- Chimera-dev - RBVI Mailing Lists

how to export the volume data which is stored in the memory?
by Zhiheng Yu 03 Dec '07

03 Dec '07

Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng

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Re: [chimera-dev] Chimera-dev Digest, Vol 46, Issue 7
by Jean-Didier Maréchal 28 Nov '07

28 Nov '07

Hi Eric, both information have been of great interest for me. I actually read Walt mail when it came to the list, though, I forgot about it afterward... Thanks JD On Tue, 2007-11-27 at 12:00 -0800, chimera-dev-request(a)cgl.ucsf.edu wrote: > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: Different models (Thomas Goddard) > 2. Re: Molecular Editing: metal ion chelation (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Nov 2007 14:27:08 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Different models > To: Marco Mernberger <mernberger(a)Mathematik.Uni-Marburg.de> > Cc: chimera-dev(a)cgl.ucsf.edu > Message-ID: <474B483C.3050804(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Marco, > > The Chimera volume path tracer tool has some similarity to your > proposed Chimera tool. It allows you to place markers on volume data > and connect them up. The markers could represent molecules, domains, > ... and are implemented as a Chimera molecule, so all the coloring, > selecting, hiding/displaying capabilities of molecules are available to > the user. > > The volume path tool is implemented all in Python in directory > > chimera/share/VolumePath > > Look specifically at the markerset.py file which defines classes > Marker_Set, Marker, and Link that are wrappers for Chimera Molecule, > Atom and Bond. > > Tom > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Nov 2007 15:59:09 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Molecular Editing: metal ion chelation > To: Jean-Didier Mar?chal <jeandidier.marechal(a)uab.es> > Cc: chimera-dev(a)cgl.ucsf.edu > Message-ID: <629CBC57-7D4F-4612-A50E-DD80312697D9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi JD, > Unfortunately, Chimera isn't really being as smart here as you are > giving it credit for. Many PDB files specify coordination bonds in > CONECT records. Chimera identifies those bonds and converts them to > pseudobonds (otherwise its atom-typing code, which depends on correct > covalent bonding, would get the bonded atoms wrong). So PDB files > that do not identify the coordination bonds with CONECT records (e.g. > 1lwx) will not have any coordination bonds in Chimera. > I'm wondering if what you are hoping to do is along the lines of > this previous mail to chimera-users: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001529.html > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Nov 23, 2007, at 9:30 AM, Jean-Didier Mar?chal wrote: > > > Hi Eric, > > > > Thanks for that. I have been able to get a bit further. > > > > To follow with my problem, I have one question more though. > > Basically, I > > would like to know how chimera "Recognizes" metal chelation and > > coordination bounds. > > > > What I see is that when you open a pdb with a metal ion, the program > > places correctly "semi bounds" corresponding to coordination > > interactions. Unfortunately, I work with a series of protein > > structures > > where metals do not adopt a typical geometries (ex: 1lwx). First, I > > would like to be able to improve the number of acceptable metal > > geometries, but my questions are: how does chimera recognize the right > > geometry of the metal ions? Is it implemented in a python module? > > It is > > a C++ code? > > > > All the best, > > JD > > > > > > > > > >

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Molecular Editing
by Jean Didier Pie Marechal 26 Nov '07

26 Nov '07

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Different models
by Marco Mernberger 26 Nov '07

26 Nov '07

Hi there, i have a question concerning a kind of extension, i'm considering ... I'm a PhD student using chimera for the depiction and comparison of chemical and protein structures. I'm wondering if i could implement an extension that would allow me a self-defined type of molecule model, where the atoms are replaced by self-defined centers representing specific functional groups in a molecule. Could you give me a hint, how to do that? I mean, what kind of class do i have to change in order to define such a model and to load a corresponding file type? Thanks in advance, Marco Mernberger

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Re: [chimera-dev] [Chimera-users] Angles
by Eric Pettersen 06 Nov '07

06 Nov '07

On Nov 6, 2007, at 7:38 AM, Greg Pintilie wrote: > yes, try: > > chimera.selection.currentAtoms() > > this will return a list of the currently selected atoms in the > Chimera viewer. > > > For your purposes, it sounds like you want vectors between every two > atoms that you subsequently select. Watch out however, that the list > returned by the above command need not be in the order that you made > the selection. I noticed that in general the selection routines return > atoms in arbitrary order, independent of the selection order or their > position in the structure. Not sure if there is any way to enforce any > kind of order? chimera.selection.currentAtoms(ordered=True) This returns the atoms in the order they were selected. It's not the default since it involves a possibly-expensive sorting operation and because many uses of the current selection don't care about the ordering. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] chimera python shell
by Eric Pettersen 31 Oct '07

31 Oct '07

On Oct 31, 2007, at 3:44 AM, Ondrej Marsalek wrote: > hi, > > i wanted to ask whether there are any plans to change the idle python > shell in chimera for something else. i would be interested in > something with completion and editable history, ideally ipython > (http://ipython.scipy.org/moin/) > > i tried to add ipython to the python embedded in chimera but did > not succeed. > > i will be grateful for any information or personal experience with > this. We didn't have any plans to change the shell, no. Looking at ipython, it seems quite nice and probably would be slightly better than Idle. Keep in mind that you can essentially get editable history in Idle by scrolling the window back to the command(s) you want to repeat, inserting the cursor after them, and hitting Return. That will insert those commands at the end of the Idle shell where you are free to edit them before hitting Return to execute. I'm going to put "adding ipython" to my to-do list, but it probably will take a while to get to since there are a lot of other features that need adding that seem to offer more "bang for the buck". Unless other people chime in about how adding it would be important to them... I know you tried to add ipython yourself, but if you want to try again you need to look at what we do with the Idle shell to get it to work in Chimera. Particularly the file <chimera installation>/share/ Idle/__init__.py (and ChimeraExtension.py in the same directory). There's some stuff in there to prevent quitting Idle from quitting Chimera, and to get output to stop going to the Reply Log and go to Idle instead (the pushReply() and popReply() calls). The ChimeraExtension.py is for getting Idle to show up in the Tools menu as described in one of the Programmer's Examples (http:// www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html -- the "Working with the Chimera Extension Manager" example). --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Origins in CCP4 and MRC maps
by Bernard Heymann 23 Oct '07

23 Oct '07

We have an issue with disparity of the interpretation of CCP4 and MRC density maps in Chimera. The CCP4 and MRC file formats are very close in specification, and in particular the definition of the origin is the same. However, when I open both formats of a density map in Chimera, the origins given in the Volume Viewer do not agree and the maps are located in different places. The first issue is how the origin is specified. In the 3DEM community, we proposed that the origin is defined as the location of the physical coordinate origin within the framework of the map, expressed in voxel dimensions. In Chimera (build 2422), the origin for the MRC format is consistent with this definition while for the CCP4 format it is not. Example: I have a map with dimensions 100x100x100, an origin at 50x50x50 and sampling of 2 angstroms/voxel. In both the CCP4 and MRC versions the relevant fields are: nxstart = -50, nystart = -50, nzstart = -50. The origin as defined for 3DEM is thus the negative of these fields. In Chimera, the origin is given as {50,50,50} for the MRC format file, while for the CCP4 format file it is {-100,-100,-100}. Suggestion: The origin given in the Volume Viewer for the example should be either {50,50,50} specified as voxel units, or {100,100,100} specified in angstroms, for both file formats. Identical maps in the two formats should be superimposable when the origin specifications are the same. Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892-8025 Tel. 301-451-8241, Fax. 301-480-7629

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CHIMERA new features
by Sacha De Carlo 22 Oct '07

22 Oct '07

Dear developers, a HUGE thank you for making CHIMERA the best rendering/molecular viewer/structure analyzer software there is out there! I am a big fan of your soft and I just wanted to thank you to create such a professional environment and easy to use graphic interface to create stunning snapshots and making our work look so good :) THANKS THANKS THANKS !!! Sacha P.S. if you ever make a cycling jersey with the UCSF Chimera logo on it, I'll the first to buy it :) -- PLEASE HELP ME RAISE FUNDS FOR MY AIDS LIFE CYCLE 7. Please donate online: http://www.aidslifecycle.org/1162 __o _`\<,_ (O)/ (O) ====================================================== Sacha De Carlo, PhD Molecular, Cellular and Developmental Biology Dept. NCRR 3DEM and Hoenger Labs, Campus Box 347 University of Colorado Boulder, CO 80309 Phone: (303) 492-5471 e-mail: sacha(a)bio3d.colorado.edu URL: http://www.planetesacha.com ======================================================

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Benchmark scores
by Gabor Papai 07 Sep '07

07 Sep '07

Hi! The benchmark scores of my PC are: CPU Information Processor (CPU): Intel(R) Core(TM)2 CPU 6600 @ 2.40GHz Speed: 2 401,96 MHz Memory Information Total memory (RAM): 2,0 GB Total Swap: 4,0 GB OS Information OS: Linux 2.6.20-1.2952.fc6 i686 System: Fedora Core release 6 (Zod) Display Info Vendor: nVidia Corporation Model: Quadro FX 1500 Memory: 256 MB Benchmark scores surface 839 mesh 809 contour 179 solid 435 recolor 161 Test was done: 07 Sept. 2007 Chimera 2422 I don't know whether these scores are good or not, I'm not familiar with them. Bye, 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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Pickle a molecule object?
by Francis E Reyes 31 Aug '07

31 Aug '07

Is it possible to pickle a molecule object? >>> pickle.dumps(molecule) Traceback (most recent call last): File "<pyshell#32>", line 1, in ? pickle.dumps(molecule) File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/ pickle.py", line 1386, in dumps Pickler(file, protocol, bin).dump(obj) File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/ pickle.py", line 231, in dump self.save(obj) File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/ pickle.py", line 313, in save rv = reduce(self.proto) File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/ copy_reg.py", line 69, in _reduce_ex raise TypeError, "can't pickle %s objects" % base.__name__ TypeError: can't pickle Molecule objects >>> --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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IMAGIC-5 and Chimera
by michael 13 Jul '07

13 Jul '07

Dear programmers/developers of Chimera! I am writing because many of our users display their 3D results obtained with our IMAGIC-5 software with your Chimera program. We would be interested to create a more direct coupling to Chimera which I believe would be to everyone's advantage. We as the Image Science company maintain and distribute (free of charge) a universal data conversion program called EM2EM which most people in the 3DEM ("3D electron microscopy") community use to convert their results into various formats such as MRC/CCP4 that is compatible with Chimera directly. The data format of our IMAGIC-5 software is comparable to MRC/CCP4 but is a bit richer because it also supports sequences of 3D volumes in a file. Is it possible to achieve a closer integration with your Chimera program? And if yes, how can we proceed? Thank you and kind regards Michael Schatz Image Science www.ImageScience.de www.ImageScience.de/imagic www.ImageScience.de/formats

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Fwd: [Chimera-users] Reading a data set from a text file
by Elaine Meng 14 Jun '07

14 Jun '07

Hi Kyaw, The only ways I can think of are: - create a VRML file describing a surface with those points, read into Chimera - write a Python script to be opened in Chimera that reads in the numbers and generates a Chimera surface model However, I do not know the details about how to do either of these things. Others, feel free to chime in! 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: > Hi Dr. Meng, > > I am sorry for my vague question. > > I have a table of numbers in a text file and I'd like to read in > those numbers and convert them into cartesian coordinates so that > they can be displayed as a surface in Chimera. > > If you could give me some suggestions on how to do it, I'd really > appreciate it. > > Thank you, > Kyaw

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Protein to ligand shortest distances?
by khar6039＠mail.usyd.edu.au 21 May '07

21 May '07

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 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [chimera-dev] Placing Chimera markers
by Thomas Goddard 23 Apr '07

23 Apr '07

Hi Karin, There is no programming documentation for Chimera markers and marker sets. You can place a marker at position p = (x,y,z) using import VolumePath VolumePath.place_marker(p) Its radius and color and which marker set it is placed in and whether it is connected to an already selected marker is determined by settings in the volume path tracer dialog. If you don't want to use tho`se dialog settings you can instead use code like: xyz = (5.2, 1.2, -4.2) rgba = (0,0,1,1) # red, green, blue, opacity in range [0,1] radius = 2.0 mset.place_marker(xyz, rgba, radius) Here mset is a marker set. You can get the current marker set shown in the path tracer dialog using code: from VolumePath import volume_path_dialog d = volume_path_dialog(create = True) mset = d.active_marker_set if mset == None: mset = d.new_marker_set_cb() All of the marker routines are in chimera/share/VolumePath/gui.py chimera/share/VolumePath/markerset.py The markerset.py file defines the Marker_Set, Marker, and Link classes that hold the path data. The marker positions are obtained using mlist = mset.markers() for m in mlist: print m.xyz() Markers need not be connected. If they are connected they need not be in a single path. Three or more links can connect to a single marker. To find the links use: llist = mset.links() for link in llist: m1, m2 = link.marker1, link.marker2 # the two linked markers print m1.id, 'connected to', m2.id Hope this gives you some ideas to start with. Sorry for the poor quality of the path tracer code. Suggestions for improving it are welcome. Tom Karin Gross wrote: > Hi Tom, > > I have some questions concerning the makers and markersets in chimera. > > First of all, is there any programmer documentation for the markers? > > I want the users to be able to place markers directly onto my plane. Is there > any possibility to get the coordinates for each marker and place markers with > specific x-,y-, z- coordinates? > > The next feature I want to offer is, that the user is able to define a > path(connected markers) within a volume and then the plane should follow this > path through the volume. > Therefor I need some infomations about the paths, how they are stored?, can I > get out the path for moving my plane onto it?, etc... > > Thanks for your time > -Karin >

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Building a multimer model
by Benjamin G.S. Horsman 07 Apr '07

07 Apr '07

Hello, My name is Benjamin Horsman and I am a student at the University of Toronto. I have what should be a basic (possibly naive) question regarding protein modelling that I was hoping you might be able to answer for me or point my in the right direction. I have been studying the structure of a bacterial protein complex, trying to understand how it interacts with several known binding partners. The complex is known to be a hexameric homomultimer. Recently the structure of the subunit protein was solved. However, only the monomeric form of the protein was determined, and the corresponding PDB file does not contain coordinates for the multimer (i.e., no BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a model of the hexameric complex for visual inspection and for some docking studies. What would be the best way to accomplish this? There are several structures in the PDB of hexameric protein complexes composed of subunits with very close structural alignment to my protein of interest, differing in two regions of the protein that are outside of the multimer binding regions. I believe that my protein complex posses very similar or nearly identical geometry to these known complexes. Is there any way to basically insert my protein into this geometry? Can this be done in Chimera? If not, is there any program or web server that allows this to be done? Or are you aware of a better way to get this done? Thank you for your time. Any help is greatly appreciated. Benjamin Horsman

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additional SimpleSession variable to facilitate session merging
by Eric Pettersen 02 Apr '07

02 Apr '07

For what I imagine are the very few people who have written extensions that save their state into sessions and that restore their own models from sessions, you should know that I have added a variable to the SimpleSession module named "modelOffset". During a normal session restore, modelOffset is zero. During a session restore where pre-existing models haven't been closed (i.e. the session is being "merged" with the current models) modelOffset is a positive integer that should be added to restored model IDs (not sub- IDs) to avoid collision with currently-open models. This is explained in further detail in the Programmer's Guide example for sessions: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ Main_SessionSave.html Let me know if anything is unclear... --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Camera changes in chimera 1.2348
by Greg Couch 27 Feb '07

27 Feb '07

There used to be three attributes, given in the same units (only ratios where used), eyeSeparation, viewDistance (distance to the screen), and screenWidth (the idea was to scale it to the actual window width, but that was never done). The default values were given in inches: 2.0, 30.0, and and 13.0, respectively. The effective field of view was just under 25 degrees. Now, there is an explicit fieldOfView attribute, because chimera maintains the field of view when resizing the graphics window. Of the original three attributes, only eyeSeparation remains, and it is given in millimeters, and the latter two are replaced with screenDistance and windowWidth. The windowWidth value is automatically computed when the graphics window is resized which in turn adjusts the screenDistance based on the field of view. If the screenDistance is explicitly set, then the field of view angle is recomputed. Defaults for the new values, are 50.8 mm for the eyeSeparation, and 25 degrees for the fieldOfView. - Greg

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New chimera development snapshot available
by Greg Couch 26 Feb '07

26 Feb '07

See <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> for details (this will be accurate for the next few days, after that read the release notes that are bundled into the chimera snapshot). The snapshot uses NumPy instead of Numeric python, so some third-party extensions may break (eg., parts of EMAN). Other highlights include intial support for PDB 3.0 (remediated PDB) format and built-in POV-Ray raytraced image support. Enjoy, Greg Couch UCSF Computer Graphics Lab

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Re: [chimera-dev] [Chimera-users] programmatic representation
by Eric Pettersen 13 Feb '07

13 Feb '07

Hi Randy, The second argument to Midas.represent() is polymorphic, and if it is a list then is is expected to be a list of atoms. You're giving it a list of models, which results in the 'drawMode' attribute of those models being set (to no effect). Perhaps the polymorphism of the second argument could be improved to handle lists of models (or residues), but right now it doesn't. My suggestion is to use a Selection object based on your list of models, which Midas.represent () can handle, perhaps like so: self.model = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.model) from chimera.selection import ItemizedSelection sel = ItemizedSelection() sel.add(self.model) Midas.represent('cpk', sel) --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Feb 12, 2007, at 12:28 PM, Randy Heiland wrote: > I'd like to be able to set the representation (wire, stick, bs, > cpk) of > a model programmatically, in this case, from a plugin. I was > trying the > following, but the newly displayed model would always be displayed in > wire: > > self.model = ReadSDF.readSDF(tmpfile.name) > chimera.openModels.add(self.model) > > #Midas.represent('stick', self.model) > Midas.represent('cpk', self.model) > > Suggestions? > thanks, Randy > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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NumPy in Chimera
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Chimera Extension Writers, If you have written Chimera extensions that use Numeric Python you will need to convert them to instead use NumPy to work with future versions of Chimera. NumPy provides almost all the same routines as Numeric but some function and module names have changed. We are switching Chimera over from Numeric Python to NumPy and will have a Chimera snapshot out in one to three weeks that uses NumPy. We envision having a Chimera production release that uses NumPy in perhaps 3 months. The change was necessary because Numeric is no longer maintained. Numeric will no longer be included with Chimera because dynamic library name space collisions with NumPy occur on the Mac because of certain Chimera compilation options. The conversion of Chimera code was not much trouble, but we had to also convert third party packages that are included with Chimera (PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular surfaces) and that took some work. Thanks for your patience. Tom

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large data structures in conditional blocks makes baby Python cry
by Eric Pettersen 17 Jan '07

17 Jan '07

This is actually applicable to any Python code, but is especially relevant to extensions that save data in Chimera sessions: the Python bytecode compiler has a limitation of a maximum of a 16 bit offset in a jump instruction. This means that you don't want to have 64K worth of characters in a single conditional block of code (i.e. if/else, loops, try/except). Otherwise you will get the somewhat opaque: SystemError: com_backpatch: offset too large So if you have data structures that may be potentially large when written to a session file, try to place their definitions in the session file outside of conditional blocks. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] SDF format
by Eric Pettersen 15 Dec '06

15 Dec '06

On Dec 15, 2006, at 5:45 AM, Randy Heiland wrote: > Eric, > May I ask how you go about developing plugins for Chimera? > Specifically, is > there a trick to *not* having to quit/restart chimera when testing new > changes made to the plugin module? May I ask what IDE you use for > developing your Python code? I'm currently using eclipse, but I'm > always > curious to hear of others' experiences. > > Thanks, Randy Hi Randy, I always go the "restart Chimera" route. Chimera typically starts much faster the second and subsequent times since many of it's shared libraries are already loaded into memory. Supposedly you could use Python's "reload" function to load the new version of your module, though I've personally found that to be a bumpy road (though I haven't really tried it recently). You would definitely want to read the documentation for the reload function to get the most out of it, and would probably want to be aware of the caveats noted here: http://pyunit.sourceforge.net/notes/reloading.html As far as an IDE, I pretty much work in the stone age -- inserting print statements as needed! Perhaps others would have suggestions... --Eric

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opening models
by Eric Pettersen 15 Dec '06

15 Dec '06

On Dec 15, 2006, at 1:07 PM, Randy Heiland wrote: > Eric, > Need a bit more help on this... how can I invoke this reader > programmatically from my plugin and display the model in the viewer > window? Til now, with PDB formatted files, I've done: > > fp = open(tmpfile.name, 'w') > fp.write(pdbstr) > fp.close() > self.model = chimera.openModels.open(tmpfile.name, type='PDB', > identifyAs=id[0]) If your temp file's name ends in '.sdf' then you don't have to supply a 'type' keyword to openModels.open(). If not, then with the code I gave you the 'type' would be "Structure Data Format" (it's the "fileType" variable in ReadSDF/fileInfo.py). You might want to import that variable and use it instead of a fixed string, because in the next release of Chimera the string will be "MDL MOL/SDF" since I enhanced the reader to handle MOL files as well. Also, openModels.open() always returns a _list_ of models, even if the input only creates one model. > Now I have a 'pdbstr' that's really an sdf format, and when I try to > substitue type='PDB' w/ 'SDF', it doesn't recognize it. > > And when I try the following, it doesn't complain, however no model is > displayed: > import ReadSDF > > fp = open(tmpfile.name, 'w') > fp.write(sdfstr) > fp.close() > self.model = ReadSDF.readSDF(tmpfile.name) The readSDF() function returns a list of models. To add them to the list of open models, use chimera.openModels.add(), probably like this: self.models = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.models) --Eric

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Re: [chimera-dev] C/C++ libraries in Chimera
by Elaine Meng 06 Dec '06

06 Dec '06

Hi Viktor, Actually, I'm the one person on the Chimera team that doesn't do programming! I'll share your mail with the chimera-dev(a)cgl.ucsf.edu list (for programmer/developer issues) - I believe it has a handful of subscribers in addition to the Chimera team members, and this set of people may have some valuable insights. 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 Dec 6, 2006, at 9:28 AM, Viktor Hornak wrote: > Dear Elaine, > > sorry to write directly to you and not to chimera list but I have a > question which is rather off-topic. It concerns developing C > extensions in Python, and I don't even mean specifically for > chimera (at this time), but in general. I know that you guys (I am > not sure who specifically on chimera team does this sort of a "hard > core" programming work) develop a lot of extensions (.so libraries) > that can be called from Python and thus you must have a lot of > experience doing it. I attempted a couple times to write C > extensions in Python as described in Python extension guide but > always got burned by reference counting, programs crashing at > allocating memory or releasing pointers, etc. In other words, there > must be a better/easier way to write extensions. All I need is to > transfer integer/float variables and arrays to or from Python to my > C subroutine, e.g. I just need to wrap my existing C subroutines > and pass arrays back and forth between C and Python (I guess Python > lists versus C arrays). I was hoping someone on your team could > point me to the right direction. I saw people use SWIG (that looked > rather complex though and an overkill for what I need), or Pyrex, > etc but I wasn't sure which solution was worth picking up in terms > of time I have to spend to learn it and future support (so that the > project doesn't disappear in a year). > I would really appreciate if you could provide any hints or point > me to some resources. > > Many thanks for your help and sorry for such an unrelated question!!! > > Cheers, > -Viktor > > -- > =================================================================== > Viktor Hornak > Center for Structural Biology Phone: (631)632-1439 > SUNY at Stony Brook Fax: (631)632-1555 > Stony Brook, NY 11794-5115 E-mail: viktor.hornak(a)sunysb.edu > ===================================================================

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_surface module
by Karin Gross 12 Oct '06

12 Oct '06

Hi, I've tried to display several three-dimensional geometric surfaces in Chimera. I've described the surfaces as sets of quadrilaterals. In Chimera-1.2199 it works, but in Chimera-1.2255 it gives me this error message: ***error: Triangles array second dimension must = 3, got size 4****. Is desribing surfaces as sets of quadrilaterals not supported anymore? Thanks -Karin --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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