February 2010 - Chimera-users - RBVI Mailing Lists

Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Rendering a vector/axis
by Richard Stanton 23 Feb '10

23 Feb '10

Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich

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Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Defining planes & Thermal ellipsoids
by David Chenoweth 22 Feb '10

22 Feb '10

Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning. Thanks again for adding all these features, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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How are chains paired in morphing?
by Thomas Goddard 22 Feb '10

22 Feb '10

Bobby Laird showed me a homo-tetramer with chains A, B, C, D that when morphed between two states with the Chimera morph conformations tool swapped two of the monomers. In other words the 4 chains from one state weren't correctly paired with the 4 chains from the other state so two monomers exchanged positions during the morph. The tetramers were built from dimers 1pfk and 2pfk by using the symmetry of the unit cell with other software (coot?). How does morph conformations decide which chains to pair? Tom

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Which Mac daily build to use
by Thomas Goddard 21 Feb '10

21 Feb '10

> on another note: which of the daily builds should I be using? aqua, > aqua-intel, intel-cocoa, intel-cocoa-64. > > not sure on the + & -'s > > do not mind taking some crash risks to push sw dev objectives and reporting. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA Hi Matt, The Mac Chimera builds are far too numerous now. I recommend the 64-bit Cocoa build. That is what I use. It has one very serious issue right now that pressing Option-e or Option plus many other other characters will immediately crash Chimera. It is a Tk Cocoa bug that I reported but I need to put a fix into Chimera while I wait for the Tk developers to fix it. If that sounds too dangerous use the Chimera Aqua build (32-bit only). That uses the Mac Carbon API which is the older Mac API that Apple says they will not provide 64-bit support for. So we will replace that with Cocoa in the Chimera 1.5 release in a few months. My least favorite choice is Mac X11 which is not the native Mac windowing system and is the least well supported. That Chimera version will also be eliminated in the future. For the 32-bit versus 64-bit Chimera Cocoa you should use 64-bit if you have Mac OS 10.6 (Snow Leopard) or 32-bit for older Mac OS versions. We don't offer 64-bit Mac Chimera on Mac OS 10.5 or older Mac OS versions. Mac OS 10.6 is the first version of Mac OS that uses 64-bit by default. I've measured performance of 64-bit Mac Cocoa Chimera and it is as good as 32-bit. For the Chimera 1.5 release we hope to only be offering two production Mac Chimera versions 32-bit and 64-bit Cocoa. The X11 version will be in the unsupported category and the Aqua (= Carbon) will be gone. Tom

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centroid measurements typo
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Centroid measurements
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, The centroid feature is great, but I would like to select two centroids of a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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command line writing PDB files
by Matthew Dougherty 19 Feb '10

19 Feb '10

Is there a command line string for writing out selected atoms as a PDB file? thanks, matt Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================== ==================================

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distance measurements
by Bala subramanian 19 Feb '10

19 Feb '10

Friends, Greetings. I have 5Aromatic residues and 4 aliphatic residues in a loop. I want to calculate the CA distance between between each of Aromatic with the CA of each of the aliphatic residues in a single command. Can i do it in some fancy way. I have tried distance command but it takes exactly two atoms. Any example script would be of great help to me. Thank you, Bala

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