- Chimera-users - RBVI Mailing Lists

atoms/residues within a certain distance of another structure
by Terry Nelson 12 Jun '07

12 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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atoms/residues within a certain distance of protein
by Terry Nelson 11 Jun '07

11 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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Re: [Chimera-users] dock prep in batch mode?
by Eric Pettersen 11 Jun '07

11 Jun '07

On Jun 9, 2007, at 7:52 AM, figo wrote: > I have seen your solution to the dock > prep in batch mode (http://blur.compbio.ucsf.edu/pipermail/dock- > fans/2007-May/001043.html ) , but when I run the command : > chimera --nogui pdb:1gcn dockprep.py , the chimera want to Fetch > protein 1gcn from web site www.rcsb.org, I have download the > entire PDB, so how can I specify the PDB path to the chimera? Thanks. If you have the PDB files laid out the same way that the RCSB distributes them (e.g. entry 1GCN is in gc/pdb1gcn.ent) then Chimera will automatically look in /mol/pdb and /usr/mol/pdb for them. To have it look elsewhere you need to edit the file <your Chimera installation>/share/chimera/pdbDir and follow the reasonably simple instructions contained in that file. The drawback is that you will need to do that edit every time you install a new Chimera. Putting a better mechanism in place is on our to-do list. Other alternatives include putting the full path to the PDB file in your command, or putting all the files you need into one directory and using the PDB preferences (Favorites...Preferences...[change to PDB category]) to get Chimera to look in that directory. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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rmsd and display queries
by bala 09 Jun '07

09 Jun '07

Hello, 1) Basically i hav three conformations (only 3 pdb) of the same molecule picked up from three different regions of a simulated trajectory. I hv to calculte rmsd and superimpose structure. I tried the emsemble match but it seems that it can work on only two conformation. Kindly suggest me how i can overcome this. 2) Is it possible to create a substructure (subset) of a molecule and do rmsd calcutn and superimposing only on the substructures for the conformations i have.

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New to the board
by Campbell, Patrick 08 Jun '07

08 Jun '07

Hello, I am a grad student and have only been recently been introduced to Chimera. I have a quick question which I hope, someone will be able to assist me with. I am looking at a pdb protein, 2NEF which is composed of 40 NMR structures. I was able to isolate one of the chains and was wondering if a. It is possible to change part of the sequence on the chain (from AAAA to EEEE for instance). b. Is it possible to then use the changed sequence (B) to morph it against the original 3d sequence (A) c. Is it possible to align the changed fragment of B with the original A d. Could the changed sequence (B) be saved for future use or does one have to go through the process of creating it each time it is used on CHIMERA? thanks much pat

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Re: [Chimera-users] rmsd and display queries
by Elaine Meng 08 Jun '07

08 Jun '07

On Jun 8, 2007, at 12:06 AM, bala wrote: > Hi Elaine, > Thank you for your inputs. I think i didnt mention my second query > reg. substructure creation clearly, > I hve a 20 mer duplex RNA, i want to visualize only a few base > pairs at the middle. Is there any way that i can select, display > and do actions only the portion of interest and undisplay other > portion > Bala Hi Bala, Of course. The general procedure is to (1) select what you are interested in (2) invert the selection so now it contains only what you are *not* interested in (3) hide or delete the selection (if you're confident you won't want the other parts, deleting will make later steps simpler) (4) if you only hid rather than deleting, now select the parts of interest again, and use the Actions menu to work with those parts There are many different ways to do each step, too many to describe in this mail. Below, I'll just give an example using commands, but be aware that selection can also be done with Ctrl-click and arrow key operations, or with the Select menu, or using the Sequence tool: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html Commands example: open 6bna sel :4-8.a,5-9.b sel invert delete sel Then carry on with what is left, using commands or the menu as you prefer. I hope this helps, Elaine ----- 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

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Re: [Chimera-users] IMOD mesh/surface colors
by Elaine Meng 07 Jun '07

07 Jun '07

Hi Jeff, There are two general reasons why the *displayed* marker radius and link radius might not equal the values shown in Volume Path Tracer. In the following explanation, atom = marker and bond = link. (1) The atom or marker is in the "ball" representation rather than "sphere." displayed ball radius = (ball scale)(atom radius) where the default ball scale is 0.25. You could - change the atom to the "sphere" representation, which uses the full radius. "Actions... Atoms/Bonds... sphere" or the command "repr sphere sel" will change the selected atoms to the sphere representation. or - stay in the "ball" representation but change the "ball scale" factor to 1.0 (I'll describe how to get to this parameter below) (2) Similar to the markers, displayed bond or link radius = (stick scale)(bond radius) You could make sure that the "stick scale" factor is 1.0. It probably already is, since that's the default. Of course, the bond or link should also be the stick representation, not wire. Volume Path Tracer automatically makes them sticks when the radius is >0, however. In the Model Panel, if you click the IMOD contours model (or any molecule model) on the left and "attributes..." on the right (or just double-click the model on the left), that opens the molecule model attributes panel. In there you can see and change the ball scale and stick scale values. In your example file trial2.mod, I selected a few markers and links and set all their radii to 20. After I changed the marker to sphere, it did match up in size with the connected link. The more I zoomed in, the better it looked. It may be a level of detail issue if they don't look matched up when zoomed out. You can increase the number of subdivisions used to draw the spheres/cylinders with subdivision quality in Effects (under Tools... Viewing Controls). The parallel links did not quite touch, however, but since you said the contours were approximately 40 A apart, I think it is working correctly! If you still have trouble, though, let me know. I hope this helps, Elaine ----- 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 On Jun 7, 2007, at 12:12 PM, William Jeffrey Triffo wrote: > thanks Elaine, > > another thing I noticed, when I change the marker (atom?) radius in > Volume Path Tracer, it does not appear to change quite right. For > instance, if I set the 'Link' radius to something like '20', and > likewise the Marker radius to '20', they will not be the same size. > > In general when making marker sets, this is not the case, and the > radius acts the same between the two settings. For these markers, > the contours were place approx. 40 A apart, so a marker (or link) > radius of '20' should make the contours 'kiss' when viewed as a > marker set, correct? > > thanks for your prompt response, it would make sense that I would > miss the color setting instructions on the actual page for the tool... > > -Jeff

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Saving images with the povray option
by jean-francois menetret 07 Jun '07

07 Jun '07

I am trying to save images with the povray option using chimera2416, but the camera viewpoint is lower than the center of the scene, so that I just see the bottom of the scene. Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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IMOD scaling and alignment
by Tom Goddard 05 Jun '07

05 Jun '07

Points placed in IMOD may not have proper scale and alignment when opened in Chimera together with the original MRC map. There are some IMOD settings that can fix this. Jeff wrote: > great, > > I don't know if I replied earlier or not, but if the issue comes up > with anyone else, setting the magnitude of the IMOD model (which a > user would typically do in the IMOD tool 3dmod) to be equal in > magnitude to the pixel size listed in the MRC header of the > desired/corresponding volume map is enough to ensure the proper > scaling; the default for units in 3dmod appears to be nm, while in MRC > files it is generally Angstroms. Applying a translation equal to the > origin offset that chimera uses in the MRC header is then sufficient > to co-register the two. > > -J

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Little help to write a python script
by Eduardo Sanz Garcia 05 Jun '07

05 Jun '07

I have previously written command scripts for chimera. Now, I need to do something more complicated that, I believe, is not possible to do from the command line. This is the task: I have a list of 100 electron density maps. 1- I want to display each map, one by one. 2- Change the default threshold. 3- Save an image of the current volume. 4- Close the current volume and open the next model. Has anyone done this before? An example of a python script that can do this or something similar could help me a lot. Thanks in advance.

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Volume segmentation question
by Toby Starborg 05 Jun '07

05 Jun '07

Dear Chimera users. I am new to using chimera, so this question may seem a bit simplistic. I'm trying to use Chimera to examine EM tomographs of fairly busy data sets. I'd like to be able to divide the data into separate features so that I can better understand which parts are noise and which are structural (segmentation). So far I have found the "Pick Surface Pieces" tool is very useful for colouring the surface of features of interest. I have also found it useful to colour some surfaces with 0 opacity to remove items that are in the way, but I would prefer to do this in a more permanent fashion sot that I can return to a data set and quickly compare structures. I have also tried using "Volume Path Tracker" with "Color Zone" and "Split Map by Color" (after adjusting the voxel size to angstroms rather than nm to give a reasonable volume segmentation). My question is would it be possible to alter "Pick Surface Pieces" so that it colours (or tags in some way) all of the voxels within the chosen mesh, so that it would then be possible to split the map into separate compartments that could be saved and examined separately? This would also offer the ability to use different threshold levels to examine different features. I realise that this is more of a wish list than a trouble shooting question, but I'd also appreciate any input from more experienced Chimera/tomography users. Thank you for your help. Toby S -- Dr T Starborg FLS, University of Manchester Michael Smith Building, Rumford Street, Manchester,M13 9PL. UK tel:+44(0)161 275 1557 fax +44(0)161 275 1505

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(no subject)
by Газизов А.С. 04 Jun '07

04 Jun '07

Hello everybody. Is there Fe2+ ion in Chimera? I'm trying to add charges to hem molecule and it always appears to be Fe3+ (and Add Charge tool reports "There is odd number of electrons..." and fails).Assigning odd overall charge helps (i.e. +1, +3, etc), but I need +2...

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problem with chimera-->followup
by Vinay Kumar 04 Jun '07

04 Jun '07

Hello all, Firstly. Greg, Thank you. Though, i have been using the linux OS for quite sometime, i still have a few doubts about upgrading and these sort of things. I have actually gone to mesa3d, OpenGL, and DRI websites. but they contain terms which i am not acquainted with. I have downloaded, MesaLib 6.4.2 and tried installing it as per their instructions, only to find the installation stopping with some error. ( i shall post the error in the next email.) I would like to know, if the installation went well, would i have upgraded X11?? With regards, Vinay. ps- MesaLib 6.5.3 was available, but 6.4.2 was stated to be a stable release hence opted that.

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problem with chimera
by Vinay Kumar 01 Jun '07

01 Jun '07

Hello all, I have been using chimera and dock6.0 on a RHL9.0 system. More recently if i perform simple processes like coloring a molecule in chimera, the display goes blank and also logs me out of the session. meaning, i come back to the graphical login for my system. I am unable to proceed any further as repeated attempts to do simple tasks simply logs me out. Kindly help with suggestions. With regards, Vinay.

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Volume thresholds in Chimera
by Tom Goddard 01 Jun '07

01 Jun '07

Huang, Ren-Huai wrote: > Hi, > > Thanks for your help before. > > Chimera runs smoothly in my Linux computer. It generates very nice images for > EM reconstruction map. > Could you explain the concepts of thresholds of contour used in Volume > histogram? What is the value mean? > Thanks very much in advance, > > Ren-Huai > Thomas Goddard wrote: > Hi Ren-Huai, > > The map values shown in the Chimera volume viewer dialog are the > values that come from the file. Typically the map files do not have > any meaningful normalization. There is currently no facility for > instead showing values in standard deviation units. Chimera also does > not report the mean. These capabilities are on our requested features > list (entry #88). http://www.cgl.ucsf.edu/chimera/plans.html > > The histogram shows the distribution of map data values. The height > is the logarithm of the number of grid points with values in a small > value range. > > Tom >

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Software tools wiki pages
by Bridget Carragher 01 Jun '07

01 Jun '07

Hi there, In preparation for an announcement to go out about the JSB Software Tools Special Issue I am asking people who have entries on the 3DEM Software Tools wiki pages to update these if possible - eg. can you update the ref from the current "in press" to the right reference and also just check that the entry is otherwise up to date. Thanks, Bridget P.S. The url for these pages is: http://en.wikipedia.org/wiki/ Software_tools_for_molecular_microscopy in case you don't have it handy. ------------------------------------------------------------------------ ---------------------------------------------------------- Bridget Carragher, Associate Professor Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, La Jolla, CA 92037 tel: (858) 784-9070; fax: (858) 784-9090; bcarr(a)scripps.edu; http:// ami.scripps.edu National Resource for Automated Molecular Microscopy: http:// nramm.scripps.edu ------------------------------------------------------------------------ ----------------------------------------------------------

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ESP grid is offset from original PDB coordinates??
by Kenward Vaughan 30 May '07

30 May '07

I was playing with esp results yesterday from Delphi on several structures, and ran a quick calculation on 2ace. To my surprise, the results as visualized as a solid under volume viewer were very obviously offset from the structure itself. They stand alone to one side of the original. I've attached a small jpg of this. I'm using the latest Linux production version (beta version 1 build 2415) on an amd64 box (Debian Sid, kernel 2.6.20). I hope there is a simple explanation... ;-) I am no expert with Delphi, so something may be odd there. I used a couple of the siz/crg files, with the same results in each case, so I suspect something in the original pdb file is messing things up? Cheers! Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???

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Python script for reading volume values at atom positions
by Tom Goddard 30 May '07

30 May '07

Hi Terry, Here is a Python script to read a volume map and a PDB file and print the values of the map interpolated at the atom positions. It will work without the Chimera graphical user interface. I tested it in Chimera 1.2415. Tom # ----------------------------------------------------------------------------- # Script that opens PDB and map files and prints the map values interpolated # at each atom position. Can be run without graphical user interface: # # chimera --nogui avalnogui.py # def map_values_at_atoms(pdb_path, map_path): # Open map file. # File name has to have file suffix indicating volume format. from VolumeData import open_file data = open_file(map_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map = Data_Region(data, full_region(data.size), '', ro) attribute_name = data.name.split('.')[0] # Open PDB model(s). from chimera import openModels molecules = openModels.open(pdb_path, 'PDB') # Interpolate map values at atom positions. from AtomDensity import set_atom_volume_values for mol in molecules: set_atom_volume_values(mol, map, attribute_name) # Print values. for mol in molecules: for a in mol.atoms: v = getattr(a, attribute_name) print '%-15s %12.4g' % (a.oslIdent(), v) # ----------------------------------------------------------------------------- # map_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.omap' pdb_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.pdb' map_values_at_atoms(pdb_path, map_path)

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Color in Chimera
by Albion Baucom 25 May '07

25 May '07

How do I determine the exact color value of a model from a previous session? I want to open a session, determine the color of a selected chain, and then color another chain that exact color. I can't seem to find an "eye-dropper" or other comparable tool to determine the color value (RGB, hex, etc). Thanks. Albion

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Chimera release candidate
by Elaine Meng 24 May '07

24 May '07

Hello everybody, A new version of Chimera (1.2415) is available for all platforms: http://www.cgl.ucsf.edu/chimera/download.html It is a candidate for a production release we plan to make in about a week. Many new features have been added since our last production release (1.2304, October 2006), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/1.2415/docs/relnotes/snapshot.html Here are just a few of the changes since last October: - embedded POV-Ray for production of glossy, shadowed images including labels - ability to supersample or to use POV-Ray when recording movies - new input formats: MDL MOL/SDF, Gromacs trajectories - new Fetch by ID types: EDS (fo-fc) electron density difference map, PQS predicted biological unit - Presets menu with display settings for interactive Chimera use or generation of publication images - Side View includes "top view" for interactively adjusting stereo parameters and perspective - expanded morphing capabilities - new Fit Map in Map tool - new windowsize command - updates to handle new naming conventions in the remediated PDB Enjoy! (and do let us know right away via "Report a Bug" or chimera- bugs(a)cgl.ucsf.edu if you find any problems) Thanks, Elaine ----- 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

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Re: [Chimera-users] fit map in map
by Thomas Goddard 24 May '07

24 May '07

Hi Gabor, There are no Chimera commands to fit one map into another, but it can be done with a Python script. I've attached a Python script that I made by piecing together code from gui.py and __init__.py from directory chimera/share/FitMap. Tom Gabor Papai wrote: > Hi Tom, > > Can the fit map in map tool be used without the GUI and retreive back > only the transformation matrix? > Bye, > Gabor > # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)

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Electrostatical surface of a virus
by Eduardo Sanz-Garcia 23 May '07

23 May '07

I need to visualize the electrostatic surface of a virus. I don't know how to do it. I was thinking in the following sequence of instructions: 1. Use the DelPhiController to generate the potential map (*.phi) for the asymmetric unit. 2. Use Multiscale Models tool to generate the 60-related units. Is this a logic sequence ? Any hint would be appreciated. Thank you.

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Mac stereo
by Greg Couch 23 May '07

23 May '07

To deal with the issue that the Mac OS X's X11 doesn't work with stereo very well, we have decided to release an Aqua version of chimera concurrent with production releases of the X11 version. The Aqua version will be labeled as a snapshot because we still recommend using the X11 version (the user interface works much better than the Aqua version). But if you need stereo, multisampling (full window antialiasing), or background transparency/opacity, then you need to use the Aqua version. Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] Virus Images for the MSD Database
by Tom Goddard 23 May '07

23 May '07

Hi Jawahar, Unfortunately Chimera is not able to save images without displaying the graphical user interface. The image saving code grabs the image directly from the main window OpenGL graphics buffer, so it also will not work if the main window is covered or iconified. Greg Couch once made a special version of Chimera for Linux using the OSMesa graphics library that could do all the graphics off-screen including saving images. But I don't see that version in the Chimera download archive, and I believe it was made more than a year ago. We recently added raytraced image capture using POVray. Since that does not use the OpenGL graphics it should be able to work in nogui mode but a Chimera bug report indicates that does not work http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3678&database=chime… and is expected to be difficult to fix. Unfortunately the only option at this time is to have the Chimera window appear to save an image. Tom Jawahar Swaminathan wrote: > Dear Tom, > We are interested in making virus capsid pictures for the MSD Database > atlas pages using chimera. For this purpose, I was recently provided > with a script from Cathy Lawson (RCSB) which makes really pretty > images of viral capsids. I attach the script given by Cathy below. > > However, since we would want to run chimera in an automatic manner > (ideally with the --nogui) option, I've been trying to run the script > with --nogui and this appears to conflict with the module tkgui which > is called in the program. > > So my question: is it possible to make images without necessarily > opening up a GUI ? > > I would be really grateful if you could clear this us.. > > best regards, > > Jawahar Swaminathan > PDB Depositions > Macromolecular Structure Database > EBI

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Problem with DCD not containing periodic box info when I use MD
by Antoine Daina 22 May '07

22 May '07

Hi Eric, I got a "DCD format error 9" returned by MD Movie in Chimera 1.2304 when trying to see the trajectory of a Charmm simulation without periodic box info. Can we easily fix it ? Antoine Daina, PhD, University of Geneva.

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