- Chimera-users - RBVI Mailing Lists

Showing data set axes
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera supports a format for making geometric objects called BILD described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Below is a 6 line BILD file that when opened in Chimera shows cylindrical arrows for the X (red), (green), and Z (blue) axes in the style of the program VMD. I made the axes 20 units long, with radius 1 and cone shaped tip with a radius of 2. Tom ----- File axes.bld: .color 1 0 0 .arrow 0 0 0 20 0 0 1 2 .color 0 1 0 .arrow 0 0 0 0 20 0 1 2 .color 0 0 1 .arrow 0 0 0 0 0 20 1 2 > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 17:30:29 -0800 > > i figured some of that but is good to hear it from the source. > > one last question - if i want to make an origin with axes (like a CAD > program might have) so i don't get lost after rotating my volumes a jillion > times and have to click 'orient', is there a way for me to make a > marker-based model (two markers for each axis) and put it slightly > off-origin (like in the -,-,- octant) so that i have a visual on my axes as > i rotate the scene? > > as in, is there a simple way for me to hand-write a marker model that i can > just load and fix to the scene? > > thanks, > > -jeff

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X11 updated for Mac OS X, stereo now?
by David Belnap 02 Nov '06

02 Nov '06

Apple has released an update for X11 with the following comment: This update addresses several issues in the X11 for Mac OS X package, enabling it to better handle: - GLX stereo visuals - offscreen rendering to GLX Pbuffers and Pixmaps I downloaded it and tried to run Chimera (beta version 1 build 2199 2006/01/24) in stereo. It didn't work. Does the X11 update have the stereo-in-a-window capability now that Chimera needs? Is there a newer version of Chimera that will run in stereo on the Mac? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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Re: [Chimera-users] Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera clipping and other tools use xyz coordinates and do not use voxel or pixel measures. The volume dialog region bounds panel and the volume dialog step size are exceptions where voxel index positions are used. The notion of a voxel is only relevant to density maps, not atomic models and clippping applies to all kinds of data, not just maps. Screen pixels are a 2 dimensional concept so it is an awkward measure to use especially with perspective 3-d viewing for measuring lengths. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 14:30:30 -0800 > > does this mean that I can't refer to a given coordinate by pixel/voxel > location without resetting the voxel size to '1 1 1' (which I might not want > to do - does chimera not keep the mrc file (or other voxel data) inside of a > similar kind of array) > > > -----Original Message----- > > From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] > > Sent: Thursday, November 02, 2006 1:46 PM > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Chimera length units > > > > > > Hi Jeff, > > > > Chimera does not know what units you are using, the data > > coordinates are just numbers as far as it is concerned. If > > you open a PDB atomic model the coordinates are always > > Angstroms. If you open a density map, say an MRC file, the > > header may include the voxel size. That value could be in > > Angstroms or nanometers. Often maps don't have the true > > voxel size in the header, often they say it is 1. In such > > cases you can use the Chimera volume dialog menu entry > > "Features / Origin and Scale" to set the voxel size in > > Angstroms or nanometers so that the map can be aligned with > > other models or maps. If you open a PDB model in Angstroms > > and a map with the scale set in nanometers then the map will > > look 10 times smaller than it should be relative to the model. > > > > Tom

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Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera does not know what units you are using, the data coordinates are just numbers as far as it is concerned. If you open a PDB atomic model the coordinates are always Angstroms. If you open a density map, say an MRC file, the header may include the voxel size. That value could be in Angstroms or nanometers. Often maps don't have the true voxel size in the header, often they say it is 1. In such cases you can use the Chimera volume dialog menu entry "Features / Origin and Scale" to set the voxel size in Angstroms or nanometers so that the map can be aligned with other models or maps. If you open a PDB model in Angstroms and a map with the scale set in nanometers then the map will look 10 times smaller than it should be relative to the model. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Date: Thu, 2 Nov 2006 13:26:11 -0800 > > thanks Tom, > > sorry for a goofy question, but how do I know what units chimera is using > (for measuring distances, having the output is nice in Angstroms, but > sometimes (like with orienting a clipping plane) using unitless/pixels is > more handy for displacements/etc) > > thanks, > > -jeff

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Per-model clipping plane command
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, There isn't yet a Chimera command for per-model clipping. Below is some Python code that can do it. Open a density map and then open this Python code in Chimera to clip it. Some more code can make it loop through different depths. There is some trickiness to making it update the graphics window in such a loop. Ask for details if you want that. Tom > From: Jeff > To: <goddard(a)cgl.ucsf.edu> > Subject: per-model clipping plane question (or similar) > Date: Thu, 2 Nov 2006 10:54:26 -0800 > > hi Tom, > > was wondering if I can control the per-model clipping plane > orientation/parameters/etc via command line or shortcuts - > > would like to be able to methodically push a clipping plane in 'slab mode' > through my model to compare it w/ other 2D/projection tools I use - I know I > can click 'orient' on the model and it will orient to a default > position/rotation (and I can click orient on the per-model clipping plane > and therefore register them both), but is there then a way that I can > specify (say, along one axis, like z) where the slab/clipping plane is > positioned, like in pixels? > > can I control the angular position of the clipping plane via command line, > too? > > thanks, > > Jeff ----- Python code clip.py. # ----------------------------------------------------------------------------- # Python function to control per-model clipping (like menu entry # Tools / Depiction / Per-Model Clipping). The clip plane rotates with # the model (PDB structure, density map, ...). # # Parameters: # model is a Chimera Model # origin is (x,y,z) of point on clip plane. # normal is (nx,ny,nz) pointing towards clipped (invisible) half of plane. # slab_thickness is in data length units (usually Angstroms). # # Origin and normal are relative to the data coordinate system, for example, # the x,y,z coordinates of a PDB atoms or axes of a density map. The clip # def set_clipping(model, origin, normal, slab_thickness = None): p = model.clipPlane from chimera import Point, Vector p.origin = Point(*origin) p.normal = Vector(*normal) model.clipPlane = p model.useClipPlane = True if slab_thickness == None: model.useClipThickness = False else: model.clipThickness = slab_thickness model.useClipThickness = True # ----------------------------------------------------------------------------- # Cap holes left when clipping a surface. Controls graphical interface # shown by menu entry Tools / Depiction / Surface Capping. # # Parameters: # cap_color is (r,g,b) or (r,g,b,a) where values in range 0-1 # cap_mesh is True or False for mesh or solid cap appearance # cap_subdivision of 2 makes cap mesh twice as fine for detailed coloring. # cap_offset in data length units (usually Angstroms) for large models # sometimes needs to be larger to avoid cap itself being clipped due to # finite floating point precision in OpenGL. # def show_surface_caps(show, cap_color = None, cap_mesh = False, cap_subdivision = 1, cap_offset = 0.001): from SurfaceCap.gui import capper_dialog d = capper_dialog(create = True) d.Close() use_color = (cap_color != None) if use_color: d.use_cap_color.set(use_color) d.cap_color.showColor(cap_color) if cap_mesh: d.cap_style.set('mesh') else: d.cap_style.set('solid') d.subdivision_factor.set(cap_subdivision) d.cap_offset.set(cap_offset) d.show_caps.set(show) # ----------------------------------------------------------------------------- # Example using set_clipping(). # from chimera import openModels mlist = openModels.list() m = mlist[0] set_clipping(m, (.5,0,1), (0,1,1), 8) show_surface_caps(True, (1,0,0), True) # Red mesh caps

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Chimera under FreeBSD
by Devon Ryan 01 Nov '06

01 Nov '06

Has anyone had success getting chimera to run under FreeBSD? I can get the linux version to start (under the linuxulator), but it crashes after ~20 seconds when the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel architecture. Thanks -- Devon Ryan | dpryan(a)sg.uchicago.edu Neuro Grad Student, Ptacek Lab | dpryan(a)phy.ucsf.edu University of Chicago '02 | dpryan(a)alumni.uchicago.edu www.dpryan.com | dpryan(a)dpryan.com ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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question regarding chimera 1.2304-wim32.exe
by AJ Campbell 31 Oct '06

31 Oct '06

I have tried installing Chimera several times on my Windows machine but keep receiving an error message saying "Outline highlight not supported by hardware", any advice would be appreciated. ~ Arthur

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atom name balloons
by Greg Pintilie 31 Oct '06

31 Oct '06

I was wondering why in the new release of Chimera ballons no longer pop up when the mouse is placed over an atom and is left there... is this an option that has to be set somewhere? I found it extremely usefull and now am missing it... Greg

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problems with starting Chimera
by Mareike Goeritz 30 Oct '06

30 Oct '06

Hello, I'm interested in using Chimera, but after downloading and installing the software I'm unable to launch the program. I always get the following error message: "Microsoft Visual C++ Runtime Library: Assertion failed! Program: C:\Program Files\Chimera\bin\pythonw.exe File: togl.c Line: 2994 Expression: res==TRUE For information on how your program can cause an assertion failure, see the Visual C++ documentation on asserts (Press Retry to debug the application - JIT must be enabled)" I'm not familiar with C++, so I don't know what to do. Does anybody know what might be missing or what's the problem? Thank you for your help!! Mareike -- ******************************** Dr. Mareike Goeritz Department of Chemistry, MC 164-30 California Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 (626) 395-6032 Tel (626) 683-8753 Fax goeritz(a)caltech.edu ********************************

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Chimera, 3dsmax, blender
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Lydia, It's been years since I've had access to a 3dsmax license, so I can't really make good comparisons between it and Blender. Fundamentally, they serve the same role, so I expect you would find using them similar, especially compared to PyMOL, Chimera, etc. Before getting into the benefits, you should be aware that compared to any software truly designed for chemical modeling, Blender has some serious drawbacks. There is no pre-existing set of structural tools that is standard for chemistry modeling software: if you want ribbons, you have to write a procedure that will generate them. I'm assuming you're already familiar with this, though, since you're using 3dsmax. As another sizeable negative, CSG in Blender is still somewhat flaky. I seem to remember having far fewer problems in 3d studio, even back around ~R5 or 6. On the benefit side, Blender's plugin/scripting system is extremely free of restrictions. The scripting system is pure Python, and many Python "plugins" are available. The true plugins are done in C, but are currently restricted to some post-processing features. You could also use the scripting system to access C libraries. These features really help to make up for the lack of built-in chemistry-centered tools. The other reason why you might prefer Blender over 3dsmax is that the scripting and plugin system is very much like Chimera, so if you're using both it's only one system to learn. Jonathan > Message: 8 > Date: Mon, 30 Oct 2006 14:47:06 -0800 > From: "Lydia Jablonski" <lydka(a)uoregon.edu> > Subject: [Chimera-users] Exporting VRML, Using Blender > > Jonathan and Greg- > > Thank you for your suggestions. I wanted to at least try them before I responded. > > Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible. > > Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up. > > Any more pointers would be much appreciated. > > -Lydia

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Toolbar and Favorite on PC
by jean-francois menetret 30 Oct '06

30 Oct '06

Hello all, when running chimera on my PC (windows XP), my toolbar stopped being displayed. If I uninstall and reinstall chimera, my toolbar comes back until the next reboot. How can I fix that ? Is there to restore my preferences after launching chimera? Regards Jean-Francois 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] Chimera-users Digest, Vol 42, Issue 19
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although this does not relate to your question on licensing, is there any particular reason you're using such a complicated workflow? Chimera can be used to generate basic geometry (sphere/cylinder) from PDB files via povray, but so could any import system you have for the 3D modeling software. You would also lose the benefit of chemistry-centered structure for manipulation or selection: chains, residues, etc. I've been using Blender to handle complicated chemical models for a while now, and it wasn't that difficult to implement the import of various data types. With BioPython pdb files become trivial, and volumetric data sets are (very) difficult but possible. Jonathan > Hello- > > Do any of you have an idea of how much a single commercial license for Chimera would cost? > > I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max. > > Thanks, > > Lydia Jablonski

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changing center of rotation
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although I haven't used EMAnimator, you can set the center of rotation within Chimera using the Set Pivot action: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot There's also Tools/Movement/Rotation, and lastly, you can edit structures to insert artificial points at extreme high/low XYZ locations, which will in effect manually set the center used via the 'center of models' option. I wouldn't recommend the last option unless you have a good reason to do so, but it does work. Jonathan > Message: 1 > Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST) > From: wendy ochoa <wencryo(a)yahoo.com> > Subject: [Chimera-users] rotating molecules for movies > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <20061030195242.57847.qmail(a)web37306.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? > Thanks > > > >

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Re: [Chimera-users] viewing grid density
by Thomas Goddard 30 Oct '06

30 Oct '06

Bala reports that the problem was in an Amber input file. > From: "bala" <bala(a)igib.res.in> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] viewing grid density > Date: Fri, 27 Oct 2006 19:59:38 +0530 > > Hello Thomas and Elaine, > > Thank you for your information. I rechecked the amber input files and i = > found a mistake there in rms fitting the coordinates in my trajectory. > > regards, > Bala

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Re: [Chimera-users] rotating molecules for movies
by Thomas Goddard 30 Oct '06

30 Oct '06

Hi Wendy, Here are some Chimera commands that are useful for making movies with Movie Recorder: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Here's a fancier Chimera movie script example. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com Here is the documentation for the Movie Recorder dialog and movie command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom

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rotating molecules for movies
by wendy ochoa 30 Oct '06

30 Oct '06

Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? Thanks

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generating electrostatic potential map
by bala 27 Oct '06

27 Oct '06

Hello all, I want to generate the electrostatic potential map using Chimera. I tried through Delphi controler, however i am repeatedly getting an error as follows. I have successfully installed Delphi. Can someone suggest me what is wrong. __________DelPhi V. 4 Release 1.1 ______________ | | | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | many dielectric regions, multisalt ionic | | strength, different probe radii, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | | Recompiled on Linux and PC | | January 2002 -------- Walter Rocchia | |__________________ ___________________| DelPhi V. 4 program started on Fri Oct 27 2006 at 14:55:00 opening parameter file /tmp/tmpvpgS8V At least 30 nonlinear iterations atom radii read from file /usr/people/ojha/BALA/chim_amber.siz unknown header format in radius file: O5' A 1 1.7210 First it showed the same for H5 atom [which was the first atom in the siz/charge file], then i just tried by deleting the first line in the radius and charge file. Then the same error is coming for the second atom O5' in the file. Thanks in advance, Bala

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viewing grid density
by bala 26 Oct '06

26 Oct '06

Hello all, 1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same. 2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc. 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it. Bala

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To except box information in MD movie
by Atsutoshi Okabe 25 Oct '06

25 Oct '06

Hello, I viewed Amber format trajectory files ( topology/parameter file and trajectory file ) by MD movie. But I got the figure( attached file) I didn't intend. I think the reason is to read box information in the Amber trajectory file . How can I except the box information in MD movie window ?

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To color atoms
by Atsutoshi Okabe 24 Oct '06

24 Oct '06

Hi, I visualized one ligand molecule (a kind of sugar) written by PDB format within chimera. But all atoms have non color(attached file ) I want to color these atoms (i.e. the oxygen has red .) Could you please teach me how to color atoms?

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1.2304 production
by Eric Pettersen 23 Oct '06

23 Oct '06

We haven't received any major bug reports for the release candidate, so we have promoted it to a production release (1.2304) which includes a few quite minor bug fixes and some documentation improvements relative to the release candidate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Movie - Display Spheres
by Jared Godar 20 Oct '06

20 Oct '06

Hello, I am trying to use the 'represent spheres' command to draw attention to specific residues in a model that is displayed as a ribbon. I would like to first show the ATP binding site of the molecule with magenta spheres, then show the three residuse which get phosphorolated. Currently, I am able to display one of these elements or the other as spheres, but not both at the same time. I've tried to use a single represent sphere command to specify all of the desired atoms, but can't seem to get the context right, represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 & #0::ATP weren't working. Help on the syntax to simultaneously display the two commands listed below which are currently mutually exclusive would be appreciated. #SHOW ATP: color magenta #0::ATP; color magenta #0::mg; represent sphere #0::ATP #SHOW PO4 Residues show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red #0:432; represent sphere #0:426,431,432 Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

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Dock?
by S Joshua Swamidass 19 Oct '06

19 Oct '06

Hello, Are there any plans to develop a gui frontend for DOCK using chimera? Josh

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force fitting a protein into select volume in a EM reconstruction
by jayant_jacques 17 Oct '06

17 Oct '06

hi! Is it possible in chimera to choose a particular part of a EM envelope and a protein and fit them? AS the protein that I am trying to fit into the map finds a better fit else where in the EM envelope, after I painstakingly align it to the place where its supposed to be!!! Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

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release candidate
by Eric Pettersen 17 Oct '06

17 Oct '06

We've made a release candidate (version 1.2303) available for download. It has many new features relative to the previous production release (1.2199). The features/improvements are listed here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2303.html Please let us know if you encounter any problems with the release candidate. If no major problems surface in the next few days, we will promote the candidate to production release status. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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