- Chimera-users - RBVI Mailing Lists

defining a putative binding site
by Francesco Pietra 18 Feb '09

18 Feb '09

Hi: I need to define a putative binding site for a smaller protein upon a larger one. The task is creating a table of likely interactions between residues of the larger proteinseparated by less than 5 A from those of the smaller protein. Deriving from molecular dynamics, all residues for both proteins are in the same pdb file, alongside lipid, water, etc. I wonder whether the most appropriate way is to separate in two different pdb files the lines belonging to the two different proteins. Then: sel #0:20,30-40,55 & #1:1701-1793 z<5 where "0" is the larger and "1" is the smaller protein. If OK, can the results be obtained in a table form? Thanks francesco pietra

2 1

Re: [Chimera-users] color changes
by Elaine Meng 17 Feb '09

17 Feb '09

On Feb 17, 2009, at 1:15 PM, Jean-Paul Armache wrote: > hello, > i have one question concerning color manipulation in chimera. > every pdb file one opens gets a specific color (if set so). so, > having a few of them open, one can distinguish > between them color-wise. > now, when one selects the files, it is possible to change the color > via actions->color. this indeed changes all > of the things selected, and if the whole pdb was selected, all the > chains there. when one looks then into the > model panel, the old colors are still there - untouched. this would > be reasonable in the case when only parts > of the pdb were selected and re-colored. however if one selects > whole files and changes the colors - is it > possible to have these colors changed also in the model panel? and > is it possible to revert to the old color > once changed through this action menu? > > best regards, > jean-paul armache Hi Jean-Paul, It is because there is a coloring hierarchy: the Model Panel shows the model color, but you can also set atom colors, whichoverrule and hide the model color. As you found, Actions... Color and the "color" command set the atom colors (otherwise you would not be able to make different parts of the same model different colors). If you already colored the atoms of a model, you can "uncolor" some or all of them to reveal the model color using the command "~color". Another way is to choose "Actions... Color... from editor" and then click the "No Color" button in the Color Editor. (The Color Editor can be found in the menu under Tools... Utilities) You can change the model color with the command "modelcolor" or by clicking on the square color wells in the Model Panel to call up the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/coloring.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html> 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

1 0

surface view of large file in chimera
by G.-Q. Hu 17 Feb '09

17 Feb '09

Hello, I am trying to show a large file by surface view in chimera. But I found that the structure lost the detail and the surface was smoothed. I guess there is a sampling problem for large file. Is there any way to view the large file at the original resolution? Thanks. Guiqing

2 1

Volume->Fit in Map question
by Keren Lasker 17 Feb '09

17 Feb '09

hello, Is there a way to fit a density map to a pdb rather than a pdb to a density map ? Or in other words, that in the end of the fitting procedure the map would move to best fit the model rather than the other way around. thank you, Keren Lasker.

2 3

configuration file for chimera
by Bala subramanian 17 Feb '09

17 Feb '09

Dear chimerians, Sorry if this question has been asked before. Where can i fix the default parameters for chimera. I explored the preferences option in favourites menu and set chose some preferences. In addition to that I want to the following like setting the color of carbon atoms as green as default setting the color of hydrogen atoms as white as default setting some macros setting the command line option when the chimera starts up (every time i go to favourites and click command line to invoke it) and other settings something like the configuration file used for vmd (.vmdrc ). Thanks in advance, Bala

3 2

stereo view
by Francesco Pietra 16 Feb '09

16 Feb '09

Hi: I would greatly appreciate advice about the following requests (between "".."") by the referees (interaction between two proteins; graphics by chimera): 1) "there is way too much wasted black space in figures". As the complex of proteins is elongated along one axis, I found it unavoidable to have wasted space around. Perhaps using a white background in the hope that white is less offending than black? Or is it a way to tailor the background according to the shape of the object? 2) "a stereoview might be helpful for better understanding". How to fulfill this request with chimera I have no idea. 3) "a molecular surface representation of the docking site would be useful". I read on passing about molecular surfaces on this forum. Is that feasible for the highly complex situation of 3D perspective with so many atoms at different "layers"? Thanks indeed for answering francesco pietra

3 2

Consurf .chimerax file under linux
by Boaz Shaanan 16 Feb '09

16 Feb '09

2 1

Re: [Chimera-users] Chimera 3D labels
by Elaine Meng 16 Feb '09

16 Feb '09

On Feb 16, 2009, at 6:53 AM, nettles wrote: > > Dear Elaine, > I'm thinking this should be possible, but don't know how to do it. > Can the labeling function in Chimera could be made more spacially > flexible? > > An example is below. The residue label coordinates are anchored to > a fixed 3D point that may, or may not be desirable for a given > view. Can this be adjusted? > > It looks like these references may be set at centroids. Maybe one > could have a toggle switch that sets the anchor projected a certain > distance from a C-alpha along the viewing vector. That might give > quick access unified text float-over > > Thanks again for such a great tool. > Jim [attachment removed by Elaine] Dear Jim, I am frequently irked by the same issue. Currently residue labels are anchored at the centroid of the displayed atoms, whereas sometimes it would look better if they were anchored at the alpha- carbon. I've previously created a bug report about this. Longer term we would also like them to be movable with the mouse, but that also can't be done currently. Here is the bug/request tracking info: http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6866 http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/167 One current workaround is that you can label some particular atom in the residue with residue information. However, currently that atom must be explicitly displayed (won't work to label some backbone atom if ribbon is shown and suppresses that atom... which I've also complained about!). Commands to do that: labelopt info residue la @ca [or if ribbon is shown, "la @cb" instead if you can live without the glycine residue labels] 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

1 0

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')

1 0

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

1 0