- Chimera-dev - RBVI Mailing Lists

loading files
by Lars Kunert 12 Oct '03

12 Oct '03

Hi! First of all thanks for your replies to my previous questions, they were really great! when i open a file (mol2) with openmodel... how do I influence into which slot/subslot ( I suppose that are not the right terms, but I hope you know what I mean) the molecule (molecules) are loaded. I want something that loads mol2-file containing one molecule into slot X subslot Y and a multimol2 file containing Z molecules into slot X starting at subslot Y How do I delete a model (or one specific molecule in a model) from a slot (subslot) - ( by slot/subslot - numbers and/or by name)? Thanks for your help Lars

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sideview eye positioning
by Tom Ferrin 12 Oct '03

12 Oct '03

Greg, During a demo at the "visualization of large complexes" workshop that Tom Goddard and I attended this weekend, I tried to zoom in close to a single protein within bluetongue virus. But what happened was that the eye position ended up behind the yon clipping plane, and the virus particle suddenly shrunk to a tiny dot. It was not easy to get back to the previous display without opening a command line window and doing a "reset." Can't 'unreasonable' eye positions be prohibited within sideview? --tom

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database access
by Lars Kunert 10 Oct '03

10 Oct '03

Hi referring to my previous mail... what I am really doing is to write some kind of database interface. I see there basically three approaches - the first two are basically short-time workarounds ( I have decided to use the first one) there third would be the "real stuff" first) My plugin accesses the db and creates a temporary file - then it tells chimera to load it. Advantage chimera can use it native (and probably fast) reading routines... second) The plugin fetches the data form the db and builds up the molecule in chimera by use of the python-interface... third() I tell chimera to access the database X, use password Y, and run select / or call a stored procedure. the stored-procedure or (for older mysql a linked extension function) could build up an input-format chimera understands from the actual data. the select-version would be a bit ugly cause we would need several of them or place some file-blobs in the bd. I hope your are interested to do some thing about approach three... Sincerely Lars

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again Chimera and Dock
by Roberto Sanavio 03 Oct '03

03 Oct '03

Greetings to all, I'm a novice user of Chimera, and I downloaded it recently with the intention to use it also for calculating molecular surfaces as input for UCSF DOCK.From the documentation I haven't understood if the latest version of Chimera is able to do that. on Thu, 19 Dec 2002 Eric Pettersen wrote, answering to Eckhart Guthöhrlein , same date: "The current version of Chimera (12/02; build 1602) doesn't have the capability to prepare an ms file suitable for DOCK, though we anticipate that capability being in the next release (~ 3/03). " If, as I suspect, it's still not possible this use of Chimera, could you tell me if and when it will be?Do you perhaps know of alternatives still functioning on WindowsXP systems ( I'm a novice even about SGI ) or the better choice for me is still to study how to run old DMS on Irix? Thank you for your patience, Roberto Sanavio Politecnico di Milano tel. +39-031-513453 cell. +39347-5894996 e-mail: rsdag(a)libero.it

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...some questions
by Lars Kunert 26 Sep '03

26 Sep '03

Hi I have got a couple of questions. After loading a couple of molecules (files) into chimara: >>>opened = chimera.openModels.open('xxx.mol2') How do I access the name of the file, the model was loaded from? How can I find out if a model/molecule is active and on the screen? If not , who can I make it active, and zoom to it? How do I display a set of spheres, together with with some edges connecting them. I do like to show some kind of pseudo-molecule/graph. Can I display an ellipsoid? - Do I have to construct it from triangles? I want to display a binding pocket, can I limit the amount of data displayed before the proterin is shown the first time? I have got some problems with the calculation of surfaces (1dwd always crashs...). Is it possible to limit the surface-calculation to an connected area (pocket). By the way, the tutorials are great, but the reference manual will probably need some efford... Thanks a lot for your help, Lars

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colors...
by Lars Kunert 26 Sep '03

26 Sep '03

Hi I do like to color some molecules/atoms I figured out, that I create a color like this: >>c=chimera.Color() >>c=(1,0,0,1) But when I apply this to all the atoms of a molecule, I end up with the following error-message: >>> for a in m.atoms: a.color=c Traceback (most recent call last): File "<pyshell#66>", line 1, in ? for a in m.atoms: RuntimeError: __wrappy__ is missing >>> I suppose, that colors like "red"are predefined somewhere, where? Are the different color-levels modell/molecule/atom are just fancy stuff for the interactive user? - I colored a molecule first (interactive) "byatom" and then tried to alter the coloring by hand: >>m.color=c it did not work, I had to alter the color atomwise... is color-byatom a function? How can I call it? Is there a way to "switch on"a history function in the buildin IDLE? Copy and paste do also not work within the IDLE. I allways have to copy and paste via an editor...

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mol2-parser reorders entries
by Lars Kunert 24 Sep '03

24 Sep '03

Hi! I do like to reference chimera-atoms from my extension. I have the problem that chimera reorders the atoms (and probably also the bond entries) of mol2 files. Which of the following workarounds would you suggest: - resort all my mol2-files -> will only work if the resorting ist stable - use a dictionary -> puts some unwellcome functionallity into my python-wrapper - refer by name -> mol2-atom names do not have to be unique and will be slow without a dictionary or is there a way to switch it of??? Thanks Lars

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Re: chimera
by Thomas Goddard 16 Sep '03

16 Sep '03

Hi Matt, Below is example python code to start Chimera and open PDB 1zzz. For it to work you have to set the LD_LIBRARY_PATH environment variable before running python to include the chimera/lib directory. If you start it from your own Python program you can pass Python objects directly to Chimera. This is simplest if your program uses Tkinter, since Chimera needs the Tkinter event loop to run in order to update the graphics and accept user input. Tom # # Need to set LD_LIBRARY_PATH environment variable to <chimera-home>/lib # before running python2.2. # # On linux your python2.2 must have the dl module. This module is not # standard on linux. It is included in the Python included with Chimera. # chimera_home = '/usr/local/chimera-1700' import sys import os.path sys.path.insert(0, os.path.join(chimera_home, 'share')) sys.path.insert(0, os.path.join(chimera_home, 'lib')) os.environ['CHIMERA'] = chimera_home import chimeraInit chimeraInit.init([], eventloop = False) import chimera chimera.openModels.open('1zzz', 'PDBID') # Will download from web. chimera.tkgui.eventLoop() # Doesn't return until Chimera quits -------------------------- > Date: Tue, 16 Sep 2003 22:12:26 -0500 > From: Matthew Dougherty <matthewd(a)bcm.tmc.edu> > To: goddard(a)cgl.ucsf.edu > Subject: chimera > > Tom- > > I was wondering if I can run chimera using an embedded python. > If so can I send python data objects to it through my main program? > > Matt > > ------------------------------------------ > Matthew Dougherty/713-747-5433 > National Center for Macromolecular Imaging > Baylor College of Medicine >

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should we change the chimera help files on Windows?
by Greg Couch 16 Sep '03

16 Sep '03

>From the python devlopment mailing list summary: "This discussion also brought up the question of whether a .chm help file for the Windows distribution would be worth using instead of including the HTML distribution of the documentation as it stands now. It was agreed that it was a good thing to have since it allowed for better searching. Tim Peters also discovered the install went faster since it would not have to copy a ton of individual HTML files." Better searching would be nice, although we do provide searching on the web site. Faster installs would be nice, too. So I'm not proposing that we do this anytime soon, but that we keep this idea in the back of our heads. And if someone comes across a tool that maintains two forms of help files (html and cbm), please share that information. - Greg

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automatic checkForChanges
by Eric Pettersen 02 Sep '03

02 Sep '03

I'd like to suggest that chimera.openModels.{open,add,close} all automatically run chimera.update.checkForChanges() as they finish (suppressable by supplying a 'checkForChanges=False' keyword argument to the functions). Right now, developers who aren't "in the know" will write scripts that loop through structures, opening and closing them and performing operations, and because they don't know to call checkForChanges the scripts will typically fail due to running out of memory. Also, some other operations (surfacing) will fail if checkForChanges isn't called after a model is opened. There are other times when checkForChanges needs to run, but those are relatively rare compared to these openModels functions. It seems to me that making this change makes normal scripting less error-prone while allowing for the uncommon case of wanting to suppress the checkForChanges. Opinions? Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Object lifetimes
by Thomas Goddard 07 Aug '03

07 Aug '03

Here are some notes about how Chimera makes sure C++ and Python objects are not prematurely deleted. The current mechanism is fragile. Tom Object lifetime problems ------------------------ Chimera's current mechanism for knowing when to delete C++ and Python objects has problems. Here's the basic example atom.color = MaterialColor(red, green, blue) This code results in the C++ Atom object saving a pointer to the C++ MaterialColor object. The trouble is that the Python MaterialColor object needs to be referenced so it does not get deleted. If the Python MaterialColor gets deleted then it will delete the C++ color and the Atom will hold a bad pointer, the program will crash. The way this is currently handled is that object attributes wrapped by WrapPy have a reference to the most recently set value. So the Python atom object above will have a atom.__cached_color attribute. The trouble with this solution is that object attributes do not exist for all the C++ pointers saved by the C++ objects. For example, openModels.add([Molecule()]) This causes the C++ OpenModels object to save a pointer to the C++ Molecule. But what keeps the Python Molecule from being deleted? The OpenModels object has no attributes giving the models, and even if it did the WrapPy cached value would not be updated by the above call. I don't know what reference keeps the Python Molecule from being deleted. Maybe Greg know. If the Python molecule is deleted it will delete the C++ molecule and OpenModels will hold a bad pointer. The core of the problem is that there is no bookkeeping of pointer references in C++. The current WrapPy mechanism is just a bandaid that makes the system work but it is very fragile and error prone. Also caching all the attribute values may be why creating Python atoms and bonds is so slow. Also one has to be careful to not make attributes that do large computations. That is unexpected behaviour. I don't think there is any simple fix. Making the C++ code include pointer book-keeping code is a big burden on the C++. Making wrapped C++ objects objects hold a reference to the Python object is another solution (Sparky does this). So the Python object can never be deleted unless you call a special C++ function, like molecule.destroy(). This is a burden to the Python programmer, and is unexpected behaviour in Python.

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PDB opening and coloring optimizations
by Thomas Goddard 07 Aug '03

07 Aug '03

Here are some tests I did to investigate speeding up opening large PDB models and coloring large molecules. Tom Optimizing PDB model opening and coloring ----------------------------------------- Opening PDB file optimization ----------------------------- I tested making Chimera open PDB files and display the molecule without creating Python atoms, bonds and residues. The molecule displayed about 4 times faster: Open 1jj2 (~100,000 atoms) current chimera: 26 seconds Open without Python atoms, bonds, residues: 6.5 seconds Open in PyMol: 3 seconds These times are on Linux, P4 2.2 GHz, 1 Gb memory. The Python atoms, bonds, residues are created when they are needed, for example, if the atoms are colored. To avoid a freeze there could be an idle procedure that creates the Python atoms, bonds and residues. This optimization requires the following code changes. 1) The b-factor, occupancy and serial number from the PDB file are saved as Python attributes. These would need to be C++ attributes. 2) WrapPy fetches all attributes and makes a reference to them, eg molecule.atoms, molecule.bonds, .... I commented out those lines that would cause Python atoms, bonds and residues to be made. WrapPy does this to make sure objects aren't deleted prematurely. In the case of atoms, bonds and residues this is not a problem because the C++ object keeps a reference to the Python object so the Python object cannot be deleted until molecule.destroy() is called. 3) chimera/__init__.py replaces bonds to metals with pseudo-bonds. A C++ routine to find metal atoms with bonds is needed to avoid creating all the Python atoms and bonds. 4) Atom, bond and residue created triggers don't happen when the molecule is opened with this optimization. Some Chimera features rely on the triggers happening immediately, for example, surface categorizer wants to recategorize atoms whenever bonds are created or deleted. Like the metals complex code, this would have to be done in C++ to avoid creating all Python atoms and bonds immediately when a file is opened. Also the bond triggers should probably indicate when the bond is created, not just when the Python bond is created. So triggers should fire on C++ bond creation. Currently the TrackChanges code keeps a set of the Python objects instead of C++ objects so this would cause all Python bonds to be created on file open. Changes 1), 2) and 3) are small and easy. Change 4) is a more serious problem that needs more consideration. Perhaps the solution for 4) is to keep the trigger and TrackChanges as is, but make surface categorization an idle task. It creates category names for menu entries that could be added to menus whenever the computation finishes. Memory use for PDB models ------------------------- About 2/3 of memory used is C++ atoms/bonds and 1/3 is Python atoms/bonds. VSZ (Mb) RSS (Mb) Chimera start-up 188 23 1jj2, no Python atoms/bonds/residues 360 (grew 172) 167 (grew 144) 1jj2 with Python atoms/bonds/residues 437 (grew 77) 243 (grew 76) These Redhat 8.0 memory use numbers from unix command ps suggest most of the memory is in the C++ data structures, rather than the Python atoms/bonds. Atom coloring optimization -------------------------- Here's a summary of some tests I did coloring atoms and bonds of 2btv (~50,000 atoms) a single color. More details are in a chimera-dev mailing list posting from June 2003 with subject coloring speed. Color atoms/bonds using Actions menu: 1.70 sec Breakdown: Building display list: .88 sec Python color setting: .66 sec Clearing track changes: .11 sec I tested alternate version of the Python color setting code: Minimal for loop for a in m.atoms: a.color = color for b in m.bonds: b.color = color took .52 seconds. The Actions menu code is a little slower because the color assignment is done with a function call. Using setattr() is slower. Using map() is slower. Using C++ set_atom_color() function for a in m.atoms: set_atom_color(a, color) for b in m.bonds: set_bond_color(b, color) took .27 seconds. So attribute setting done by WrapPy may not be as fast as it could be. Using C++ routines color_atoms(atoms, color) color_bonds(bonds, color) where atoms and bonds are lists took .10 second. I believe this time is all taken adding atoms/bonds to the TrackChanges stl::map<PyObject*>. I did similar test for the Python part of "color by element". Coloring atoms by element type: 3.5 sec Breakdown: Build display list and TrackChanges: 1 sec Python code to set colors: 2.44 sec Here are times for various versions of the Python color setting code: Actions menu color by element: 2.44 sec Optimized python coloring: 1.11 sec C++ routine: .12 sec The optimized Python uses a Python dictionary mapping element numbers to Chimera color objects. The current Actions menu version is slower because it maps element numbers to color names, and fetches the color object for each atom. The C++ routine color_atoms_by_element(atom_list) is a simple translation of the Python version. If the display list and track changes overhead is reduced by a factor of 10 (which I believe is not too hard), then moving some Python loops to C++ will make a significant improvement in response time. Besides coloring this could help with atom/bond show/hide, representation changes, large selections like chains or selecting all atoms.

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quartinary structure
by Correia, Manning 31 Jul '03

31 Jul '03

Dear Sir/Madam I am trying to reconstruct an ion channel molecule (1p7b). The molecule was submitted to pdb in the alternate form (1/2 molecule). Can I recreate the complete molecule in Chimera. If not do you know a program that I can use to import the reconstructed molecule into chimera. Secondly, can I tag a series of residues one at a time but not in a sequence? So far I am really enjoying your program. Manning Correia Manning J. Correia, Ph. D. Jehu M. Robison Distinguished Professor of Otolaryngology and Physiology & Biophysics and Anatomy & Neurosciences Telephone: 409-772-(2708), 5883, 9802 Fax: 409-772-2694 e-mail: mjcorrei(a)utmb.edu ---------------------------------------------------------------------- "Are you still wasting your time with spam?... There is a solution!" Protected by GIANT Company's Spam Inspector The most powerful anti-spam software available. http://www.giantcompany.com <http://www.giantcompany.com/>

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