- Chimera-users - RBVI Mailing Lists

1.5.2 release [fix for registration problem]
by Eric Pettersen 26 Jan '11

26 Jan '11

Hi everyone, As of a few days ago, the registration-verification certificate that has shipped with every version of Chimera for the last ten years expired. Consequently, any Chimera use after that would bring up the registration-request dialog regardless of how recently that version of Chimera had been registered. On top of that, the expired certificate caused new registrations to fail, so all you good people who were trying to help us out by registering your versions after this bug appeared were stymied. We have just released Chimera 1.5.2, which has a permanent fix for this problem. You can download it from: http://www.cgl.ucsf.edu/chimera For users who prefer not to upgrade immediately, we expect to have a solution for existing older versions in a week or less. We will send another email with details when that solution becomes available. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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electrostatic potential in active site at an interface
by Boaz Shaanan 26 Jan '11

26 Jan '11

Hi I need your advice on the following: I have an active site which is located at the interface between two subunits. The cofactor in the active site makes interactions with residues from the two subunits. I have a few mutants and would like to display their effect on the electrostatic potential around the cofactor in order to explain changes in the activity of the enzyme. I have a electrostatic potential calculated both in apbs (.px) and delphi (.phi) on the basis of whole dimer structure. My first question is whether those potential maps are relevant for displaying in chimera the potential in an inner part of the protein or should I calculate the potential over the interface region that I'd like to be displayed. If the latter is correct my second question how do I get a surface (molecular or accessible) depiction of this region. I tried several options in chimera (following some examples in the gallery) but none seems to be doing it right. I probably miss something. I would be grateful for any clues on how to go about this. Thanks for your help, Boaz Boaz Shaanan, Ph.D. 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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rotation centers
by Benoit Zuber 26 Jan '11

26 Jan '11

Hi, I have a set of density maps and PDB models. I have displayed the maps side by side. Each map has a pdb model docked in it. I would like to make a movie where each map rotates around its Z axis. Each pdb should rotate around the Z axis of its respective map. I tried: set independent roll z The problem is that the center of the pdb models is not the same as the center of their respective maps. Is there a way to group one pdb with one map so that they rotate around the same center? Or is it possible to set the center of rotation of a PDB to the same value as the center of rotation of the map? Thanks in advance Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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registration
by Francesco Pietra 25 Jan '11

25 Jan '11

I have replaced previous installation of CHIMERA with chimera alpha version 1.6 (build 32272) 2011-01-06 08:36:33 GMT. I have attempted to register at the request but the answer is that no regular installation is seen. So, at any start I have to kill the request. francesco pietra

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Chimera Question
by graemeg＠rci.rutgers.edu 24 Jan '11

24 Jan '11

Hello Chimera Feedback Team, For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it. Sincere Thanks, Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology

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selection (from distance) among PDB files after docking
by Damien Larivière 24 Jan '11

24 Jan '11

Dear all, I have numerous PDB files resulting from a docking run. From crosslinking experiments, we know here that one way to select among all the solutions is to identify the PDB files for which the distance between some residues of interest is lower than a specific value: distance between Res 246 in chain B and Res 131 chain C < 17 A distance between Res 162 in chain B and Res 135 chain C < 24 A The two constraints must be respected. So, is it possible to write a script which: - opens one by one the pdb files, -calculates the two distances for the current pdb file, - send in the reply log the name-number of this PDB file if it respects the two constraints? Then, I would just have a look to the reply log in order to know the pdb files to study in depth. Many thanks for your help Damien

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Re: [Chimera-users] font size in pull-down menus
by Greg Couch 24 Jan '11

24 Jan '11

The font size of the menus matches that of other applications on Windows. To change the size, bring up the Display Properties dialog (right-click on background, or via the Control Panel), switch to the Appearance tab, and change the font size, then Apply to see the change. If you only want to change the menu font size and leave the fonts alone (e.g., the window names and the names of icons), you can click on the Advanced button, select the Menu item, and change the font size. -- Greg On 01/24/2011 05:56 AM, Boaz Shaanan wrote: > Hi, > > Is there a way to change the font size of the pull-down menus? For > some reason on the Windows (XP) v.1.5.1 they seem smaller to me. > Nothing in terms of graphics (or my eyesight) has changed since I > upgraded to 1.5.1 recently. > > Thanks, > > Boaz > > Thanks, > > Boaz > > > Boaz Shaanan, Ph.D. > 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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rotate command
by Alexandra Deaconescu 24 Jan '11

24 Jan '11

Hi everyone: I am sure this can be done in Chimera, but I just could not find the proper command - I want to simply rotate a pdb file by let's say 90 degrees. Now, if I want to also rotate a map (so both map and pdb at the same time), what would I use? Can anyone help? Many thanks!!! Bests, Alex Alexandra Deaconescu, Ph.D. ----------------------------------- Research Associate, HHMI c/o Grigorieff Laboratory Brandeis University http://people.brandeis.edu/~deacona For mail: Brandeis University 415 South St., MS 029 Rosenstiel Center Waltham, MA 02454 For packages (FEDEX): Brandeis University 415 South St., Kalman Receiving Dock Waltham, MA 02454

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how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

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Display only selection
by Damien Larivière 20 Jan '11

20 Jan '11

Dear Chimera team, I'm identifying a complex between two proteins thanks to crosslink data. I have the following questions: 1/ I would like to select two residues that belong to two different chains and highlight them in the viewport. By using the sequence tool and then ctrl/shift+drag, I can select two residues (ex: 45 and 246 of chain A), they are highlighted in the view. But when I operate this way with res 45 of chain A and res 246 of chain B, only one remains highlighted in the view port. One way to sort this out would have been to rename all the chains with the letter A. But once the residues are highlighted, I have to measure the distance between them, then to make one chain active and then to move it and try to fit crosslink data (I hope I'm clear:-\ ). Is it possible to directly select and highlight in the viewport residues of interest belonging to different chains? 2/ Supposing that I can select and highlight in the viewport residues of interest belonging to different chains: How can I display only them in the viewport (and hide all the others)? The technical goal behind these questions is to better appreciate visually the distance between residues of interest and, thanks to the distance tool, to move one protein with respect to the other and fit crosslink data. Many thanks for your help. Damien

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