- 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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Density map in Chimera
by Pancera, Marie (NIH/VRC) [C] 17 Feb '10

17 Feb '10

Hi, I opened an electron density map in chimera. For some reason it is forming a box and I am not quite sure how to get the density outside of the box (to cover symmetry molecules etc...) Thanks for helping me with that. Best regards, Marie

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copyright permission
by M P Williamson 17 Feb '10

17 Feb '10

Hi folks. I am getting near to the end of writing a book called How Proteins Work (to be published by Garland, hopefully this fall). I would like to include a figure showing anisotropic B factors for a protein, and the best image I have come across is of heme on your website, http://www.cgl.ucsf.edu/chimera/feature_highlights/ellipsoids.png I would like to include this image in the book. Could you let me know if there are copyright restrictions on the image, and how you would like me to refer to it? Thanks Mike Williamson

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help
by Giuseppe Falini 17 Feb '10

17 Feb '10

Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe

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writing a trajectory to multiple pdbs
by Dan Gurnon 16 Feb '10

16 Feb '10

Hi everyone, How would one write a trajectory read into MD Movie to a series of pdb files instead of one large file? I don't see a suitable option specified for the "write" command, and for "Save PDB" it seems the option of multiple files is only available when multiple models are selected. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Hydrogen Atoms
by Elaine Meng 16 Feb '10

16 Feb '10

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am working on calculating the Solvent accessible Surface Area on > the antigen interaction region. I am confused about adding/removing > hydrogen's, my question is will there be a change in SASA if you > have or not have hydrogen's atoms added. > Thank You. > -Thiru > Hi Thiru, Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere. There will be more small bumps on the surface when there are hydrogens. Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I think surface area calculations are usually done on structures without hydrogens. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)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 P.S. you may want to use "measure buriedArea" (or maybe you are already doing that): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAr… >

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reference for saving pdb
by Samuel Coulbourn Flores 12 Feb '10

12 Feb '10

Hi Guys, I'm having what I am sure is a trivial problem. When I save my PDB coordinates, I am asked what the reference is, and choose a density map. But when I read those coordinates back in, they are translated/rotated from where they should be and no longer match the density map. Can you tell me what is the correct procedure for setting the reference? Thanks Sam

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Row interleaved stereo and Zalman monitors under Linux
by David Bhella 12 Feb '10

12 Feb '10

Hello again! I have just installed a Zalman M220W monitor on one of our workstations under OpenSuse 11.1, after a small amount of fiddling to get it working with dual head mode it seems to be behaving. In Amira it gives beautiful 3D, although the assignment of left and right eye views seems fairly random, as Amira has the option to reverse left and right eye views this is not a problem. In Chimera however with row interleaved stereo I seem to always get the views the wrong way around. It took me a while to work out why it didnt seem to be giving good depth and it was quite disconcerting to look at while viewing cryoEM 3D reconstructions, however with a pdb file it was quite obvious that my right eye was getting the left eye view. There only seems to be the option of reversing the views for sequential stereo however.... I would be grateful if anyone could advise me on how I can fix this. Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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Shadows
by David Bhella 12 Feb '10

12 Feb '10

Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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session writing
by Jean-Paul Armache 11 Feb '10

11 Feb '10

hello, i would like to ask whether it would be possible to save sessions with relative path, instead of absolute one ? it is a bit complicated to move the sessions between different platforms with the absolute one. thank you, best, jp armache

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Re: [Chimera-users] 64-bit version of Chimera for windows
by Tom Goddard 11 Feb '10

11 Feb '10

Hi Pu, Greg Couch in our lab is working on a 64-bit version of Chimera for Windows 7. It should be available in a month or two if we don't run into overwhelming difficulties. Tom > Hi Tom, > > Do you have 64-bit version chimera for windows. Our computer manager asked me > this question. > > Happy Chinese New Year. > > Best regards > > > Pu Qian > > >

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Peptide Builder in 1.4x
by nettles 10 Feb '10

10 Feb '10

Hi All, I was very excited to download the 1.4 version of Chimera with it many improved features yesterday. However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x) Thought you would like to know. I appreciate your excellent software. Thanks, Jim Nettles

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measure crossing angles for axes
by Tom Duncan 09 Feb '10

09 Feb '10

I have used the "measure rotation" command to create several axes. In each case, a marker set (to show the axis) is generated that consists of 2 pseudoatoms and 1 bond. Is there a simple way to measure the crossing angle between 2 such axes? If the marker set had 3 atoms, I could probably use the Axes/Planes tools to do this. Thanks, Tom

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BCC CHARGES
by emrys.fslife.co.uk 08 Feb '10

08 Feb '10

Hi folks Is it possible(within Chimera) to get the dipole moment of low-molecular weight ligands alongside their calculated BCC atomic charges? Best wishes E.Thomas

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Chimera/VMD visualization difference
by Keith Battle 08 Feb '10

08 Feb '10

Hello Chimera team, I recently conducted a MD simulation of a 12-mer peptide adjacent to a hydroxyapatite crystal using NAMD 2.6. When I viewed the output coordinates from the simulation in pdb format using Chimera 1.4, the protein ribbon was broken and the hydrogens of certain residues were not bonded but in close proximity. All of the non-bonded hydrogens were colored purple by default. The waters of the system and the crystal looked normal. Overall, the protein looked distorted. I decided to visualize the peptide using VMD 1.8.7 and to my surprise the protein ribbon was intact with all hydrogens bonded to their respective residues. Any insight into why this difference occurred would be greatly appreciated. Best, Keith Battle Research Technician University of South Alabama

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Align the molecule
by snoze pa 08 Feb '10

08 Feb '10

Dear Chimera Users, I am wondering if it is possible to align the molecule along the X-Y or Z axis. I want to place the molecule, along a line joining N to C terminal line. Idea is to place a molecule along this line(N to C line) which is X or Y or Z axis. Thank you, S

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