- Chimera-dev - RBVI Mailing Lists

Importing modules causes crashes
by Mateusz Dobrychłop 23 May '13

23 May '13

Hello, I'm writing a Chimera extension that uses modules that it imports an external module. To do this, I append the sys.path with a path to the directory where the module is placed and then I just import it. And then Chimera crashes. The line with the import is the one that directly causes the crash. I'm attaching a screenshot of the error that Chimera throws when I run it with --debug option. I have no idea what might be wrong. Thank you for your time, Mateusz

2 1

Trajectory and MD Movie GUI
by Alex 18 Apr '13

18 Apr '13

Dear all, I'm developing a plugin and would like to add frames to a model on the fly and being able to use the trajectory (MD Movie) GUI to navigate among the frames. Unfortunately, I can't find a way to instanciate the dialog MovieDialog (Movie/gui.py) with a model already opened. It seems that I have to use an Ensemble object (Trajectory/__init.py__) but its constructor requires another ensemble, and the Ensemble objects seem to be created inside MovieDialog's constructor. I'm rather confused right now and would appreciate some help on the matter. Thank you in advance, Best regards, Alex Tek --------- Alex Tek, Phd Department of Cell and Molecular Biology BMC Box 596 SE-751 24 Uppsala Sweden

3 3

ligand
by Muhammad Ali 16 Apr '13

16 Apr '13

sir When I retrieve a ligand structure in SDF files from PDB site, it contains many ligand, how to get a single ligand ??? also ligand files are why not available in PDB files ?? I have to covert them in Chimera.....

2 1

IDLE : code completion under MAC OS X
by Benjamin SCHWARZ 12 Apr '13

12 Apr '13

Hello, I started to develop simple python/chimera scripts. The manual is rather poor on these aspects (btw, is there a doxygen somewhere ?), and therefore the code completion in the chimera IDLE shell is particularly useful… Unfortunately, on my MAC (OS X), it appears to be messy : the TAB key triggers the usual "completion scrollable list window" on both my windows and linux (debian) machines, but not on my MAC. Note that I am still able to scroll through the "invisible" choices by pressing TAB and then using the up and down arrows, it is just that I cannot see the list, which is a bit annoying to have a clear view at once. I guess this has more something to do with the IDLE configuration than with chimera itself, but I don't know how to dig that up, so if you have any idea how to solve this I'd be pleased to read from it. --Ben

2 1

Pseudobonds and gap detection
by Ibai Gazpio 10 Apr '13

10 Apr '13

Dear, We are developing a chimera extension and I would like to know if there is a way to detect or select those models which have an internal sequence gap, represented by the program as a pseudobond in order to distinguish them from those who haven't. Is there a function to do that? Thank you very much and congratulations for the program. Sincerely Ibai

2 1

3dconnexion
by Dougherty, Matthew T 03 Apr '13

03 Apr '13

Hi, I am starting to build a matrix of USB HID devices using controllermate on a mac. I am planning to use two 3dconnexion devices. one to handle 6D translation/rotation, and the other to manage color/lighting; or maybe left hand for trans and right for rotation, etc. . The current driver in chimera only sees one device. If I touch the first USB 3dconnexion device plugged in, it behaves as expected. Touching the second device, chimera acts as though it is the first device. So the driver is not keeping track of the number of devices. In controllermate I can see both devices and can program them independently. For example, I will be able to remap these signals to my choosing and pass it on to a chimera extension I am developing. The second problem I am having is when chimera starts up it exclusively grabs the low level driver, ignoring the the high level driver which incorporates context management. Consequently controllermate is unable to intercept and modify the signal before passing it on. A good reason to do this would be creating deadband zones, or a user defined response curve, or integration with multibutton panel like the logitech g13 so that I can modulate the response (eg, 0.1x,1x,10x,100x, etc). How do I disable 3dConnexion so that it will not load in chimera? I could wipe out the code, but would prefer minimally screwing with chimera base code which is a headache for daily builds and has a risk factor of unforeseen consequences. Something in preferences would be helpful. In a related question on preferences, the scroll wheel is tied to camera zoom. I would like to remap that as a movement in z. Generally I like to keep my scale factor at 1; I find heavy or casual use tends to get me into camera problems. Is this possible? at the moment I disable the scroll wheel. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

3 6

changing position for a residue using python
by Jean-Didier Maréchal 27 Mar '13

27 Mar '13

Hi all, I have a problem with a prot and it seems that renumbering could help. I'd like to automatically add 230 to the residue number of the aa of my second chain. As I feared, when looping other residue to change res.id.position, my script fails as position can not be modified. How could I do this? Should I delete position and re-create it? Best JD

4 3

Re: [chimera-dev] [Chimera-users] Import Chimera Modules
by Tom Goddard 18 Mar '13

18 Mar '13

Hi Jon, I'm switching this discussion to the chimera developer mailing list since it is so technical. I'm wondering why you want to run Chimera in your own Python. Often people want that so they can install their own custom Python modules and use them with Chimera. We recommend just using the Chimera Python for that and installing your other modules into the Chimera Python. That saves you a lot of grief trying to do what you did -- set up the environment to get Chimera to start in another Python. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Import Chimera Modules From: Jonathan Williams To: Tom Goddard Date: 3/18/13 2:37 PM > Hi Tom, > > Good news: I got the chimera modules to import! > > I think that you were correct about having an older > libfreetype.6.dylib that was being used instead of Chimera's version, > probably from my Enthought Python Distribution . Overall I believe > that my EPD was making things harder for me. So I removed the EPD > from my system, set all of the environment variables per the Chimera > IDLE, added ~/Resources/lib and ~/Resources/share to PYTHONPATH, and > now I'm in business. > > Thank you for your help and suggestions! > > Jon > > > On Mar 18, 2013, at 12:49 PM, Tom Goddard <goddard(a)sonic.net > <mailto:goddard@sonic.net>> wrote: > >> Hi Jon, >> >> Chimera includes the version of libfreetype.6.dylib it needs. The >> error must mean you have another older libfreetype.6.dylib on your >> system that Chimera is getting instead of its own version. The first >> thing would be to try to locate where the other libfreetype.6.dylib >> is. I guess Chimera starts on your machine, so somehow it gets the >> right library. That suggests that you do not have the environment >> variables that control library loading setup in the same way as >> Chimera does. I'd suggest you start Chimera, open the IDLE shell >> window (Tools / General Controls) and print all the environment >> variables seen by the running Chimera using for example >> >> import os >> for k,v in os.environ.items(): >> print k,v >> >> and see if those differ from what you are trying outside Chimera. >> >> Tom >> >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Import Chimera Modules >> From: Jonathan Williams >> To: Tom Goddard >> Date: 3/18/13 8:05 AM >>> Hi Tom, >>> >>> Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH >>> variable, and I think this took care of my original problem. >>> However I have encountered a new error: >>> >>> ImportError: >>> dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, >>> 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib >>> Referenced from: >>> /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib >>> Reason: Incompatible library version: _chimera.dylib requires >>> version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 >>> >>> This seems like I just need to update my FreeType libraries, but I >>> have not had a chance to try this yet. If you have any other >>> suggestions, those would be appreciated, otherwise I'll send an >>> update when I get a chance. >>> >>> Thanks again, >>> >>> Jon >>> >>> >>> On Mar 15, 2013, at 7:02 PM, Tom Goddard <goddard(a)sonic.net >>> <mailto:goddard@sonic.net>> wrote: >>> >>>> Hi Jon, >>>> >>>> Maybe the trick is Chimera uses environment variable >>>> DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or >>>> DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that >>>> sets the environment variables >>>> >>>> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.… >>>> >>>> and a comment on this code change says "Use >>>> DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so >>>> system frameworks will get system versions of shared libraries." >>>> >>>> Tom >>>> >>>> >>>> >>>> On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: >>>> >>>>> Hello, >>>>> >>>>> I am currently trying to import Chimera modules into a non-Chimera >>>>> python installation. I have referenced previous messages from >>>>> this mailing list >>>>> (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html) >>>>> and have added the relevant paths to Chimera in the >>>>> LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. >>>>> >>>>> However when I try to import Chimera, Midas or "import >>>>> chimeraInit" followed by "chimeraInit.init([])" I receive the >>>>> following error: >>>>> >>>>> >>> import chimeraInit >>>>> >>> chimeraInit.init([]) >>>>> Traceback (most recent call last): >>>>> File "<stdin>", line 1, in <module> >>>>> File >>>>> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", >>>>> line 594, in init >>>>> import chimera >>>>> File >>>>> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", >>>>> line 16, in <module> >>>>> from _chimera import BBox, Camera, Color, ColorGroup, >>>>> DirectionalLight, LODControl, Lens, LensViewer, Light, Material, >>>>> MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, >>>>> OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, >>>>> PositionalLight, Selectable, SharedState, SpotLight, Sphere, >>>>> Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >>>>> ImportError: >>>>> dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, >>>>> 2): Symbol not found: __cg_TIFFClientOpen >>>>> Referenced from: >>>>> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>>> Expected in: >>>>> /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib >>>>> in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>>> >>> >>>>> >>>>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build >>>>> 38197) for 64bit Mac. >>>>> >>>>> Any help or advice would be greatly appreciated, >>>>> >>>>> Jon Williams >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Following on new atom types (again)
by Elisabeth Ortega 18 Mar '13

18 Mar '13

Dear Chimera dev. Team, I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported". As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens. Probably I'm modifying the wrong files... Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it? Thank you so much for your time and your patience. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

3 2

Following on new atom types.
by Jean-Didier Maréchal 15 Mar '13

15 Mar '13

Hi, I am following on Elisabeth's question on the 23rd of january regarding setting up new atoms. I have added platinum (for cisplatinum) as a new atom type and proceed as you recommended (calculate the charge on isolated species and generate the covalent bond for the first coordination sphere of the metal). I have though two questions: 1. when running the minimization I have the following message: Atom whose IDATM type has no equivalent Sybyl type: #-2147483648.-2147483648:1@PT1-CPT (type: Pt) Although the minimization still proceed, I'd like to do things right. Could you tell me where I could change the sybyl atomtype. I looked with the idle the idatmType of this atom and it gives me Pt+. I don't understand what is wrong. 2. I'd like to rapidly change the charges of the cisplatinum using charges calculated with ab initio calculations. I was thinking to change these values from the idle changing the charge attribute previous to minimization. Does it sound correct? What would be the easiest way you would reckon? Best regards, JD **************************** Dr. Jean-Didier Maréchal Associate professor The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://g <http://asklipio.qf.uab.es>ent.uab.cat/jdidier<http://ent.uab.es/jdidier>

3 3

Chimera binary code issue
by jupiter 13 Mar '13

13 Mar '13

Hi, I have been reading Chimera document on Chimera web site and I am understanding that Chimera is better to run with hardware accelerator, but we don't have GPUs in our virtual machines, we have to use mesa and we are using xlib-glx driver for remote VNC connection. One major issue I am currently investigating is that the binary Chimera code can perform 3D rotation in mesa DRI driver, but very poor performance when using mesa xlib-glx driver on CentOS 6. Please correct me my following assumptions and options to rectify the problem: (1) Binary code could be hard linked with mesa DRI driver, the solution is to remove the hard link, or replace some libraries. (2) Chimera may not be able to run on mesa xlib-glx driver at all, no possible workarounds, no solution. (3) Chimera can be used with xlib-glx driver if we can build Chimera source code with mesa xlib-glx driver. I understand you don't encourage people to build Chimera from source code, nor do I wish. But if that is the only choice which can fix the problem, would you please point me instructions and procedures how to build the source code on Linux? I've looked at README.bootstrap from svn source code, but Thank you. Kind regards. Jupiter

3 7

neighbors
by Elisabeth Ortega 12 Mar '13

12 Mar '13

Dear Chimera Dev. Team, There is any way to select the neighbors of a selected atom without drawing the bond? If it is not possible... could you tell me how draw and erase bonds using a python function? Thank you for your time. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

2 1

2-D projection of volume in Chimera
by Jesus Montoya 04 Mar '13

04 Mar '13

Hi, Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. While a "solid" representation of the volume is similar, it is not exactly what I need... Thanks!

3 2

question
by Paola Peshkepija 25 Feb '13

25 Feb '13

Good afternoon, I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. Thank you in advance for your help! Paola

2 1

Electrostatic coloring using Chimera
by Daniel Lee 19 Feb '13

19 Feb '13

To Chimera Developers, Hello, this is Daniel Lee from University of Utah Department of Pharmaceutics and Pharmaceutical Chemistry. I am currently working as a Teaching Assistant in a DNA/Protein modeling class for graduate students. We are using UCSF chimera 1.17 to explore molecular structures. I have a hard time trying to get the system to show electrostatic surface with colors matching to the electronegativity. I followed the tutorials however it seems really difficult to reproduce what the tutorial did. Surface/binding analysis did not had the preselected electrostatic potential file. I looked through the system files however did not find anything. Would you be able to assist me with this issue? The PDB model I was exploring was 2KTZ and 2KU0. I used the fetch function to download this file. Thank you, Daniel

2 1

Chimera Problem
by Neil Bugeja 19 Feb '13

19 Feb '13

Dear Sir/Madam I am using Chimera as part of my thesis. I need to find a homology model for the human muscarinic M1 receptor. However, it always tells me service is down or an error when loading from uniprot. Am I doing something wrong? The Uniprot ID is P11229 and I get fetch ID failed Thanks -- Neil Bugeja

2 1

Add new Amber parameters
by Elisabeth Ortega 22 Jan '13

22 Jan '13

Dear Chimera dev. team, I have to use my own set of Amber99 parameters because I'm working with transition metals. I'm testing if I can minimize a benchmark system that contains one copper atom coordinated to 6 water molecules. To do it, I don't use any script, I use directly the tool "minimize" present in Tools-> Structure Editing. To do so I edited the frcmod.ff99SB file with the atom, bond, dihedral... all the fields that frcmod.ff99SB ask to me. That didn't work (Element "Cu" is not currently supported by MMTK). Then I followed the instructions here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… and I put a file called "cu" with the required data in: lib/python*/site-packages/MMTK/Database/Atoms I tried again, and the same problem. In the same webpage, there are instructions of how can we edit the Amber parameters files present in: bin/amber11/dat/leap/parm I put my parameters in frcmod.ff99SB and I also tried to put it in frcmod.ff03, but it fails again. How can I solve this problem and perform the minimizations? I'm using both windows(x64) and linux(x86) versions of Chimera 1.6.2 (build 36855) but I planned to finish the testing with Chimera 1.7 that contains by default the Amber12 package. At the bottom of the message there is the mol2 file and the parameters that I'm testing. Thanks in advance for your time. Elisabeth O.-C. My mol2 file is: @<TRIPOS>MOLECULE cuh2o.mol2 19 12 1 0 0 SMALL AMBER ff99SB @<TRIPOS>ATOM 1 CU 0.0581 0.0224 0.0049 CU 1 UNK 2.0000 2 OH -2.2040 0.0438 0.0019 O.3 1 UNK -0.8230 3 OH -0.0067 -0.2388 2.1919 O.3 1 UNK -0.8370 4 OH 0.0041 0.2849 -2.1820 O.3 1 UNK -0.8450 5 OH 2.2006 0.0021 0.0073 O.3 1 UNK -0.8270 6 OH -0.0248 -2.4186 -0.2871 O.3 1 UNK -0.8330 7 OH 0.0202 2.4645 0.2971 O.3 1 UNK -0.8420 8 H15 -2.6953 -0.0699 0.6640 H 1 UNK 0.4010 9 H16 -0.6665 -0.1584 2.6929 H 1 UNK 0.4170 10 H18 -0.6618 0.2534 -2.6804 H 1 UNK 0.4330 11 H19 2.6899 -0.0779 -0.6612 H 1 UNK 0.4240 12 H20 0.6422 -2.9163 -0.2996 H 1 UNK 0.4180 13 H14 0.6417 2.9769 0.0874 H 1 UNK 0.4200 14 H17 -2.6936 -0.1186 -0.6513 H 1 UNK 0.4180 15 H22 0.6497 -0.1530 2.6964 H 1 UNK 0.4220 16 H21 0.6504 0.1511 -2.6890 H 1 UNK 0.4130 17 H13 2.6872 -0.2103 0.6483 H 1 UNK 0.4060 18 H24 -0.6602 -2.9263 -0.1105 H 1 UNK 0.4160 19 H23 -0.6488 2.9572 0.3459 H 1 UNK 0.4200 @<TRIPOS>BOND 1 18 6 1 2 14 2 1 3 10 4 1 4 9 3 1 5 8 2 1 6 19 7 1 7 6 12 1 8 17 5 1 9 16 4 1 10 15 3 1 11 13 7 1 12 5 11 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 RESIDUE 4 A UNK 0 ROOT And my initial trial of parameters that I write in the mod file is (I put the same than Fe atom parameters written in the file frcmod.heme_ff94 only to test if that works): MASS CU 63.55 BOND CU-OH 200.00 2.0 ANGLE CU-OH-HO 35.00 120.00 OH-CU-OH 50.00 90.00 DIHEDAL X-OH-CU-X 1 0.00 0.00 2.0 NONBON CU 1.2 0.05 0.00 -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

3 2

new Programmer's Example
by Eric Pettersen 15 Jan '13

15 Jan '13

The examples in the Programmer's Guide now include one that discusses the basics of how to measure various atomic-level quantities. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

How to install? - continued
by pythonchemia Gazeta.pl 14 Jan '13

14 Jan '13

hi, Mr Eric and Greg I would like to thank you for your valuable suggestions. In fact, it would be better to use the Chimera 1.6. 2 or 1.7. Thank you Mr. Greg and Eric. Yours sincerely - Janusz Grabowski

2 1

Re: [chimera-dev] [Chimera-users] How to install ?
by Greg Couch 10 Jan '13

10 Jan '13

And it would help to use a more recent version of Chimera, either version 1.6.2 or the 1.7 release candidate. The newer releases have newer versions of Python and MMTK embedded in them with the associated improvements and bug fixes. -- Greg On 01/10/2013 11:30 AM, pythonchemia Gazeta.pl wrote: > > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW.

1 0

Re: [chimera-dev] [Chimera-users] How to install ?
by Eric Pettersen 10 Jan '13

10 Jan '13

Hi Janusz, Chimera has its own self-contained Python environment, so in order to install these packages so that you can use them from within Chimera you will need to use Chimera's Python whenever the installation procedure for a package calls on you to execute a Python script. For a script with no arguments that would be: chimera --nogui installation-script.py and for scripts with arguments: chimera --nogui --script "installation-script.py argument1 argument2 ..." On non-Mac platforms you can find the chimera executable in: <your chimera installation>/bin On Macs it is in: Chimera.app/Contents/Resources/bin While the 1.5 version of Chimera is nice enough, I would encourage you to upgrade to the 1.7 release candidate, which has many improvements. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 10, 2013, at 11:30 AM, pythonchemia Gazeta.pl wrote: > Dear Chimera Team ! > > I intersted in chemistry. I use chimera 1.5 software for personal purposes, non - commercial. > Chimera is a very usefull Tool. I like it :). I know Python language a little. I'm beginner programmer. > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW. My website is pythonchemia.aq.pl > I have some questions: > > 1 - How to install pDynamo library ? from https://sites.google.com/site/pdynamomodeling/home for Chimera 1.5 automatically or manually ? > > 2 - How to install OpenBabel library ? from openbabel.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > 3 - How to install Biopython library ? from http://biopython.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > Please help me ! - I wait on answer. > Sorry for my english > > Yours sincerely - Janusz Grabowski > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Hello~ how to make a 3D structure for a number of family genes
by tao zhao 03 Dec '12

03 Dec '12

Hello,I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family.It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next. Could you please give me some instruction?Thank you very much. Tao ZhaoNorthwest A&F University,Yangling, China

2 1

atom.anisoU does update as expected for MD trajectories
by Ryan Harrison 26 Nov '12

26 Nov '12

Dear Chimera team, I've encountered a problem with atom.anisoU. Since class Atom is implemented in C++, and I don't have the technical sophistication or nerve to build chimera from scratch after the dire warning, [1<http://www.cgl.ucsf.edu/chimera/sourcecode.html>] I seek council. I'm using PDB ANISOU to store orientation information from a coarse grained model. Using PDB MODEL and PDB ENDMDL I output trajectory information. PDB atom coordinates and aniso change with each frame in the trajectory. When visualizing a coordSet in the trajectory, atom.coord() updates as expected... # m1 is a model with ANISO information >>> m1.activeCoordSet = m1.coordSets[2] >>> m1.atoms[1].coord() chimera.Point(-0.268, 0.002, 0.08) *# <~~~ As expected from PDB file* >>> m1.activeCoordSet = m1.coordSets[10] >>> m1.atoms[1].coord() chimera.Point(0.012, -0.276, -0.043) *# <~~~ Changes as expected from PDB file* However, atom.anisoU does not update as expected [2<http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007246.html>, 3<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-December/003377.html>]. It is always the PDB ANISO information from the last model (last MD trajectory) in the file... >>> m1.activeCoordSet = m1.coordSets[2] >>> m1.atoms[1].anisoU *# <~~~ ANISO for last model in PDB file, not model 2 * array([[ 0.0296, 0.0182, 0.0201], [ 0.0182, 0.0844, -0.0055], [ 0.0201, -0.0055, 0.1258]], dtype=float32) >>> m1.activeCoordSet = m1.coordSets[10] >>> m1.atoms[1].anisoU *# <~~~ Again, ANISO for last model in PDB file, not model 10* array([[ 0.0296, 0.0182, 0.0201], [ 0.0182, 0.0844, -0.0055], [ 0.0201, -0.0055, 0.1258]], dtype=float32) The result is visualizations with proper coordinates (update properly for each frame in trajectory) but inaccurate ellipsoids (ANISO does not update; fixed as last frame / last model). *Work around 1 (Failed):* Since *aniso* takes spec atom-spec as an input, I tried specifying a model and position in trajectory. Unfortunately, this doesn't seem to be possible [4<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> ]. *Work around 2 (Tedious):* Since *aniso* can take submodels, I import (cannot use nifty MD Movie tool) as sub-models instead of as a trajectory. I can then apply aniso to each submodel, which works as expected, and switch submodels on/off sequentially to make a movie (5<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003800.html>). This is not ideal since I'm missing out on the ease of use of the MD Movie tool, and it's very cumbersome to move through a stack of submodels to emulate a trajectory. Thank you for your time and please help! Best, Ryan -- Ryan M Harrison Wolfson College University of Oxford NIH-Oxford Graduate Partnership Program http://graylab.jhu.edu/~ryan/ http://www.linkedin.com/in/rmharri

2 1

sort a list of residues based on the id.position values
by Jean Didier Pie Marechal 26 Oct '12

26 Oct '12

Hi guys, how could I sort a list of residues based on their id.position value? thanks a lot jd Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Octubre 18, 2012 9:00 pm Assumpte: Chimera-dev Digest, Vol 102, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.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: Moving a residue and an VRML object (Tom Goddard) > 2. Re: Moving a residue and an VRML object (Greg Couch) > 3. Re: Moving a residue and an VRML object (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 17 Oct 2012 13:25:18 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F142E.4080906(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The arrow you drew has no idea that the atoms have moved, so of > course > it doesn't move with them. If you just want to rigidly rotate the > whole > molecule in Python you can change the matrix that places it in space > > mol.openState.xform = xf > > instead of changing the coordinates of atoms. Then you could > rigidly > move the VRML model in the same way so that the arrow stays in the > same > position relative to the molecule. > > vrml.openState.xform = xf > > If you are not moving the molecule rigidly then you really do need > to > move individual atoms and then you will have to delete the old > arrow and > make a new arrow if it is intended to have its ends follow certain > atoms. > Tom > > > -------- Original Message -------- > Subject: [chimera-dev] Moving a residue and an VRML object > From: ladam > To: chimera-dev(a)cgl.ucsf.edu > Date: 10/17/12 4:45 AM > > Hi all, > > I have a problem associating a vrml object an a molecule : > > Let's say I have an arrow created using the bild format to which > I gave > > 0.0 0.0 0.0 coordinates. > > This arrow and the molecule translate/rotate together using the > mouse.> Now if I translate / rotate my molecule using the setcoord > command on > > the atoms in a python script, the arrow won't follow up the > molecule.> I tried the addAssociatedModel command to link the arrow > and the > > molecule but still the same result. > > How can I handle this? > > Thanks for your attention > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 17 Oct 2012 15:21:35 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Tom Goddard <goddard(a)sonic.net> > Cc: chimera-dev(a)cgl.ucsf.edu, ladam <ladam(a)smbh.univ-paris13.fr> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F2F6F.30800(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Salut, > > The other trick is to give the VRML model the same model id and > submodel > id as its associated model. Then the openState is identical, so > there > would be no need to copy the transformation matrix. Again, this > only > works for rigid rotations. > > -- Greg > > On 10/17/2012 01:25 PM, Tom Goddard wrote: > > The arrow you drew has no idea that the atoms have moved, so of > course > > it doesn't move with them. If you just want to rigidly rotate > the > > whole molecule in Python you can change the matrix that places it > in > > space > > > > mol.openState.xform = xf > > > > instead of changing the coordinates of atoms. Then you could > rigidly > > move the VRML model in the same way so that the arrow stays in > the > > same position relative to the molecule. > > > > vrml.openState.xform = xf > > > > If you are not moving the molecule rigidly then you really do > need to > > move individual atoms and then you will have to delete the old > arrow > > and make a new arrow if it is intended to have its ends follow > certain > > atoms. > > > > Tom > > > > > > -------- Original Message -------- > > Subject: [chimera-dev] Moving a residue and an VRML object > > From: ladam > > To: chimera-dev(a)cgl.ucsf.edu > > Date: 10/17/12 4:45 AM > >> Hi all, > >> I have a problem associating a vrml object an a molecule : > >> Let's say I have an arrow created using the bild format to which > I gave > >> 0.0 0.0 0.0 coordinates. > >> This arrow and the molecule translate/rotate together using the > mouse.>> Now if I translate / rotate my molecule using the setcoord > command on > >> the atoms in a python script, the arrow won't follow up the > molecule.>> I tried the addAssociatedModel command to link the > arrow and the > >> molecule but still the same result. > >> How can I handle this? > >> Thanks for your attention > >> > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > ------------------------------ > > Message: 3 > Date: Wed, 17 Oct 2012 15:26:03 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <C66C5891-76C8-4D20-B82E-572E6F919DF2(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Oct 17, 2012, at 3:21 PM, Greg Couch wrote: > > > Salut, > > > > The other trick is to give the VRML model the same model id and > submodel id as its associated model. Then the openState is > identical, so there would be no need to copy the transformation > matrix. Again, this only works for rigid rotations. > > ...and the simplest way to do this is to supply the "sameAs" > keyword, with the associated model as the argument, to the > openModels.add() or openModels.open() call that you use. > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

2 1

Problem with m.openState.xform.getCoordFrame() ?
by ladam 24 Oct '12

24 Oct '12

Hi all, I noticed this : >>> >>> print m.openState.xform 0.23153 -0.972828 0 0 0.972828 0.23153 0 0 0 0 1 0 >>> print m.openState.xform.getCoordFrame()[0] 0.23153 0.972828 0 >>> print m.openState.xform.getCoordFrame()[1] -0.972828 0.23153 0 >>> print m.openState.xform.getCoordFrame()[2] 0 0 1 >>> Looks like there is a problme with signs here between first two elements [0] and [1] with respect to m.openState.xform or am I missing something? Bye -- -------------------------------- Patrick Ladam Maître de Conférence Université Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 mail: ladam(a)smbh.univ-paris13.fr -------------------------------

2 1