Hi again, When using the python shell, I am often struggling to find the attribute for the atoms I work on. for at my list with the selected atoms, I caught that at[i].name gives the atom name of the entry at[i], at[i].residue provides with the name residue.chain, etc. Where can I find in the programmer's guide the full list of available attributes? What would be the way to ask for the serialNumber from the IDLE? Thanks lot JD On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request@cgl.ucsf.edu wrote:
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Today's Topics:
1. Re: distance (Elaine Meng)
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Message: 1 Date: Thu, 21 Feb 2008 09:00:37 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] distance To: "??" <lynnwuchao@gmail.com> Cc: chimera-users@cgl.ucsf.edu Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A@cgl.ucsf.edu> Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed
Hi!
The distances are listed in a separate dialog - choose "Tools... Structure Analysis... Distances" from the menu to open that dialog. You can adjust the number of decimal places in the measurement, and there is a "Save" button if you want to save distances or other measurements to a text file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Feb 20, 2008, at 11:38 PM, ?? wrote:
Hi, folks, I select two atoms and measured their distance using the command distance and can see the exact distance value in the graphic interface, but when I go the log file i can not find it. Can anybody give me a hand and tell me why can I find it? Thanks.. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi JD, I don't know if/where there is a complete list for programmers, but the User's Guide "atom specification" page includes tables that list several attributes of atoms, residues, and molecule models. Maybe you saw these already. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html To see the lists, click the links on the left: Atom, Residue, Model. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Feb 22, 2008, at 7:28 AM, Jean-Didier Maréchal wrote:
When using the python shell, I am often struggling to find the attribute for the atoms I work on. for at my list with the selected atoms, I caught that at[i].name gives the atom name of the entry at[i], at[i].residue provides with the name residue.chain, etc.
Where can I find in the programmer's guide the full list of available attributes? What would be the way to ask for the serialNumber from the IDLE? Thanks lot JD
On Feb 22, 2008, at 7:28 AM, Jean-Didier Maréchal wrote:
Hi again,
When using the python shell, I am often struggling to find the attribute for the atoms I work on. for at my list with the selected atoms, I caught that at[i].name gives the atom name of the entry at[i], at[i].residue provides with the name residue.chain, etc.
Where can I find in the programmer's guide the full list of available attributes? What would be the way to ask for the serialNumber from the IDLE?
Thanks lot JD
Hi JD, dir(a) will list the attributes of 'a'. help(a) will produce documentation for the attributes of 'a' that come from the C++ layer (but not ones that were added in the Python layer). 'a' could be a class rather than an instance. For example, help(chimera.Atom) lists the methods/attributes of Atom and provides some info about them. We do what we can to keep the programmer's guide up to date, but for attributes (since they get added/changed pretty frequently) it is better to query with help()/dir() than to fall back on the relatively static programmer's guide documentation. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
The Chimera programming reference manual is automatically generated from the code and says little about what the available methods and attributes do. But it does at least name them. Here are the web pages for Atom, Residue and Molecule: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/generated/_c... http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/generated/_c... http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/generated/_c... I found this looking in the programmer's reference guide, under module _chimera, and scroll to the end of that long page for links to the different kinds of objects. Tom
A delayed addendum... Some attributes are not included in the Programmer's Guide lists or what you get from help() in IDLE: atoms: areaSAS, areaSES, bfactor, charge, occupancy, serialNumber residues: areaSAS, areaSES, isHet (the latter is in help but not the current Prog. Guide list) molecule models: display (not in Prog. Guide list for Molecule because inherited from Model) Some attributes do not come from the C++ layer, and some do not exist until you do something particular in Chimera (areaSAS and areaSES are assigned when molecular surface is generated; charge is assigned when Add Charge is used; etc.). Also, new attributes you have created with Define Attribute are not listed. Generally the Render/Select by Attribute tool will list these atom and residue attributes, however. Elaine ----- Elaine C. Meng, Ph.D. meng@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 Fri Feb 22 13:07:42 PST 2008 Eric Pettersen wrote:
dir(a) will list the attributes of 'a'. help(a) will produce documentation for the attributes of 'a' that come from the C++ layer (but not ones that were added in the Python layer). 'a' could be a class rather than an instance. For example, help(chimera.Atom) lists the methods/attributes of Atom and provides some info about them. We do what we can to keep the programmer's guide up to date, but for attributes (since they get added/changed pretty frequently) it is better to query with help()/dir() than to fall back on the relatively static programmer's guide documentation.
On Feb 22, 2008, at 1:36 PM, Tom Goddard wrote:
The Chimera programming reference manual is automatically generated from the code and says little about what the available methods and attributes do. But it does at least name them. Here are the web pages for Atom, Residue and Molecule:
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ generated/_chimera/__init__/Atom.html
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ generated/_chimera/__init__/Residue.html
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/ generated/_chimera/__init__/Molecule.html
I found this looking in the programmer's reference guide, under module _chimera, and scroll to the end of that long page for links to the different kinds of objects.
participants (4)
-
Elaine Meng -
Eric Pettersen -
Jean-Didier Maréchal -
Tom Goddard