January 2013 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

5 7

Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

3 5

font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

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

2 1

Write DMS missing from Tools->Structure Editing menu? (v 1.6.2 and v 1.7)
by Duncan Napier 31 Jan '13

31 Jan '13

Hi, My first posting here, and I have come here after google searching high and low about this. I understand that Write DMS is now a standard part of Chimera, but I am (or more correctly, the users I support) not able to access or use it from the Tools->Structure Editing menu. I installed the binaries (x86_64 and x86) from the UCSF Chimera site, but none of them seem to have Write DMS functionality. I am running Ubuntu 12.04.1 LTS (Precise) on a Dell Vostro 486 PC, Intel Core i7-2600 3.4 gHz, 8 Gb RAM, 1 Tb SATA HDD, Video AMD Radeon HD 6450 1GB DDR3. What am I doing wrong? You can click on this link for a screenshot of what I see (its an XMing screenshot, but the view is the same in Ubuntu) http://www.sfu.ca/~dgnapier/post/chimera-DMS.jpg Any suggestions much appreciated! -- Thanks, Duncan.

2 2

1.7 production release
by Eric Pettersen 30 Jan '13

30 Jan '13

Hello everybody, The official 1.7 production release of UCSF Chimera is now available: http://www.cgl.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). Note: 1.6 was the last version to support Mac PPC and OS X 10.5. New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. More details are given below; see release notes for the full list: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html Graphics, Depiction: * faster loading of large molecules * faster graphics on many systems; target frame rate raised to 60 fps * interactive shadows: finer quality; available on more systems * glossy default lighting, better control over contrast * users can create custom presets * 2D Labels can have backgrounds (colored rectangles beneath) * PipesAndPlanks can color SSEs uniquely, show arrowheads * Actions...Color menu works on axis, plane, and centroid objects * CASTp pocket display omits small surface fragments * "surface" and "sop" command options to hide small fragments Animation: * Animation tool allows placing scenes and simple actions (rock, roll) along a timeline to define a movie * new output movie formats H.264, VP8/WebM, Theora * "play" command to animate complex motions like radial explosion * "transparency" command to set transparency of atoms, ribbons, etc. without otherwise changing their colors, can be applied gradually * "movie" command usability improvements * "perframe" allows embedding other commands directly, substituting variables other than frame count, executing at multiframe intervals * "roll" and "turn" command options for precession motion Structure Analysis and Modeling: * AmberTools updated to v12, default charges etc. now Amber ff12SB * "click-to-center" mouse mode (default Ctrl-right button) * "show distances to nearby residues" added to atom context menu * interface to Modeller for building missing segments * interface to APBS Poisson-Boltzmann electrostatics calculations * interface to PDB2PQR charge and radius assignment * interface to AutoDock Vina single-ligand docking * ViewDock support for AutoDock/Vina .pdbqt, GOLD .mol2 files * MD Movie can calculate average structures, plot RMSD vs. frame, read GROMACS .xtc format; occupancy calculation can treat atoms as VDW spheres (as opposed to points only) * Build Structure bond length slider, bond angle control * Multalign Viewer can use a subset of the existing sequences (rather than all) to guide alignment of a new sequence; the Region Browser lists individual-sequence regions separately (now that a sequence can have many UniProt annotations) Density Maps: * Volume Viewer orthogonal planes feature * Volume Tracer default mode includes placing markers on planes * "fitmap" option to fit multiple models independently * "vop cover" can extend a map using its symmetries Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Measure inertia?
by Yen-Ting Lai 30 Jan '13

30 Jan '13

Hi, What's the formula that's used by "measure inertia"? I found a paper: An ellipsoidal approximation of protein shape. J. Mol Graph (1983) Does the "measure inertia" use the same method? Thank you! Yen

3 3

Command Patch problem
by mahad iou muddei addò 30 Jan '13

30 Jan '13

Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence: 1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR 2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I need to create a structure like this: RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHF *RD*SSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I know the position of the aa involved but after i launch the command trough command line it gives me errors like match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation What am i doing wrong? Thanks, sincererly Mahad

2 7

Selection and deleting
by Zhixue Zhu 29 Jan '13

29 Jan '13

Dear Sir/Madam: I just installed Chimera 1.7. However, I can not select individual atom or a group of atoms and then delete them. Please give some advice and instructions. Regards Zhixue

2 1

placement of metal ion in the protein model
by si yang 24 Jan '13

24 Jan '13

Good day to you, currently i am using Chimera to do some bioinformatics analysis, i want to put zinc ion into my predicted protein structure at the known binding sites, but i try to insert :Tools/structure editing/add ion/, but the option did not consists of zinc ion, hence may i know what are the alternative ways to introduce the zinc ion in order to facilitate the downstream application such as docking?? Hopefully can hear from you as soon as possible.... thank you -- Zhao Yang

2 2

Using Select with multiscale models
by Peter.Durr＠csiro.au 24 Jan '13

24 Jan '13

Hi I am using Chimera to try to visualise and then highlight the position of several amino acid mutations on a virus capsid. I have managed to use the Multiscale module to build the capsid from a PDB file. My next step is to select the residues of interest. I am able to use the Select command to find the residue within the icosahedral asymmetric unit - e.g. "select #0:14.A" However, when I apply the same command to the modelled surfaces, it doesn't work. More specifically when I run "select #1:14.A" at the command line - nothing happens - not even an error message. However, I can hunt around in the modelled surfaces on the screen and then use the mouse to interactively select the residue of interest - so Chimera seems to know which residues are which on the modelled surfaces. Thanks in advance for any guidance on how to deal with this problem. Peter Durr

2 1

Chimera-users January 2013