- Chimera-dev - RBVI Mailing Lists

minimize in IDLE and command line
by Elisabeth Ortega 07 Apr '11

07 Apr '11

Dear Chimera Dev. Team, I have a problem when I'm trying to launch "minimize" in the Python IDLE. If I write in the IDLE: >>> import MMMD >>> MMMD.base.Minimizer(chimera.openModels.list(modelTypes=[chimera.Molecule]),nsteps=0) I get (in the IDLE): <MMMD.base.Minimizer instance at 0x9e0978c> But if I write in the command line: minimize nsteps 0 I get (in the IDLE and in the message bar): >>> Initial energy: 475.211926 Anybody has any idea about that? Kind regards. Elisabeth Ortega - Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona

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Molecular energy
by Elisabeth Ortega 05 Apr '11

05 Apr '11

Dear Chimera Dev. Team, I'm trying to add energy calculations in my script. To do so, I started with the class Minimize, defining nsteps as 0 but I think that it is not so tidy. In chimera/share/MMMD/MMTKinter.py I found the function minimize and a line that says: msg = "Initial energy: %f" % self.universe.energy() . My question is... How can I invoke this self.universe.energy() in order to get the energy? I tried to write a new class in MMMD/base.py and a new function in MMMD/MMTKinter.py in order to obtain a function like "MMMD.base.energy()" to write in my script but I think that I am doing it more complex that it is... Anyone has any idea for doing it successfully? Thanks, Elisabeth Ortega-Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona.

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Re: [chimera-dev] [Chimera-users] Energy Minimisation Citation
by Konrad Hinsen 28 Mar '11

28 Mar '11

On 28 Mar, 2011, at 5:26 , Nancy wrote: > I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? The minimization code used by Chimera comes from MMTK, whose reference is this paper: http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2 The force field is some dialect of Amber, though I don't know which one exactly is used by Chimera. I hope someone else can provide that information. Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------

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minimizer
by Elisabeth Ortega 17 Mar '11

17 Mar '11

Dear Chimera Dev. Team, I have a question about the Minimizer. I want to use it in the Python/IDLE to calculate the initial energy of a system during the execution of one of my scripts, but I don't found any way to call the function Minimizer and obtain the numeric result without show the addCharge window if I have a metallic system. What can I do to call this function correctly? Thank You Elisabeth Ortega Universitat Autònoma de Barcelona

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Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

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Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 15 Mar '11

15 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

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clashes and contacts with hidden models
by Elisabeth Ortega 28 Feb '11

28 Feb '11

Dear Chimera dev. Team, I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? Thank you for your time. Elisabeth Ortega-Carrasco Universitat Autònoma de Barcelona Spain

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Re: [chimera-dev] [Chimera-users] Surface electrostatic and hydrophobicity.
by Miguel Ortiz Lombardia 29 Jan '11

29 Jan '11

Le 28/01/2011 20:37, Elaine Meng a écrit : > and there is nothing like a "hydrophobic potential" Dear Elaine, In fact, such a thing does exist, have a look here: http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html and here: http://www.moldiscovery.com/docs/vsplus/grid.html I tried long ago to import GRID maps to Chimera but faced two problems: 1/ GRID did not provide a real "volume object", but one that would actually have non-zero values only on grid points corresponding to the solvent accessible surface, which is not implemented in Chimera (and the vdwdefine +1.4 trick is not good enough here) 2/ Eventually, GRID became part of a big package that needed a big licence fee... How this potential is calculated was published long ago (see the second web page above and Goodford's cite in the first one) It would be truly useful if it was implemented in Chimera (if you still have slots in your wish-list) I can enter a feature request if you want... Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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menubar
by Elisabeth Ortega 25 Jan '11

25 Jan '11

Dear Chimera Dev Team, I created a new item in the menu bar but my question now is how can I put options in the new bar? As you know, to put any option in the menu 'Tools' we "only" have to copy the new folder in chimera/share/ . I'm trying to do the same with my new item but the only way that I found to do so is modifying the ChimeraExtension.py file of VolumeMenu. Exists any other possibility much easier than that? Thanks. Elisabeth Ortega Universitat Autònoma de Barcelona (UAB)

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Re: [chimera-dev] modify the menu bar
by Eric Pettersen 21 Jan '11

21 Jan '11

Hi Elisabeth, I guess my recommendation is to structure your code like an extension, so that Chimera will execute a ChimeraExtension.py file at startup that you've written. Normally, you put code into a ChimeraExtension.py file to do all the stuff to get your extension into the Tools menu, add a command version, etc.. but the code in that file can actually be almost anything. Just put your code to add your top-level menu in there instead of normal extension-adding code. Let me know if you need more details. --Eric On Jan 21, 2011, at 10:58 AM, Elisabeth Ortega wrote: > Hi Eric, > > I'm testing the two options. Your option works only when I execute > ">>chimera mymenu.py" .How can I auto-execute your code when I start > Chimera? > > Thanks > > 2011/1/21 Eric Pettersen <pett(a)cgl.ucsf.edu> > Hi Elisabeth, > As Tom says, the code he refers to is really more complex than you > need. Just do this: > > from chimera.tkgui import addMenu > myMenu = addMenu(label="menu name") > > to create a top-level menu that you can add items to. An example of > its use in Chimera itself is in the _getAliasMenu() function in > Midas/midas_text.py. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > &nbsp p; http://www.cgl.ucsf.edu > > On Jan 21, 2011, at 9:20 AM, Tom Goddard wrote: > >> Hi Elisabeth, >> >> There is some code in Chimera that makes a new top-level menu >> called >> Volume that is a copy of the Tools / Volume Data submenu. That >> Volume >> menu is displayed using menu entry Tools / Volume Data / Volume >> Menu on >> Menubar and if you show it it is remembered in the Chimera >> preferences >> file so it will appear every time you run Chimera. This is a more >> complex than you need. But the main routine that would be useful to >> study is called create_toplevel_volume_menu() in file >> >> chimera / share / VolumeMenu / __init__.py >> >> in your Chimera distribution. It would be easy to make a similar >> Ch a toplevel Scripts menu and simply read all >> the files in one of your directories and made menu entries which >> caused >> the file to be opened in Chimera. If you need more help with >> writing it >> ask. >> >> Tom >> >> >>> Dear Chimera Dev Team, >>> >>> >>> I'm trying to put other option in the menu bar (File, Select, >>> Actions, >>> ... , myOption, Help) to store my own scripts. I'm doing a deep >>> search >>> on your python and C++ codes but I don't find which is the code >>> that I >>> have to modify. >>> I know that is easy to store my scripts in the Tools menu, but I >>> prefer to put my scripts in a new option of the menu bar. >>> >>> >>> Thanks a lot for taking the time to reply. >>> >>> >>> >>> Elisabeth Ortega >>> Autonomous University of Barcelona (UAB) >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > >

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