- Chimera-users - RBVI Mailing Lists

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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Tips for making density map images.
by Thomas Goddard 21 May '07

21 May '07

Here are some suggestions for making density map images in Chimera 1.2382. White background color. Set with two menu entries Actions/Color/Background and Actions/Color/White. To make white the default use Favorites/Preferences, category Background, set background color button to white and press Preferences dialog Save button. Surface smoothing. Use volume dialog Features/Surface-And-Mesh-Options and click "Surface smoothing..." checkbutton. To make this the default, turn it on then use Features/Save-default-dialog-settings. Close the surface-and-mesh-options panel before saving the settings or it will always be shown taking up alot of space. Image supersampling. Removes saw-tooth edges from saved images that are especially visible with white background. Does this by making a larger image in memory then averaging down to a smaller size. When saving an image you see many small pieces flash by in main window if supersampling is being used. To turn it on use File/Save-image, press the Image Setup button in the save image dialog, then set Supersample to 3x3 in the preferences dialog that appears. Press the Save button in the preferences dialog to make this the default. For Chimera versions after 1.2392 this will look different. Supersample will be an option on the save image dialog. Saving image same size as on screen. To make a saved image the same size in pixels as it appears in the Chimera window press the Get Pixels button in the File/Save-image dialog. In Chimera versions after 1.2392 this will be the default. Silhouette edges. To add black edges around maps that makes it easier to see when part of map is in front of another part use Favorites/Side-view, choose the Effects tab in the viewing dialog that appears, click on silhouette edges. Save raytraced image. Gives glossy appearance and shadows. Use File/Save-image and set "Raytrace with POV-Ray" to True. Make back parts of surface darker. Use Favorites/Side-view and move the right vertical yellow line towards the left. The surface gets dimmer from half way between the yellow lines to the right yellow line. Your eye position in this side view is shown as the square at the left and the red lines indicate how wide your field of view is. If you move the right yellow line (rear clipping plane) it will hide parts of the map -- everything to its right is invisible. Probably want to avoid that. Make recesses in surfaces darker to improve sense of depth. Use Tools/Volume-data/Surface-color. For spherical virus color the surface using "Radius", use 2 colors, Gray pattern, press "Set full range colormap values" to get minimum and maximum surface radius, press Color. You may need to press the Center button if the virus map is not centered at (0,0,0), and also press the "Set full range..." button again in that case. Probably you'll want to modify the minimum and maximum radius to get the best effect, also maybe adjust the two colors. For filaments use "Cylinder radius". Make recesses darker for asymmetric maps. This is a bit trickier than for spherical or cylindrical maps. For ribosomes or other asymmetric maps first create a blurred version of the map using Tools/Volume-data/Gaussian-filter. This tool has to be downloaded separately from the Chimera experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html and installed. Choose a gaussian width of about 1/3 the diameter of the surface (in angstroms, maybe 30 for a ribosome) and press Filter. Use the Tools/Volume-data/Surface-color and color the original map using the gaussian smoothed map. High values of the Gaussian smoothed map are in the interior and should be made a dark color. This makes the perception of depth dramatically better. Tom

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Re: [Chimera-users] [chimera-dev] Protein to ligand shortest distances?
by Elaine Meng 21 May '07

21 May '07

Hi Kate, The Find Clashes/Contacts tool will report all atoms near your ligand and the corresponding distances. However, it does not work with a single strict cutoff, but instead uses the atoms' VDW radii. For example, if you used a cutoff of 0.0 overlap, that would find all atoms with VDW surfaces either intersecting or just touching. It finds all the atoms meeting your specified cutoff criteria, so you would still need to look at the list of results to see which atom is the closest from each residue. There are two cutoff parameters, the amount of VDW overlap and the extra closeness allowed for H-bonding pairs. As mentioned in the manual page, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html the suggested values for these two parameters are: 0.4-1.0 and 0.2-0.6, respectively, if you only want to detect "clashes" (unfavorably close contacts) -0.4-1.0 (negative values) and 0.0, respectively, to detect contacts in general It sounds like you want the latter. Select your ligand (for example by Ctrl-click on one atom and then hitting the keyboard up arrow), open the tool (Tools... Structure Analysis... Find Clashes/Contacts), click "Designate" to specify you want to find contacts of the selected atoms (the ligand) versus all other atoms. Set the parameters to -0.5 and 0.0. In the bottom section check "Write information to reply log" and uncheck the other options. Open the reply log (it's in the Favorites menu). Click Apply and the list of results will be written in the Reply Log window. You could play around with the VDW overlap parameter and when you think you have what you want, you could use the "Write information to file" instead of the reply log. As I mentioned above, you would still have to look through the results to see the closest atom from each residue. The more negative the parameter, the more atoms will be found (including those which are further away from the ligand). There is also a command version of this tool, http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html If you really care that you include all residues with any atom within 5 angstroms, you could do an additional step first: select the ligand, then Select... Zone using 5 angstroms, then use Actions... Write List to save the names of the "selected residues" to a file. You can compare this list to the more detailed results from Find Clashes/Contacts to find the closest atom from each of the residues. I hope this helps, Elaine p.s. I'm sending this to chimera-users too because that is more for user questions, while chimera-dev is more for developer/programmer questions ----- 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 May 20, 2007, at 10:12 PM, khar6039(a)mail.usyd.edu.au wrote: > Hi all, > I'm new to chimera and would like a simple way to zone 5 Angstroms > around a > ligand and then have chimera tell me what the shortest distances are > between these residues and the ligand. Is this possible? > Cheers, > Kate

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Multiple stucture comparision
by Pankaj Barah 19 May '07

19 May '07

Dear all, I have been using UCSF Chimera for structural superpositions for last few days. But while trying to do multiple superimposition for a set of proteins, i am unable to perform it. can anybody give me any suggestion? Regards Pankaj Barah Junior Research Fellow, Phone:+91-9922346120(M) Bioinformatics Centre, +91-20-25692039(O) University of Pune, Pune 411 007,Maharashtra, India. Pankaj Borah MSc Bioinformatics Univ of Madras(HCAS) Mobile number: 09884270481(Chennai)/ 09844514157(B'lore) Home number:(03752)259201 Alt. Mail id: pankajborah(a)gmail.com Group homepage: http://groups.yahoo.com/group/bioinformatrix/ --------------------------------- Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Here's a solution!

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Pub3D database URL
by Elaine Meng 18 May '07

18 May '07

Hi everybody, In a previous message I mentioned Pub3D as a useful source of 3D coordinates (SDF files) for many PubChem entries. The URL for that server is now http://www.chembiogrid.org/cheminfo/p3d Enjoy! 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 Begin forwarded message: > From: Rajarshi Guha <rguha(a)indiana.edu> > Date: May 17, 2007 4:44:53 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Pub3D SDFs > >> I noticed that your Pub3D site has not been reachable for a while. >> ( http://rguha.ath.cx/~rguha/p3d/ ) > > Aah! My Apache redirect failed again :( > > Actually, we have a new URL for it which should be constant (and is > independent of my machine) > > http://www.chembiogrid.org/cheminfo/p3d > > ------------------------------------------------------------------- > Rajarshi Guha <rguha(a)indiana.edu> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > -------------------------------------------------------------------

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mac stereo
by Dougherty, Matthew T. 14 May '07

14 May '07

what is the status of mac quadro fx4500 stereographics on chimera? thanks, matt Matthew Dougherty *** 713-433-3849 *** National Center for Macromolecular Imaging***

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benchmark
by Dougherty, Matthew T. 14 May '07

14 May '07

nvidia quadro fx 4500 macpro Dual-Core Intel Xeon clock 2.66 GHz macos 10.4.9 pci express date 5/11/7 chimera 2382 graphics memory 512 MB main memory 2GB unknown apple graphics driver Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 4439.0 4263.0 827.0 828.0 4344.0 1201.0 11755.0 1YTI (798): 4285.0 4034.0 307.0 307.0 4119.0 475.0 3562.0 2GBP (2575): 3384.0 3217.0 103.0 102.0 3139.0 166.0 1063.0 1GOT (6449): 1833.0 1602.0 41.0 41.0 1702.0 67.0 395.0 2HMG (12189): 461.0 478.0 22.0 21.0 489.0 35.0 143.0 2PDA (18894): 271.0 293.0 14.0 14.0 297.0 22.0 76.0 1YNJ (24369): 211.0 230.0 11.0 11.0 232.0 18.0 56.0 1F4H (33805): 154.0 166.0 8.0 8.0 169.0 13.0 38.0 Matthew Dougherty *** 713-433-3849 *** National Center for Macromolecular Imaging***

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Normal Modes, arrows and more...
by Jean-Didier Marechal 14 May '07

14 May '07

Dear All, I am trying to use chimera to draw arrows of the Normal Modes vectors I previously calculated with charmm. I see different possibilities to provide chimera with the vectors, but how can I draw the arrows? I found a request on the list from Mingfeng Yang that Petter answered in october 2004 regarding a similar problem. Unfortunately the link indicated for VRML does not work anymore. What are the actual features of chimera that would allow me to do something like this ? All the best, JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

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Re: [Chimera-users] imod model viewing
by Tom Goddard 11 May '07

11 May '07

Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote: > Tom, > > I was trying to use the new IMOD file reader and must be doing something > foolish. I downloaded the newest chimera snapshot release (1.2392) and > the imod.zip file and made a new installation. I can load my IMOD > volume into chimera without any trouble. I then "opened" the IMOD model > file (it opened as an "IMOD segmentation" type). That works without > trouble, but I don't ever see the model. Even trying to use "focus" to > bring it into the field of view gives me a blank field. > > It's possible that my model is the wrong type - I'm playing with chimera > in preparation for needing to do something fancy, so I simply created a > set of spheres of different colors and different radii in IMOD, saved > that model and tried to read it into chimera. I thought I'd simply be > able to read this into chimera and see a couple of spheres, but I don't. > I'm sure I'm doing something silly, but figured I'd bother you while I > play around with it. > > David Gene Morgan > University of California at Davis >

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Question about background transparency
by Vanacore, Roberto M 09 May '07

09 May '07

What are the system requirements to run -bgopacity option in a windows machine? I've tried adding to option (--bgopacity) to the startup command but I can not get a transparent background I'm using Chimera 2.2199 Thanks! Roberto Roberto Vanacore, PhD B-3101 Medical Center North Vanderbilt University Medical Center 1161 Twenty-first Ave South Nashville, TN 37232-2372 Phone: 615-322-7306 Fax: 615-322-7381

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contour levels in Morph Map
by Gabor Papai 09 May '07

09 May '07

Dear all, Is it possible with the Morph Map tool to set the contour levels of the two maps differently? For e.g. if I would like to morph between a map, which is obtained from single particle analysis and has the right contour level of 0.2 - and a second map, which is obtained from tomography and has the right contour level of 2.2, it gives weird result. Other question: does somebody consider to make chimera able to read Imagic files? Thanks for the help! Regards, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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chain selection in a multi-conformatin pdb file.
by Hong Liang 09 May '07

09 May '07

Hi Chimera fans, 1. If a pdb file contains more then one struture, how can I select and keep just one and get rid of the rest. Such as 1X95. It is a big mess after Chimera load the the DNA pdb structure. How can I leave just one double helix? 2. Can Chimera do the extension of DNA. Such as 1X95 has the hexamer with the sequence of ATGCAT, can Chimera double it to a dodecamer with a sequence ATGCATATGCAT? It Chimera can not do that, do you know which software has such a function. I tried PyMol but did not get what I wanted. Thanks a lot. Hong

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Defining a zone around a point defined by x, y, z coordinates
by Jean-Didier Marechal 08 May '07

08 May '07

Dear all, We are having difficulties in defining a certain type of selection zones in chimera. Our problem is that we don't want to centre the zone on an atom selection but on one point of the space defined by its 3D coordinates. Typically we want to give chimera the x,y,z coordinates and select all the atoms included in a sphere of 25 angstroms around this point. How can we do so? Thanks a lot JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

3 2

Find Hbonds in batch
by Stefan Bienert 08 May '07

08 May '07

Hello Chimera fans! Is there a way to use chimera for finding hydrogen bonds for tons of molecules? I'm thinking of something like a command line script, which loads a pdb file, fetches the hbonds and writes them to a file. I got around 1000 pdb files and therefore doing everything manually is not an option ;-) greetings, Stefan -- Stefan Bienert Zentrum fuer Bioinformatik Universitaet Hamburg Bundesstrasse 43 20146 Hamburg Germany Email: bienert(a)zbh.uni-hamburg.de Phone: +49 (40) 42838 7345 Fax: +49 (40) 42838 7332

2 3

importing sdf files from PubChem
by Mark Andrake 07 May '07

07 May '07

Hey Folks, It is a relatively new feature to be able to read SDF compound structure files in Chimera. (I have release 2350 for Windows - I will be upgrading to the new snapshot that I just saw while looking around the site) Anyway - I tried with a compound sdf file that I got from PubChem (enclosed) - but seemed to have problems. At first it gave an error shown in the first lines below - and then seemed to say that it opened the files - but no atoms were displayed and no new model ID was generated and put into the Model Panel . Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf I tried various atom selections and displaying all - but it seems obvious that it has not read in atoms and bonds. I have browsed around the documentation and only found a link to the sdf file formats. (I checked this out and tried editing out two of the header lines - ) It seems the error is unexpected end of file past the header. When checking the sdf file format information it seems that the $$$$ should be the only end of file mark - and there is only one at the end of my file. I also tried the whole procedure with a different sdf file from PubChem. Can anyone recognize what is causing the error in the enclosed file? Beyond that - are there other instructions on sdf file use in chimera that I did not see in searching the documentation? Thanks in advance, Mark -- Mark Andrake, Ph.D. Research Associate Fox Chase Cancer Center ICR428 7701 Burholme Ave. Philadelphia, PA 19111 215-728-3654 mark.andrake(a)fccc.edu 16048627 -OEChem-05040716572D 113118 0 0 0 0 0 0 0999 V2000 3.4030 4.5407 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -2.2663 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.5369 5.0407 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9030 5.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9030 3.6746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -3.2663 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 10.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1864 -3.2991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1265 4.0641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8972 -2.1423 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7693 2.3693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6424 -5.4263 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0223 -3.0754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7407 5.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0148 2.0782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 2.7359 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 11.5196 1.7056 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5185 -4.0434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 18.1050 3.8579 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 4.3454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1258 0.9008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5309 1.8086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 0.7337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7573 4.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6399 5.2970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2579 1.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4553 0.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2129 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1874 2.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 4.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5901 1.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1659 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 2.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -1.2663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9007 0.0906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8338 2.9879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2329 -0.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.8123 2.7817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5436 -1.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.4801 3.5260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8757 -2.3485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4586 3.3198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7281 -5.0211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5238 -3.9406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.8470 4.5283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.5133 2.9450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8630 -5.5226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1187 -4.8548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.7139 4.0298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5076 3.0513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1208 4.4296 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2595 5.2953 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3937 5.4340 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2299 5.4876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4493 5.8870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0499 5.1064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8048 2.0774 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6405 1.2975 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9953 0.5745 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0397 -0.3012 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9154 -0.2568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4661 1.8751 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6470 1.5623 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9598 0.7432 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6611 2.7775 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.4187 3.0251 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8409 4.0776 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3409 3.2116 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 5.1607 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3258 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0432 0.7491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2075 1.5290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.9347 1.6684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.6923 1.9160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 1.9207 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 0.5437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7209 2.1377 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7321 2.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2833 -0.3973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4477 0.3826 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.0650 3.5632 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.3074 3.3156 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6860 -0.9457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8503 -0.1658 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.3386 2.4541 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.5810 2.2065 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9261 -2.0921 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0905 -1.3122 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.7114 4.1013 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.9538 3.8537 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 4.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4029 -5.9383 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2283 -6.0236 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5812 -4.5457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7551 -5.3570 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9651 4.5966 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3038 3.8392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1244 2.9876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5087 2.4313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 4 2 0 0 0 0 1 5 2 0 0 0 0 1 44 1 0 0 0 0 2 6 1 0 0 0 0 2 7 2 0 0 0 0 2 8 2 0 0 0 0 2 45 1 0 0 0 0 3105 1 0 0 0 0 9 19 1 0 0 0 0 9 54 1 0 0 0 0 10 20 1 0 0 0 0 10 55 1 0 0 0 0 11 54 2 0 0 0 0 12 55 2 0 0 0 0 13 56 2 0 0 0 0 14 57 2 0 0 0 0 15 58 2 0 0 0 0 16 59 2 0 0 0 0 17 23 2 0 0 0 0 17 27 1 0 0 0 0 17 31 1 0 0 0 0 18 24 1 0 0 0 0 18 28 1 0 0 0 0 18 34 1 0 0 0 0 19 56 1 0 0 0 0 19 57 1 0 0 0 0 20 58 1 0 0 0 0 20 59 1 0 0 0 0 21 23 1 0 0 0 0 21 25 1 0 0 0 0 21 29 1 0 0 0 0 21 30 1 0 0 0 0 22 24 1 0 0 0 0 22 26 1 0 0 0 0 22 32 1 0 0 0 0 22 33 1 0 0 0 0 23 35 1 0 0 0 0 24 36 2 0 0 0 0 25 27 2 0 0 0 0 25 37 1 0 0 0 0 26 28 2 0 0 0 0 26 38 1 0 0 0 0 27 41 1 0 0 0 0 28 42 1 0 0 0 0 29 64 1 0 0 0 0 29 65 1 0 0 0 0 29 66 1 0 0 0 0 30 67 1 0 0 0 0 30 68 1 0 0 0 0 30 69 1 0 0 0 0 31 39 1 0 0 0 0 31 70 1 0 0 0 0 31 71 1 0 0 0 0 32 72 1 0 0 0 0 32 73 1 0 0 0 0 32 74 1 0 0 0 0 33 75 1 0 0 0 0 33 76 1 0 0 0 0 33 77 1 0 0 0 0 34 40 1 0 0 0 0 34 78 1 0 0 0 0 34 79 1 0 0 0 0 35 43 2 0 0 0 0 35 80 1 0 0 0 0 36 43 1 0 0 0 0 36 81 1 0 0 0 0 37 44 2 0 0 0 0 37 82 1 0 0 0 0 38 45 2 0 0 0 0 38 83 1 0 0 0 0 39 47 1 0 0 0 0 39 84 1 0 0 0 0 39 85 1 0 0 0 0 40 49 1 0 0 0 0 40 86 1 0 0 0 0 40 87 1 0 0 0 0 41 46 2 0 0 0 0 41 88 1 0 0 0 0 42 48 2 0 0 0 0 42 89 1 0 0 0 0 43 90 1 0 0 0 0 44 46 1 0 0 0 0 45 48 1 0 0 0 0 46 91 1 0 0 0 0 47 50 1 0 0 0 0 47 92 1 0 0 0 0 47 93 1 0 0 0 0 48 94 1 0 0 0 0 49 51 1 0 0 0 0 49 95 1 0 0 0 0 49 96 1 0 0 0 0 50 52 1 0 0 0 0 50 97 1 0 0 0 0 50 98 1 0 0 0 0 51 53 1 0 0 0 0 51 99 1 0 0 0 0 51100 1 0 0 0 0 52 54 1 0 0 0 0 52101 1 0 0 0 0 52102 1 0 0 0 0 53 55 1 0 0 0 0 53103 1 0 0 0 0 53104 1 0 0 0 0 56 60 1 0 0 0 0 57 61 1 0 0 0 0 58 62 1 0 0 0 0 59 63 1 0 0 0 0 60 61 1 0 0 0 0 60106 1 0 0 0 0 60107 1 0 0 0 0 61108 1 0 0 0 0 61109 1 0 0 0 0 62 63 1 0 0 0 0 62110 1 0 0 0 0 62111 1 0 0 0 0 63112 1 0 0 0 0 63113 1 0 0 0 0 M CHG 2 6 -1 17 1 M END > <PUBCHEM_COMPOUND_CID> 16048627 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 15 > <PUBCHEM_CACTVS_HBOND_DONOR> 1 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 19 > <PUBCHEM_CACTVS_SUBSKEYS> AAADcfB/vABgAAAAAAAAAAAAAAAAAWLFiAAwYAAAAAAAAFgBQAAAHgQECAAADgjB2AQyyYMQAIKoAyXyXHDCAEAhAgAoiBk4ZJgIIDLAkZGEIAhkhCDIyAedyMAPgAQAgAACAAAACAEAAAQAAAAAAAAAAA== > <PUBCHEM_IUPAC_OPENEYE_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_IUPAC_CAS_NAME> (2E)-1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-2-[(E)-3-[1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_IUPAC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate > <PUBCHEM_IUPAC_SYSTEMATIC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate > <PUBCHEM_IUPAC_TRADITIONAL_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_NIST_INCHI> InChI=1/C43H50N4O14S2/c1-42(2)30-26-28(62(54,55)56)16-18-32(30)44(24-9-5-7-14-40(52)60-46-36(48)20-21-37(46)49)34(42)12-11-13-35-43(3,4)31-27-29(63(57,58)59)17-19-33(31)45(35)25-10-6-8-15-41(53)61-47-38(50)22-23-39(47)51/h11-13,16-19,26-27H,5-10,14-15,20-25H2,1-4H3,(H-,54,55,56,57,58,59)/f/h54H > <PUBCHEM_CACTVS_EXACT_MASS> 910.276 > <PUBCHEM_OPENEYE_MF> C43H50N4O14S2 > <PUBCHEM_OPENEYE_MW> 911.008 > <PUBCHEM_OPENEYE_CAN_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1C=CC=C3C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C > <PUBCHEM_OPENEYE_ISO_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1\C=C\C=C\3/C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C > <PUBCHEM_CACTVS_TPSA> 245 > <PUBCHEM_OPENEYE_MONOISOTOPICWT> 910.276 > <PUBCHEM_TOTAL_CHARGE> 0 > <PUBCHEM_HEAVY_ATOM_COUNT> 63 > <PUBCHEM_ATOM_DEF_STEREO_COUNT> 0 > <PUBCHEM_ATOM_UDEF_STEREO_COUNT> 0 > <PUBCHEM_BOND_DEF_STEREO_COUNT> 2 > <PUBCHEM_BOND_UDEF_STEREO_COUNT> 0 > <PUBCHEM_ISOTOPIC_ATOM_COUNT> 0 > <PUBCHEM_COMPONENT_COUNT> 1 > <PUBCHEM_CACTVS_TAUTO_COUNT> 9 > <PUBCHEM_BONDANNOTATIONS> 25 27 8 25 37 8 26 28 8 26 38 8 27 41 8 28 42 8 37 44 8 38 45 8 41 46 8 42 48 8 44 46 8 45 48 8 $$$$

3 2

Suggestion for Metal Geometry Feature
by Walter Fast 07 May '07

07 May '07

Hi Elaine (I think!), I know there is a measure angle feature in Chimera. I have been using this to define metal ligand geometries in our protein structures (for example, distinguishing between square pyramidal and trigonal bypramidal geometries). Maybe if there is enough interest, this could be an automated feature in the future where a metal ion is selected and then all of the ligands and angles are automatically displayed along with an assigned geometry. We've been using the following reference for assigning them. Just a suggestion! Many thanks, Walt -- Walter Fast, Ph.D. Assistant Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

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Re: [Chimera-users] importing sdf files from PubChem
by Elaine Meng 05 May '07

05 May '07

Hi Mark, You're welcome! I tried getting an SDF directly from PubChem, and that caused the same error you sent, again fixed by cutting and pasting the contents into another SDF file. Cutting/pasting (or otherwise getting rid of bad invisible characters) is the way to go for SDFs from PubChem, at least for now. We may take a look at those files (although I doubt there is a high demand for viewing 2D structures in Chimera!). Best, 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 May 5, 2007, at 7:32 AM, Mark Andrake wrote: > Elaine, > > Thanks so much for your fast reply. > I can see from the users group that you guys do such a great job in > responding to user questions and concerns. > > After a quick gaze and trying on my laptop chimera at home - > it looks like there must be a hidden character issue. > I also had tried MS Word and saved it as a txt file > (in case there was some problem in the browser creating the file) > but maybe MS Word does not flatten out the file with just ASCI > characters. > > Next time I will try cutting and pasting through something like > WordPad first. > > In any case your test.sdf opened fine in my laptop chimera. > Thanks so much - have a great weekend! > > Mark > > Mark Andrake, Ph.D. > Research Associate > > Fox Chase Cancer Center > ICR428 > 7701 Burholme Ave. > Philadelphia, PA 19111 > 215-728-3654 > mark.andrake(a)fccc.edu > > > Elaine Meng wrote:Hi Mark, >> I've attached the test.sdf file mentioned in my previous message. >> Best, >> 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 >> >> >>

1 0

selecting a unique ligand structure from multiple copy
by Jean-Didier Marechal 03 May '07

03 May '07

Hi everyone, I am working with different protein structures that have at least two copies of the ligand in their binding site. How could I select only one of them? (I'd like a selection specification that does not require the atom numbers if possible). Cheers JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

2 1

wwPDB Announcement: Release of Remediated PDB Data
by Cathy Lawson 03 May '07

03 May '07

***wwPDB Announcement: Release of Remediated PDB Data*** The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files. The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non- polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards. A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http:// www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp:// ftp.rcsb.org. Both sites share the same directory structure. Starting May 1, the remediated data will be served using gzip compression. Your input is very important to us. PDB users are encouraged to test the remediated data files between now and July 2007. The details of the final transition will be announced on the wwPDB website (http:// www.wwpdb.org) Detailed information about the wwPDB remediation project can be found at http://remediation.wwpdb.org. Comments about the files should be sent to info(a)wwpdb.org. Major announcements will be made at the wwPDB website (http:// www.wwpdb.org) as well as on the individual member websites.

1 0

Ligand structure minimization
by Jean-Didier Marechal 02 May '07

02 May '07

Dear all, I don't know whether my problem falls in "bug" or "user request" category, pcorry if I use the wrong list. I am preparing a course where students will perform some protein-ligand dockings. I was thinking in minimizing the ligand in chimera using the "minimize structure" tool. I have installed the 1.2356 (that's what I thought but the message in the "About UCSF Chimera" pop up window says 1.2376 actually) version of chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to have compatibility problems with numpy. I join here the message given in the reply log file: .... Charges for residue U0E determined Total charge for #0: 1.0000 Running PARMCHK for U0E1.pdb command: /usr/local/chimera/bin/antechamber/exe/parmchk -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0 -p /usr/local/chimera/share/MMMD/parm/gaff.dat Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for calculations. Numeric is only available in Chimera 1.2318 and earlier. Is there an easy way to move around this problem or should I install a earlier version of chimera for the moment? cheers, JD

2 1

How does chimera invoke msms?
by aladdin 30 Apr '07

30 Apr '07

I need to know the solvent accessible surface of a protein, that means the info of solvent accessibility of residues or atoms . If I directly run "msms" with "-af" option, I can get an .area file in which stored such information. But in chimera's surface model, I cannot find what I need. How can I get the solvent accessible info in chimera? Thanks. liren --------------------------------------------

2 1

Re: [Chimera-users] mutating amino acid side chain_deleting single atom
by Gary Laco 24 Apr '07

24 Apr '07

Hi, How can I mutate an amino acid side chain in a protein to another residue using Chimera? Also, how do I delete a single atom on an amino acid (for example a hydrogen). I looked through all the tools and did not find a way to do it. Thanks, Gary Gary S. Laco, Ph.D. Assistant Professor of Biochemistry Lake Erie College of Osteopathic Medicine-Bradenton 5000 Lakewood Ranch Blvd. Bradenton, FL 34211 Office: 941-782-5666 Fax: 941-782-5729 E-mail: <mailto:glaco@lecom.edu> glaco(a)lecom.edu

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movie and 'side view'
by jean-francois menetret 23 Apr '07

23 Apr '07

Is it possible to include the 'side view' during movie recording ? 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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Secondary Structure Editing
by anat＠chem.ch.huji.ac.il 23 Apr '07

23 Apr '07

Hi, I would like to know if it's possible to edit (manually) the secondary structure attribute of single amino acid in the computed sequence given by Chimera (e.g. from strand to helix). Thank you for your help, Anat, the Hebrew university of Jerusalem. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera-users Digest, Vol 48, Issue 17
by Puey Ounjai 21 Apr '07

21 Apr '07

Dear all; I am wondering can we manually assign secondary structure to each residues in the PDB file in chimera? Thanks Puey

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Chimera crash
by hsosa＠aecom.yu.edu 20 Apr '07

20 Apr '07

Hi, I'm having problems later with chimera. Sometimes when rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash with blue screen and reboot. It seems like a new problem as I've bee using chimera for a while and it didn't' happen before. As far as I know everything is the same in the computer. I'm running the latest snapshot release of chimera but that doesn't seem to be the problem. I deinstalled this version and installed the latest production release and got the same problem. Any ideas what the problem may be ?. Thanks Hernando System details UCSF chimera version 1.2382 (or 1.2304) OS: Windows XP service pack-2 Computer: Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.00.27.05 ForceWare version 91.36 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Transform Molecule Coordinates
by rkhayat＠scripps.edu 19 Apr '07

19 Apr '07

Hi, I was wondering if there is a stand alone version of the "Transform Molecule Coordinates" Chimera extension available. Alternatively, how will I be able to use this feature outside of Chimera? Thanks. Reza

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Re: [Chimera-users] rotating maps in chimera
by Tom Goddard 19 Apr '07

19 Apr '07

Hi Preethi, Here's what caused the misalignment when you opened "subtracted map 2", let's call that one map 3, into Chimera where the original map 2 and reoriented map 1 were already opened. When you open map 3 Chimera needed to give it an initial transformation. Maps 1 and 2 had different transforms. Chimera chooses the transform of the map with the lowest id number (shown in Model Panel, menu entry Favorites / Model Panel). Map 1 must have had the lowest id number, so it got the transform of map 1 instead of the transform of map 2. Chimera had no way of knowing that map 3 was just a modified version of map 2. When you open data in Chimera it assigns an id number to it (shown in Model Panel). The id number is 0 for the first opened data set, then 1 for the next, .... In general it assigns the lowest available id number when a new data set is opened. When restoring Chimera sessions maps get their original model id numbers in Chimera versions 1.2354 and later, but are assigned new model id numbers in older versions. Since the data sets with lowest id number determines the transform of all newly opened models it is best to think of that data set as defining the reference frame. You can use the Model Panel / Transform As... button to correct the transform of a newly opened model. In the case you described you would need to transform map 3 as map 2 to fix the misalignment. This is probably easier than editing a session file. Tom preethi(a)bu.edu wrote: > Hi Tom, > > Chris I think had already discussed with you about how we transform > the PDB files that were originally fit into a brix map so that it now > fits into an MRC file in chimera. > > I am just repeating that here because I came across a problem when I > did this. > > I saved a session in chimera where I had rotated a MRC map say map 1 > w.r.t another MRC map 2 and then used the "fit map into map" feature > to align map 1 into map 2.So I saved the session(which would save the > transformation matrix) and then used the matrix to move certain PDB > files(using "transform as"). > > Now I did some zoning and volume erasing on map 2(the unrotated map) > and then saved the resulting map and then with another program outside > chimera subtracted the zoned out volume from the whole volume of map 2. > > SO when I read in the subtracted file into chimera it is now rotated > w.r.t the map 2 instead of being read with the original matrix that > was used for map2. I fixed this problem by going into chimera session > file and maunally changing the rotation and translation values for > this map to match that of map2. > > Also, if I opened chimera afresh and didnt restore the session where I > had done all the transformations but just opened map 2 and the > subtracted map then it reads them correctly without displacing one map > w.r.t the other. > > So I was just wondering why chimera automatically rotates the > subsequent MRC files that are read into a session where a > transformation was applied to some files only ? > > -Preethi > > > > > >

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rotating 2 models side-by-side
by jean-francois menetret 19 Apr '07

19 Apr '07

How can I make two models rotate side-by-side around their respective centers using chimera ? 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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Re: [Chimera-users] Proper display of oligosaccharide
by Greg Couch 18 Apr '07

18 Apr '07

To followup, I just tried the first Human milk saccarides example on the Sweet webside, 2'-Fucosyllactose, and the PDB file it generates doesn't display at all because of the non-standard data in columns 67-72. We have decided that we're being too strict in this case and will change chimera. In the iterim, if you're on a UNIX system (Linux, Mac OS X, etc.), you can truncate the lines with the following: awk '{if (/^ATOM/) print substr($0, 1, 67); else print $0}' < original > fixed with appropriate filename replacements for original and fixed. Greg Couch UCSF Computer Graphics Lab

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Proper display of oligosaccharide
by R. Andrew Byrd 18 Apr '07

18 Apr '07

We study protein:carbohydrate interactions, and we use chimera for protein displays. We have a model built for an oligosaccharide using the SWEET server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php The file is in pdb format, but it has neither amino acid residue names nor nucleotide names. Hence, the molecule is invisible in Chimera. How could we make this a recognizable molecule so that we can examine various visualizations and modeling efforts using Chimera? Thanks! Andy P.S. I can send the file if you want.

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using different scale for 2 models
by jean-francois menetret 17 Apr '07

17 Apr '07

Is it possible to vary the scale of one model in respect to another during a movie ? 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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Re: [Chimera-users] Rotate or rock commands for making movie?
by Elaine Meng 17 Apr '07

17 Apr '07

On Apr 17, 2007, at 2:14 PM, Walter wrote: > Hi Elaine, > > I would like to make a movie using CHIMERA, but can only figure out > how to > rotate the molecule by hand and it ends up looking sloppy. Are there > command line entries for smoothly rotating or rocking a molecule? > > Thanks for your help! > > Walt Hi Walter, Sounds like you are looking for the "roll" command. http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/midas/roll.html This page lists commands especially useful for scripting movies, and links to a few example command files: http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/movies.html 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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Help with installing DMS and Chimera
by Ben Keshet 17 Apr '07

17 Apr '07

Hello everybody, I am a very inexperienced new user of Linux / cygwin and having problems in installing DMS and Chimera: 1. I am trying to install DMS but having problems with specifying correctly the pathway to the appropriate locations of the BINDIR and LIBDIR directories in the GNUmakefile. I am getting a message: "Cannot create directory. not such file or directory". I have tried it both on Linux enterprise 4 and on Windows using cygwin. My pathway includes spaces, i.e: /cygdrive/c/Documents and Settings/User Name/Desktop/dms/bin Can anyone please tell me how exactly I should enter the pathway (I think the spaces cause the problem but not sure)? 2. I am having problems running the chimera-installer.exe. file of Chimera on Linux. When I double-clicked on it, it tells me that I cannot execute the file, so as suggested in the instructions (http://www.cgl.ucsf.edu/chimera/1.2304/linux.html) I typed chmod +x 'filename' . When I checked the properties of the file after chmod, the box of 'execute' was checked (so I believe that I really changed the file's permissions). However, I am still getting the same error message when I double-click it. Does anyone know what am I doing wrong? Please consider my lack of experience in UNIX terminology if you try to answer one of my questions, Thanks a lot, Ben

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switching object on/off at the command line
by jean-francois menetret 16 Apr '07

16 Apr '07

Is it possible to switch a model on/off from the command line ? "objdisplay #model / ~objdisplay #model" sound promissing but it doesn't work ... 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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gromacs trajectory - only atoms, no bonds
by Moo Cow 16 Apr '07

16 Apr '07

I believe one has to have a very recent chimera in order to be able to read gromacs trajectories. I have "beta version 1 build 2376 2007/04/11 It is terrific that chimera can read the trajectories (without problem), but it then does not seem to join the atoms with bonds (it certainly does so for normal pdb files). My trajectory is displayed as a set of lonely unbonded atoms. I believe I checked for obvious mistakes on my part. I went to the tutorial, found the lines repr stick and so on. They gave no error message, but did not help. Many thanks for any advice. = Search for products and services at: http://search.mail.com

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