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density map in Chimera
by Fei Li 07 Sep '10

07 Sep '10

Dear Chimera-dev group, I am a graduate student of Computer Science. I come accross aome problems with the Density map (.mrc file). I noticed that Chimera use the Origin index parameters to locate the density map. I am wondering where these index numbers come from? is it read from the MRC header or does chimera do something about the information in mer header file. thank you for your help. Fei Li Old Dominion University, Norfolk, VA 23508

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Re: [chimera-dev] [Chimera-users] WIngware for Chimera?
by Eric Pettersen 31 Aug '10

31 Aug '10

On Aug 27, 2010, at 8:53 AM, Forbes J. Burkowski wrote: > Hi: > > At the risk of being a heretic, I would like to ask the following > question: > > Is it possible to use the Wingware Python IDE instead of IDLE to > edit and > execute Python scripts for Chimera? > > More information about Wingware can be found at wingware.com. > > I suppose that if Wingware is given the appropriate pathnames it could > import chimera and other needed packages. So, it could be used as > Python script editor. However, I am hoping that it could also be > used to > run and debug scripts that interact with the Chimera window. Would > this > be possible? First off: heretic! ;-) Second, the new face in our lab, Darren Weber, has developed a wiki page describing how to get the Eclipse IDE to work with Chimera: http://plato.cgl.ucsf.edu/trac/chimera/wiki/ChimeraEclipse Perhaps some of the information there could be adapted to getting Wingware to interface with Chimera. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Query about writing extensions in Chimera
by Arun Prasad Pandurangan 24 Aug '10

24 Aug '10

Dear Chimera Developers Team, Would like to know whether its possible to develop a custom application that can be added as a plug-in inside Chimera (For example like the recent program Ringer)? If so, is there any expert advice or tutorials available to develop such a custom application that depends on Chimera? Thank you. With kind regards, Arun Prasad

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adding python packages to chimera environment
by Darren Weber 20 Aug '10

20 Aug '10

This an example of getting some packages installed into the Chimera python environment. In my case, I was interested in using the spyder IDE within the Chimera python installation. http://packages.python.org/spyder/ First, get the setuptools (easy_install) package: $ sudo -i # export PATH=$PATH:/opt/UCSF/Chimera64-2010-08-05/bin/ # export LD_LIBRARY_PATH=/opt/UCSF/Chimera64-2010-08-05/lib # sh /home/dweber/Downloads/setuptools-0.6c11-py2.7.egg --prefix=/opt/UCSF/Chimera64-2010-08-05/ That gets 'easy_install' working with the Chimera python installation. Now for the spyder IDE. It requires PyQt4, so it's not trivial, but the following seems to build and install OK (against an Ubuntu package install for Qt4, not a custom build of Qt4 in foreign; the wget commands fetch linux-specific downloads): $ sudo -i # wget http://www.riverbankcomputing.co.uk/static/Downloads/sip4/sip-4.10.5.tar.gz # tar zxvf sip-4.10.5.tar.gz # cd sip-4.10.5 # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py # make # make install # cd .. # wget http://www.riverbankcomputing.co.uk/static/Downloads/PyQt4/PyQt-x11-gpl-4.7… # tar zxvf PyQt-x11-gpl-4.7.4.tar.gz # cd PyQt-x11-gpl-4.7.4 # update-alternatives --config qmake #select qmake-qt4 option # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py --no-designer-plugin --qmake=/usr/bin/qmake-qt4 ...<snip>... The PyQt Python package will be installed in /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages. PyQt is being built with generated docstrings. PyQt is being built with 'protected' redefined as 'public'. The PyQt .sip files will be installed in /opt/UCSF/Chimera64-2010-08-05/share/sip/PyQt4. pyuic4, pyrcc4 and pylupdate4 will be installed in /opt/UCSF/Chimera64-2010-08-05/bin. ...<snip>... #make #make install That should satisfy the deps for spyder. Then use easy_install to get spyder installed, like so: # /opt/UCSF/Chimera64-2010-08-05/bin/easy_install spyder Then to run spyder with a chimera-like env, the following seems to work: # export CHIMERA=/opt/UCSF/Chimera64-2010-08-05 # export LD_LIBRARY_PATH="$CHIMERA/lib/" # export TCL_LIBRARY="$CHIMERA/lib/tcl8.6" # export TCLLIBPATH="{$CHIMERA/lib}" # unset TK_LIBRARY # unset TIX_LIBRARY # export LD_PRELOAD=libotf.so # export PATH=$PATH:$CHIMERA/bin # unset PYTHONHOME # unset PYTHONPATH # $CHIMERA/bin/spyder Within the spyder interactive console, it reports running python 2.7 and I see: >>> import sys >>> sys.path ['', '/opt/UCSF/Chimera64-2010-08-05/bin', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/spyder-1.1.4-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/pyflakes-0.4.0-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/rope-0.9.3-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python27.zip', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/plat-linux2', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-tk', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-old', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-dynload', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/PIL'] >>> This is not quite the right path (and maybe LD_LIBRARY_PATH etc.), but a few tweaks get it working, i.e.: >>> sys.path.append('/opt/UCSF/Chimera64-2010-08-05/share') >>> sys.path.append('/opt/UCSF/Chimera64-2010-08-05/lib') >>> import chimera >>> chimera.version.version 'alpha version 1.5 (build 31152) 2010-08-05 19:55:24 GMT' This may not be a complete config/setup, but it's close. The spyder interface provides autocompletion, auto help-inspection, debug facilities, workspace, etc. If anyone finds a better way to do this, please let me know. There may be better ways to do this with virtualenv, see http://clemesha.org/blog/2009/jul/05/modern-python-hacker-tools-virtualenv-… Best, Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, 415-439-0619 (google voice) http://www.cgl.ucsf.edu/chimera/

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asynchronous running of Chimera extensions
by Marcin Pawlowski 19 Aug '10

19 Aug '10

Dear Chimera developers. Me and of my students are developing a chimera extension to deal with protein structures. Unfortunately, the execution of our plunging last at least 5 minutes, so during this time the chimera program is hinged. We would like to execute the program in an asynchronous way. Is it possible? Please do not hesitate to contact us if you require further information about our project. Best regards, Marcin Pawlowski

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(no subject)
by Reza Heidari 16 Aug '10

16 Aug '10

Hi, How can i display just some of residues (in form sphere) on a protein (in form ball & stick), for example: Trp38, Val66, Ala80. Please help me, thanks a lot.

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Re: [chimera-dev] [Chimera-users] alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear Eric, thanks for your suggestions. Unfortunately removing the SEQRES record did not help. I also downloaded and installed the new chimera-version today. The false numbering in the alignment still occurs. Also when I remove the SEQRES record and try with the new chimera version the false numbering appears. Quite annoying... The pdb-file is not in the protein data bank yet. Any more suggestions? Could I add "dummy atoms" in the structure? Thanks, Gesa Eric Pettersen schrieb: > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> Dear All, >> >> I observed an issue with the alignment function of Chimera. >> I loaded a crystal structure where in between a loop is not modelled >> due to low electron density- so these residues are missing in the >> structure and the numbering also has this gap. When I align this >> structure with others, the missing residues are not recognized and >> chimera just overrides the numbering so after this loop all the >> numbers in the alignment do not fit anymore to the residues they >> should belong to although the structure and numberings are shown in >> the right way in the graphics window. How can I overcome this issue? >> Should I change the pdb-file? In which way? >> >> Thanks for all responses! > > Hi Gesa, > I had a similar problem reported with 1JFF 12 days ago and haven't yet > worked on fixing it. It seems to only happen for a small subset of > structures. 1JFF has a missing loop and also exactly one missing > residue at the N terminus. Is your structure like that? Is it a > standard PDB entry (if so, what's the ID code)? I'll add you to the > recipient list for the ticket we have open in our bug database for > this (#8585) so you will be notified when it gets fixed. It'll > probably be fairly soon. > Until then the only workaround that occurs to me is for you to remove > the SEQRES records from the PDB file before you open it. Then the > Sequence viewer will depict only the residues physically present in > the structure -- no gaps (incorrect or otherwise) will be depicted. > > --Eric > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Re: [chimera-dev] question about rotations/translations in Chimera
by Thomas Goddard 19 Jul '10

19 Jul '10

Hi Julio, Chimera Python and C++ code represent rotations and translations as 3 row by 4 column matrices with the first 3 columns being a rotation matrix and the 4th column being a translation. The rotation is applied first (about 0,0,0) then the translation. Each map and atomic model in Chimera has its own local coordinate system. The placement of the local coordinate frame in the Chimera global coordinate system (z axis points out of screen, x axis horizontal on screen) is given by one of these 3x4 transformation matrices. The origin of the local coordinate system can be at any point relative to the data. It does not need to be at the corner of the map, nor in the center of the map. The position is specified in the header of many of the map file formats (e.g. MRC). With atomic models (PDB files) from crystallography the origin is usually the crystallographic origin (used for crystallographic point symmetry). There is a 3x4 transform describing how the local coordinate frame is positioned in the global coordinate system. Also for maps there is another 3x4 transform that describes how the grid is positioned within the local coordinate system. This latter transform determines where the data sits in the local coordinate frame the actual data -- the shift is determined by the origin values in map headers. The ability to rotate the grid within the local coordinate frame is generally not supported by map file formats. So if you want to save a rotated map you generally have to resample on a rotated grid -- unfortunate. The Chimera command language allows specifying rotations and translations with the "turn" and "move" commands. These do not use a 3x4 matrix since that is not very useful for hand-typed commands. Instead you can specify the center for a rotation, an axis vector and an angle. For example turn 1,1,0 30 center 150,245.5,90 coordinateSystem #0 model #1 rotates model #1 about axis (1,1,0) by 30 degrees about with center (150,245.5,90) where the axis and center are in the local coordinate system of model #0. There's a lot to know about how coordinate systems are handled in Chimera and I'd need a more specific question to advise you further. Here's a little info about transforms in Python http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q5 And here's some about the "turn" and "move" commands http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html Tom > Dear Prof. Goddard, > > I came recently to Pawel's group in UT Houston, and we were wondering > about how Chimera performs rotations and translations: in which order, > and with respect to which point (center of the map, origin of > coordinates, corner of the map...)? > > Any info that you can provide to help us clarify this will be greatly > appreciated. > > Best regards, > Julio > >

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Alignment + missing residues
by Gesa Volkers 14 Jul '10

14 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Adding atom types in the Gaff parameter files of chimera.
by Jean Didier Pie Marechal 13 Jul '10

13 Jul '10

HI guys, I am trying to add another type of atom in the GAFF parameter file that is called during the minimization process and can't find the right place. Could you give me a hand please? best, 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: Dimecres, Juny 30, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 76, Issue 4 > 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: pil background Image (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 29 Jun 2010 14:10:46 -0700 > From: Greg Couch <postmaster(a)cgl.ucsf.edu> > To: Ludovic Autin <autin(a)scripps.edu> > Cc: "chimera-dev(a)cgl.ucsf.edu" <chimera-dev(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] pil background Image > Message-ID: <4C2A6156.6070100(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Ludovic, > > This is possible, but a little tricky. It requires writing Python > code. So if I were to code a solution (and I may if you don't, but > I > need to fix a few bugs first), I'd make a chimera extension that > would > load an image into an OpenGL texture, then in the 2D drawing pass, > I'd > draw it underneath everything that is currently drawn. The reason > for > using a texture instead of a bitmap is to allow for high resolution > backgrounds for saving images. > > If you are inclined to write this yourself, code for a chimera > extension > that does OpenGL in Python can be found in the CHIMERA/share/Ilabel > package. > > -- Greg > > On 6/23/2010 2:14 PM, Eric Pettersen wrote: > > On Jun 22, 2010, at 1:25 PM, Ludovic Autin wrote: > > > >> Hi, > >> > >> I would like to know if its possible to use a PIL or a raw image > as a > >> background image. > >> And/Or can you help me figure out how to do it (maybe using some > >> volume from image functinoality). > >> Ideally, I would like to be able to update in realtime this > >> background image (either using a thread, or a callback) > > > > Hi Ludovic, > > The developer who could authoritatively answer your question > (Greg > > Couch) is out this week, so I'll take a stab at it: I don't > think so. > > :-) However, if your goal is to, say, make a movie with a > background > > you provide then you could write out image files with a > transparent > > background (described in this message: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2008- > January/002197.html) > > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008- > January/002197.html%29> > > and use most any image-processing program to compose the Chimera > > images with the background(s) you prefer. > > Despite my flippant answer in the first sentence, I don't really > know > > if it is possible to directly change the background. When Greg > gets > > back I hope he will comment on that. Perhaps you could say more > about > > what your ultimate goal is? > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > Hi Ludovic, > > Everything is possible. > >

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