- Chimera-users - RBVI Mailing Lists

viewing & comparison of multiple overlay structures
by Roberta King 03 Apr '07

03 Apr '07

Hello, I am relatively new to Chimera (and the user group), but am using it to compare ligand binding pockets for multiple (36) structures of related proteins. My proteins overlay nicely based on alignment, but I am having difficulty with the comparisons of multiple structures at once. First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? I appreciate any help provided. Roberta ******************************** Roberta S. King, Ph.D. Assistant Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island

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error parsing ATOM record when coordinate long-ish
by Miguel Ortiz-Lombardia 02 Apr '07

02 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I can't read a particular atom line that looks like: ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 C I presume that the reason is that the y-coordinate forms a continuous string with the x-coordinate. However, this line complies with the PDB format; I quote from the RCBS site: 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms I realize that this may be seldom a problem, but I think it should be tackled. In my case, this is a dummy atom to represent a dipole moment vector with quite a big magnitude. I have the same problem in the last and the previous snapshot versions of chimera (both in linux and MacOSX) Thank you in advance, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2QuF6oOrDvhbQIRApSSAJ94MwNKKsPowzYE/k61g9Yen1PArwCfSnWJ gUXmMlHVsrRuLscR3IWg/tQ= =6/U1 -----END PGP SIGNATURE-----

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error parsing ATOM record when coordinate long-ish (II)
by Miguel Ortiz-Lombardia 01 Apr '07

01 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi again, I forgot to mention that I solved my particular problem by using a bild object to depict the vector. Just thought that the parsing of the ATOM record should be fixed. Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2u7F6oOrDvhbQIRAvWJAJ9UiNDLaAv9yDbf6HPoNyhHVaGAmwCfd1SF ZHM9NIY3QX5mjFVqNdvvTQk= =Gbf0 -----END PGP SIGNATURE-----

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can 2D label font be bold?
by EJ Pone 27 Mar '07

27 Mar '07

Hi, I was wondering if there's a way to make the font of 2D labels bold. I can change the font of labels associated with atoms/residues etc thru Favorites > Preferences > Background > Label font > Bold, but I can't figure out how to do this for 2D labels. The reason I am interested is that the bold font looks really appealing in labels when I make movies, but the regular font for 2D labels looks a little bit weak. Thank you for any suggestions. EJ UC Irvine

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Re: [Chimera-users] per-model clipping plane
by Thomas Goddard 26 Mar '07

26 Mar '07

Hi Jean-Francois, There is not yet a command specifically to move per-model clip planes. But you can do it using the "savepos" and "reset" commands. These save and restore the positions of all models and the per-model clip plane positions (Chimera 1.2352 and newer). For example, you can save an initial position with command savepos p1 then move a per-model clip plane with the mouse to a new position and save that savepos p2 then to smoothly go from position p1 to p2 over 100 frames use reset p1 reset p2 100 The named positions are saved in Chimera session files. Saving of per-model clip positions when you use savepos was added very recently (March 1, 2007) so you need Chimera snapshot version 1.2352 or newer. Formerly just the model orientations were remembered. Tom jean-francois menetret wrote: > > Hi Thomas, > > is it possible to move the per-model clipping plane using a > movie-related command ? > > Jean-Francois > >

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need help to run chimera 1.2304-linux.exe
by 김소연 26 Mar '07

26 Mar '07

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saving image as stereo pair
by Boaz Shaanan 25 Mar '07

25 Mar '07

Hi, It seems to me as if the stereo pair produced when I select 'stereo pair' in save image is crossed-eye stereo (not wall-eye), or is my brain fooling me ? I certainly see a left-handed alpha helix, residues in the front going to the back and D-amino acids when I use my stereoviewer. Please advise. Thanks. Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Counting atoms within density map contour
by Tom Goddard 23 Mar '07

23 Mar '07

Hi Gary, You asked yesterday whether it is possible to count the atoms lying outside the contour surface of a EM map after fitting. This can be done although it currently requires a few steps. Here's how. 1) fit the atomic model into the map as desired. 2) Use menu entry Tools / Volume Data / Values at Atom Positions, choose the molecule and map and press the Histogram button. This shows a histogram of the map values interpolated at the atom positions. 3) Press the "Select" tab on the Render / Select by Attribute dialog and choose Attribute "value_mymap.xxx", move the rightmost green bar on the histogram to match the contour level, then press the Apply button. This procedure selects the atoms at lower density levels than the map contour level and you can see the number of atoms selected in the lower right corner of the main graphics window. You can press the up arrow key a few times to select all atoms in the molecule to see the total number of atoms. I show a picture below fitting 1i84.pdb into myosin.map where 2727 of 16070 atoms lie outside the contour surface. I colored the selected atoms outside the contour blue in the picture. Tom

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osx headers
by Randy Heiland 23 Mar '07

23 Mar '07

Out of curiosity, what is different in the ppc and intel headers for 1.2349? I see that both are available on the Source download page. -Randy

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installing chimera over an older chimera install?
by Sabuj Pattanayek 23 Mar '07

23 Mar '07

Hi, On *nix is it safe to install a newer version of chimera over a previous installation? Will this break something in the newer installation? The reason why I ask is the trouble of maintaining externally installed plugins. We could make a wrapper for the .exe unzipsfx install and re-build symlinks to an external directory of chimera plugins in the share directory, but this seems like too much trouble especially if just installing over an old installation should just "work". Thanks, Sabuj

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