runCommand('set bg_color white') # Create residue number label runCommand('2dlabel create rlab xpos 0.1 ypos 0.9') # Set display style. runCommand('repr stick #%d' % m.id) m.stickScale = 5.0 # Fatter sticks # Order residues by number and chain id. rlist = m.residues rlist.sort(key = lambda r: (r.id.position, r.id.chainId)) # Hide all atoms. for a in m.atoms: a.display = False # Show density adding one residue at a time. from MoleculeMap import molecule_map atoms = [] map = None for r in rlist: # Accumulate atoms from residue. atoms.extend(r.atoms) # Close previous map. if map: om.close([map]) # Make map. map = molecule_map(atoms, resolution, gridSpacing = .2*resolution, showDialog = False) map.set_parameters(surface_colors = [map_color], one_transparent_layer = True) map.show() # Display backbone atoms. for a in r.atoms: if a.name == 'CA': a.display = True # Update residue label text = 'chain %s residue %d' % (r.id.chainId, r.id.position) if r.isHelix: text += ' helix' elif r.isSheet: text += ' sheet' runCommand('2dlabel change rlab text "%s" color black' % text) # Draw one frame. runCommand('wait 1')

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Re: [Chimera-users] Command Line - Slecting Zone Parameters
by Elaine Meng 11 Feb '09

11 Feb '09

On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote: > Hi all, > I am trying to find all the atoms that lie within a certain > distance from a selected chains. I am able to do this by going to > select -> zone and giving the distance I want and selecting all the > atoms that met my criteria. I would like to do this on command > line. I am unable to figure it out. > Any help would be greatly appreciated. > Thank You > Thiru Ramaraj Hi Thiru, The following command would select all residues with any atom within 4.5 angstroms of your current selection: select sel z<4.5 You could use "za" instead of "z" if you want an atom-based cutoff instead of whole residues, > instead of < to get the atoms farther away, and of course, a different distance. Also, you don't have to use selections. For example, this would color all atoms within 5 angstroms of chain A red: color red :.a za<5 Description of command-line zone specification: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ atom_spec.html#zones> More examples appear in various tutorials: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ attributes.html#part2> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ squalene.html#surfaces> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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maps handling
by Benoit Zuber 11 Feb '09

11 Feb '09

Hi, I want to handle a large number of small density maps (around 1000 maps of approx 50x50x50 pixels). I need to group them (in around 5 groups). Then I need to treat all the maps of each group in a certain way. For example, I would like to change the level threshold for display, or the display style for every maps in a group at once. Also I would like to show or hide all maps of a group at once. The maps are not opened in an order related to their group. I remember someone recently suggested model 'folders' as a new functionality. Has this been incorporated in the latest versions of chimera? Even if it is the case, It would be too tedious to have to click on each individual model to assign it to a group. Similarly a simple command passed at the command line wouldn't be very elegant: I would have to write each volume number since they are unsorted. I suppose a python script would be much more appropriate. The script would have some functions to do tasks like those described above on each members of a group and a function to read group composition from a text file. I looked in chimera's programmer guide for a section on volume handling but I couldn't find much material on that. Did I miss it? What approach would you recommend? I guess I could use runCommand() but there are maybe better ways. Also the script would have to run in interactive mode. I suppose that IDLE would work for that purpose. How should I do that? Open IDLE and import my module? Where can you define the paths that chimera uses to look for packages? Thanks in advance! Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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examples of python scripts
by Bala subramanian 11 Feb '09

11 Feb '09

Dear Chimerians, Can someone help me by providing examples of python scripts written for analyzing structures inside chimera. I have seen the chimera programmers guide but i need some more scripts written for different tasks to understand the way of accessing certain residues or atoms in a structure and extracting its attributes etc. Cheers, Bala

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making movies with CMM files
by Keren Lasker 06 Feb '09

06 Feb '09

hello, Is there a way to generate a movie out of a set of CMM files ( similar to MD Movie with PDB files)? thank you very much, Keren.

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Re: [Chimera-users] [chimera-dev] alias menu
by Eric Pettersen 05 Feb '09

05 Feb '09

On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: > Dear Chimera Developers, > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol recently, > it would be great to have an option for the alias command that > allowed the particular alias to be listed in a separate window and > ran the alias by clicking on the alias name listed there. > > Best regards, > > Tim Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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script command for writing out areaSAS attribute?
by Julius Su 05 Feb '09

05 Feb '09

Hello, Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute? I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values. I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script. Thanks much! Julius

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Is it possible?
by Ahir Utsav Pushpanath 04 Feb '09

04 Feb '09

Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir

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roll command:
by Bui Khanh Huy 01 Feb '09

01 Feb '09

Dear all, I tried the roll command with my model (EM map) open: roll z 30 1 center 50,50,50 Chimera showed msg "wait_frames argument not implemented". Just wonder how to implement that command without the error? Huy

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Calc buried surface area between 2 chains
by Tom Duncan 30 Jan '09

30 Jan '09

I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan

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