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

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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 > *************************************** >

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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

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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.

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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

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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

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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

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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

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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

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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

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Chimera 1.7 release candidate
by Elaine Meng 23 Jan '13

23 Jan '13

Hello, A Chimera production release candidate (version 1.7) is available; please try it and report any problems: <http://www.cgl.ucsf.edu/chimera/download.html> 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, and interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. See the release notes for details: <http://www.cgl.ucsf.edu/chimera/1.7/docs/relnotes/1.7.html> Mac PowerPC and OS X 10.5 are no longer supported. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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periodic shift of data in a Cryo EM map
by Benjamin SCHWARZ 23 Jan '13

23 Jan '13

Hi list, Sorry for the inaccurate vocabulary, I am not really from the field. I'll try to be as descriptive as I can. My problem is that I have a cryo EM map of a protein complex with the information somehow "shifted" in the "outline box". It looks like the center of my complex was placed on one corner of the outline box, and that the whole complex is thus spread over the 8 corners of the box… All the information is thus present in the map but should be periodically translated in order to place the center of my complex in the center of the box. I can think of two ways to solve my problem, and for both I need your help : 1. how to shift periodically the content of a map ? 2. how to create a new (and bigger) map by repeating and translating one map in the 9 surrounding directions ? Thanks in avance --Ben

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selection using mouse
by francesco oteri 22 Jan '13

22 Jan '13

Dear Chimera's users, I downloaded and installed version 1.7 build 38047 and I noticed that is no longer possible to select atoms through mouse. Previously, I used the 1.6 and it was still possible using mouse for selecting atoms. I am wondering whether this function has been removed or I miss something? Francesci

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(no subject)
by Jean-Francois Menetret 18 Jan '13

18 Jan '13

Hi, I am trying to restore sessions I saved about 4 months ago but I keep getting the following message: python2.7: ../../nouveau/nouveau_pushbuf.c:274: nouveau_pushbuf_flush: Assertion `0' failed. Aborted (core dumped) PS: I am currently using chimera version 1.7 (build 38083) J-F

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colour with coulombic potential
by giulia zanetti 18 Jan '13

18 Jan '13

Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models. Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia

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Re: [Chimera-users] Homology Modeling
by Elaine Meng 17 Jan '13

17 Jan '13

Hi CE, Different or missing chain IDs are not a problem, unless they somehow cause your specification to indicate different numbers of atoms in the two structures. The example command I gave in the previous message had one structure with chain A and the other with no chain ID. Different residue numbering is also not a problem, because you enter the numbers yourself in the match command. > match #1:482-513.A@ca #0:212-243@ca However, a structure without chain IDs could cause a problem if it contains multiple chains and thus more than one residue with the same residue number. Other common reasons for an error message like this: (a) the specification syntax is simply wrong (b) one structure has "alternate locations" (for example, 2fma residue 170.A) and thus multiple instances of the same atom/residue/chain name. If I run into this, I usually delete the alternate locations (e.g. command "delete @.b" would delete all alternate locations B) and try again. You can see how many atoms each specification generates with commands like: select #1:482-513.A@ca select #0:212-243@ca It is impossible to guess without having the actual structure and seeing the exact command that you used, sorry. However, if you think it is related to chain ID, that can be changed using "Change Chain IDs" (in menu under Tools... Structure Editing) or command "changechain" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html> 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 Jan 17, 2013, at 2:26 PM, Chinaza Egbuta wrote: > Hi Elaine, > > Thank you for your prompt response. Yes, the question is actually about 3D superposition. I used the match command following the atom specification syntax described in <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>. However, I have been getting the following error message "Unequal number of atoms chosen for evaluation". > > The two models I am comparing both have the same model number but the chains are different (one is "chain A" and the other is "principal chain"). This could be because the actual homology modeling was performed on the MOE platform (chemical computing) and the chain numbers are assigned differently. Please could you let me know if I the error message is as a result of this nomenclature? If yes, please could you provide me with information on how to change the chain number? > > Thank you! > > CE

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copy file command
by Rachel Kramer Green 17 Jan '13

17 Jan '13

Hi, I am trying to save an image using the cmd line in Chimera. The command that I am using is: copy file testimage.jpg jpeg width 500 height 500 It looks like it is working. The bottom bar of the display screen says "rendering high resolution image" and then "Finished saving image(s)." However, then I cannot find a created file anywhere. Any idea what is happening to the saved file? Thanks! -- ------------------------------------------------------------------------ Rachel Kramer Green, Ph.D. RCSB PDB kramer(a)rcsb.rutgers.edu

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Re: [Chimera-users] Homology Modeling
by Chinaza Egbuta 17 Jan '13

17 Jan '13

I have a protein with multiple modules that are homologous to each other. I have generated a homology model of one module based on the structure of another. However, I need to align a specific peptide that is identical between my two modules. Is there a way to do this? Thank you. CE

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Structure minimization
by Bobo Dang 15 Jan '13

15 Jan '13

Hey All, I am trying to use Chimera to minimize a small protein with a special structure, the model has nonstandard amino acid, Also the N-terminal is connected to cyclized to one Asp side chain, is it possible to minimize this modified structure by Chimera? Thanks bobo

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Ubuntu 12.10 and Chimera update #1
by Greg Couch 15 Jan '13

15 Jan '13

Ubuntu 12.10 is still buggy, but I have found a workaround to get Chimera to work if you have AMD/ATI or NVIDIA graphics. If you change the desktop environment from the default Ubuntu environment to another, e.g., Xfce, then Chimera will work. Do do that, first install xfce4: sudo apt-get install xfce4 Then logout, and you will see an circular icon to the right of your login name. Click on that icon and choose "Xfce session" and OK. Then type in your password and you'll get the Xfce desktop environment (don't use a single panel unless you know what you're doing). And then Chimera will work as before from the desktop or the command line. There are other possible desktop environments and it appears that the ones that have a compositing window manager, e.g., kde plasma, don't work. If you are using a different desktop environment in Ubuntu 12.10 that works, please tell me about it. HTH, Greg

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Structure minimization for model with rigid body
by danashah＠post.tau.ac.il 14 Jan '13

14 Jan '13

Hi all, We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body. Is "fragment true" the best way to do that, or is there a different option? http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html#fragment Of course the "spec" option will define all the atoms which are not in the rigid body part.... Best, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Re: [Chimera-users] em fit refinement
by Feixia 14 Jan '13

14 Jan '13

Hi Tom, I have a question about multiple fit. Essentially, I have a map of a dimer. For each monomer, I have three domains. I have built models for each of the domain. I tried to fit each individual domain into the map, but found the same domain taking different orientations in different monomer, so I can't achieve 2-fold symmetry. I wonder what would be a sensible approach to fit. Also, what would be a good value to select for 'level' for the map. The map is from negative-staining data with 18A resolution. Thanks a lot! Best, Feixia -- Feixia Chu, Ph.D. Assistant Professor Biochemistry Graduate Program Coordinator Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436

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Is it possible to make an open-book diagram using Chimera?
by Amy Davenport 14 Jan '13

14 Jan '13

Hi - I want to create an open-book diagram showing amino acid interactions present in a buried surface area. I was wondering if it is possible to create these types of diagrams with Chimera without cheating by cutting the protein into two and flipping it. In my experience, it's extremely hard to get things rotated correctly when you do that. Any ideas would be much appreciated. Thank you. Amy Migliori UCSD

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Chimera crashes at launch
by Gökhan Tolun 14 Jan '13

14 Jan '13

Hi, I was running Chimera 1.7s 64bit under Windows 7 64 bit, and all was fine until I started trying it with a 3D monitor. While I was playing with stereo options, Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore. I uninstalled it, deleted its preferences folder .chimera from AppData folder, cleaned up chimera occurences from registry and reinstalled the daily version, and it still doesnt work! After launch, the error window shows: --------------------------- Chimera Launcher Error --------------------------- chimera failed abnormally; the exit code was: 1. Use the --debug command line option for the full error message. --------------------------- OK And if I launch it with the debug option, this is what I can see in the terminal (command line): Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Traceback (most recent call last): File "c:\Program Files\Chimera 2013-01-11\share\__main__.py", line 69, in <mod ule> value = chimeraInit.init(sys.argv) File "c:\Program Files\Chimera 2013-01-11\share\chimeraInit.py", line 651, in init extraArgs = tkgui.finalizeGUI() File "c:\Program Files\Chimera 2013-01-11\share\chimera\tkgui.py", line 3623, in finalizeGUI _firstStatus(lastVersion) File "c:\Program Files\Chimera 2013-01-11\share\chimera\tkgui.py", line 3528, in _firstStatus statusline.show_status_line(True) File "c:\Program Files\Chimera 2013-01-11\share\chimera\statusline.py", line 3 98, in show_status_line status.show(show) File "c:\Program Files\Chimera 2013-01-11\share\chimera\statusline.py", line 1 18, in show self.frame.pack(expand=Tkinter.FALSE, side='bottom', fill=Tkinter.X, **kw) File "c:\Program Files\Chimera 2013-01-11\bin\lib\lib-tk\Tkinter.py", line 180 8, in pack_configure + self._options(cnf, kw)) _tkinter.TclError: window ".106614152L.110482120L" isn't packed Return code: 1 Press return or enter to to exit I was planning to get something done this weekend, so Id appreciate any replies. Looking forward to the solution. Thanks and have a nice weekend. Gökhan

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heptamer
by Hossein Lanjanian 14 Jan '13

14 Jan '13

Hi every body. I want to make a heptamer of beta cyclodextrin from its monomer pdb file. is it possible to do it with the chimera software? in other words, can chimera model *heptamer, from, monomer*? -- With The Best H.Lanjanian

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How to install ?
by pythonchemia Gazeta.pl 10 Jan '13

10 Jan '13

Dear Chimera Team ! I intersted in chemistry. I use chimera 1.5 software for personal purposes, non - commercial. Chimera is a very usefull Tool. I like it :). I know Python language a little. I'm beginner programmer. I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW. My website is pythonchemia.aq.pl I have some questions: 1 - How to install pDynamo library ? from https://sites.google.com/site/pdynamomodeling/home for Chimera 1.5 automatically or manually ? 2 - How to install OpenBabel library ? from openbabel.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? 3 - How to install Biopython library ? from http://biopython.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? Please help me ! - I wait on answer. Sorry for my english Yours sincerely - Janusz Grabowski

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Showing Binding surface
by Bobo Dang 10 Jan '13

10 Jan '13

Dear Chimera Users, I am trying to use Chimera to show the binding surface between two chains in one Model and measure the area of this binding surface, but I don't know how I can select the bind surface, could anybody give me a hand? the model I am using is 4GLN from PDB. thanks a lot bobo

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Place markers
by Kim Fong 09 Jan '13

09 Jan '13

Hello, Is there an easy way to select a single residue along a chain and center a new marker on that selected residue? Thanks! Kim

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crosslinks
by Trisha Davis 09 Jan '13

09 Jan '13

We would like to show the cross links we recently observed between proteins within a complex. Is there an easy way to specify where to put these 15 cross links? In the past, when we had just a few, we drew them in and positioned them by hand. Trisha Davis

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Color surfaces
by Hernando J Sosa 08 Jan '13

08 Jan '13

Hi I thought there is was way to color density surfaces according to the assigned color of atoms close by (i.e. when there is an a atomic structure fitted into the density), but I can't remember if this was indeed possible or how to do it. Is there a way to do this ? Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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Chimera 1.7 for mac
by Pat Heath 08 Jan '13

08 Jan '13

It starts to open and then quits. User was previously running 1.5 fine. Another user on the same machine can open chimera 1.7 just fine. Makes me think there is a file that needs thrown away from the other user that was generated by version 1.5. I deleted the .chimera folder, but that didn't help. Any ideas? Thanks, Pat

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Re: [Chimera-users] Stereo 3D on non-quadro GeForce cards
by Steven Ludtke 07 Jan '13

07 Jan '13

Hmm... Since I get this in digest form, not sure how to post a reply, but it may be worth pointing out that one of the biggest advantages of the passive 3D displays becoming increasingly available is that you can do windowed 3D on Win, Mac and Linux with no drivers and no special setup at all as long as the software supports it (Chimera does). They are inexpensive, and the glasses are dirt cheap (and compatible with movie-theater 3-D). The only disadvantage is the vertical loss of resolution/interpolation, but in my mind it's a very small price to pay for the ease of setup and use. ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Professor, Dept. of Biochemistry and Mol. Biol. Those who do Co-Director National Center For Macromolecular Imaging ARE Baylor College of Medicine The converse sludtke(a)bcm.edu -or- stevel(a)alumni.caltech.edu also applies http://ncmi.bcm.edu/~stevel

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Front End for NAMD?
by Rudy J. Richardson 07 Jan '13

07 Jan '13

To whom it may concern: First, my profound thanks to the creators of Chimera for a superb research and teaching tool. I am especially grateful for the excellent interface with Modeller for doing such things as creating and optimizing loops to repair chain breaks in X-ray structures; this feature is greatly improved in v. 1.7rc. I am also grateful that Chimera can be used to visualize results of MD simulations with, e.g., NAMD. However, in addition to viewing results, it would be great if Chimera could be developed to serve as an interactive GUI for setting up, running, and analyzing NAMD simulations, including steered MD, as well. There is a real need to make MD more accessible to a wider range of scientists, and it appears that Chimera could be an excellent platform for this. I realize that VMD has co-evolved with NAMD for this purpose, but VMD lacks the integration, polish, and intuitive ease of use of Chimera. Thank you. Sincerely yours, Rudy

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Re: [Chimera-users] Circular DNA minimization
by Eric Pettersen 07 Jan '13

07 Jan '13

On Jan 7, 2013, at 10:10 AM, Damien Larivière wrote: > Dear all, > > I'm still on this subject. > > I tested the command (minimize spec :275-276.E:7-8.F fragment true nsteps 0 cgsteps 1 interval 1) suggested by Conrad or Eric in their reply to the bug I submitted. It works well. > > I attach the original structure to be minimized by Chimera (Chimera_minimization.pdb). This structure poses various problems (too long O3'-P bonds for instance) and that's the reason why I want to minimize it. > > It is interesting to note that the four distorted base rings (275 and 276 chain E, 7 and 8 chain F) occured after the Steepest Descent steps. I attach the structure as it is after 100 Steepest Descent steps (Chimera_minimization_NoConjugate.pdb). > > For your information, the summary of my user experience in this specific case: > - the Steepest descent phase repaired too long O3'-P bonds > - the Steepest descent phase generated four distorted base rings > - the command minimize spec :275-276.E:7-8.F fragment true nsteps 0 cgsteps 1 interval 1 (so just one step of conjugate gradient minimization) repaired the distorted rings. The structure at the end looks like stucturally correct. With the before-minimization structure you provided, I cannot reproduce the ring distortion -- neither with 1.6.2 nor 1.8, and neither on Mac nor Windows 64. 100 steps of steepest descent with no conjugate gradient and default forcefield choices (99SB on 1.6.2; 12SB on 1.8) results in perfectly normal-looking rings in those residues. So if we can't reproduce it, the problem may not be possible for us to solve. We'll see what we can do. > May you tell me how you identified these four distorted rings? thanks to a visual inspection of the base pairs one by one? Well, if you're as familiar with Chimera as I am, you can use the Python layer to directly answer questions that no tool directly addresses. So when I noted that breaking the circularizing phosphate bridges allowed the minimization to proceed, with a big drop in energy but no noticeable movement of the newly-freed ends, I wondered what atoms had moved. Here's how I answered that question: 1) I used MatchMaker to superimpose the structure as best as possible. Since I knew which chains to match up, I used the "specific chain with specific chain" option in MatchMaker to match chain E with E and chain F with F. 2) I opened the IDLE Python interpreter (in Tools/General Controls) so I could interactively execute Python commands. In IDLE I: 2a) Fetched a list of atoms from both models: atoms1, atoms2 = [m.atoms for m in chimera.openModels.list()] 2b) Since one structure had atoms the other didn't, I needed to set up some way of matching up the atoms in one structure to the corresponding atoms (if any) in the other structure. I made a lookup dictionary of the (residue ID + atom name) to atom for one structure's atoms, that I could later use on the other structure's atoms to determine the correspondences: lookup = dict([((a.residue.id, a.name), a) for a in atoms1]) 2c) Then I run through the atoms in the other structure, and for ones that correspond to atoms in the first structure I note the distance between the atoms: dists = [] for a in atoms2: key = (a.residue.id, a.name) if key not in lookup: continue dists.append((a.xformCoord().distance(lookup[key].xformCoord()), a)) Note that since the models have been moved by MatchMaker relative to each other, I need to use xformCoord(). Also, I put the distance first in the 2-tuple, since I know I will want to sort the list next, and sorting works on the first member of a tuple first, only using later parts of the tuple in the event of ties. 2d) Sort the distances. dists.sort() 2e) Since sorting is from smallest to largest, reverse the order. dists.reverse() Then I just examined the list. For instance, "print dists[0]" showed me that the largest movement was ~0.4 angstroms. That seemed significant. "print dists[0][-1]" showed me it was one of the atoms in the four distorted residues. I went and looked at the residue and could immediately see that the distorted ring was the problem. To try to get a handle on how many large movements had occurred (which I arbitrarily decided was 0.2 angstroms) I executed this code: len([a for d, a in dists if d > 0.2]) which told me there were 25 atoms that had moved that much. Since that wasn't an overwhelming number, I just printed them all: for d, a in dists[:25]: print d, a I could see that they were all in those four residues. So that's how I found the problem residues. --Eric > > Many thanks > > Damien > > On 04/01/2013 13:27, Damien Larivière wrote: >> Dear all, >> >> Many thanks for your help on this! >> >> Just one comment about the Steepest Descent steps that did not modify anything (RMSD = 0 as Eric or Conrad said). In fact, the structure I uploaded had already been minimized with through 100 Steepest Descent steps. It resulted in the repairing of several too long O3'-P bonds and other structural deficiencies (but not the distorted base rings). This explains the RMSD equal to 0. >> >> I have a question: >> >> How did Eric or Conrad noticed that some rings were structurally deficient? I also observed these distortions but thanks to a visual inspection and, due to the size of the structure, by chance! One can use the ADIT server to know whether structural deficiencies subsist or not but this requires to make sense of a list of number. In other words, it is not said "your structure poses problem at the sugar rings at position 255 or at base ring at position 266". You were able to tell me that base rings in residues 275 and 276 of chain E and residues 7 and 8 of chain F were deficient: Is there a way in Chimera to notice that "directly" or this is just a matter of expertize? >> >> I can't test the solution before Monday as I am away of my office. If I understand correctly: >> >> - I have to remove the phosphate bridges in order the conjugate gradient phase to start?! >> >> - I have to use the fragment option to accelerate the repair of known distorted rings thanks to the conjugate gradient steps?! >> >> I wish all of you a very happy new year! >> >> Damien >> >> On 03/01/2013 23:04, Eric Pettersen wrote: >>> Okay, the executive summary for those interested is that in a case like this where minimization gets "stuck" on a large structure you may have to minimize badly distorted parts of the structure separately first by using the "fragment" option of the minimize command (not the "freeze" option in the tool or command, which still uses the remainder of the structure in the calculation). >>> >>> --Eric >>> >>> On Jan 2, 2013, at 1:34 PM, Eric Pettersen wrote: >>> >>>> On Dec 29, 2012, at 7:40 AM, Damien Larivière wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. >>>>> >>>>> The first phase, the Steepest Descent Steps, works fine. >>>>> >>>>> However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. >>>>> >>>>> If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. >>>>> >>>>> I'm not versed in the art of minimization. Do you know the reason of this behavior? >>>> >>>> Hi Damien, >>>> I cannot reproduce this behavior. A small circular peptide (attached) minimizes fine with conjugate gradient. I need you to open a bug report (in Chimera, Help->Report A Bug) and attach the circular DNA structure. Thanks! >>>> >>>> --Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> http://www.cgl.ucsf.edu >>>> >>>> <circular.pdb>_______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > <Chimera_minimization.pdb><Chimera_minimization_NoConjugate.pdb>

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Edit and UnDo?
by Rudy J. Richardson 07 Jan '13

07 Jan '13

To whom it may concern: Although this would be a departure from the current menu structure in Chimera, would it be possible to add a conventional "Edit" to the menu that would be populated with actions appropriate for editing? In addition, either in a new Edit menu or in the current Actions menu, would it be possible to add a global "Undo" function? Thank you for your consideration. Sincerely yours, Rudy

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average pdb
by edu troche 07 Jan '13

07 Jan '13

Hi chimera users, I was wondering if there is any way to build an average pdb from an Amber MD simulation of a system that doesn't contain any biopolymer. I know there is a script within the Amber suite, to generate an average pdb, but I'm doing the MD in several parts, and then reimaging them, so I wanted to check if the results of the Amber script, that makes an average on the coordinate file (.rst) without centering the system, is the same that I could have after applying the reimaging-centering script. Thank you! -- Eduardo Troche Pesqueira <http://webs.uvigo.es/webqo3/people/eduardo.html> Tel. 986812309 Edificio E, Andar 3º, Laboratorio1 Facultade de Químicas Departamenteo de Química Orgánica Lagoas-Marcosende Universidade de Vigo

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Stereo 3D on non-quadro GeForce cards
by Gökhan Tolun 07 Jan '13

07 Jan '13

Hi, Is Chimera still quadro-only as the stereo-3D goes, and if so, is there ANY way of making it work with a non-quadro card? I have a 560 Ti SLI system with an ACER 27" 3D LCD monitor with active shutter glasses. Thanks. Gökhan

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Announcement: Release of DOCK 6.6
by Scott Brozell 04 Jan '13

04 Jan '13

We are pleased to announce the release of DOCK 6.6. DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring. The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids. Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues. The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket. In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies. For full information on what is new in DOCK 6.6, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.6.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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3DConnexion Space Navigator dead-zone
by Gökhan Tolun 03 Jan '13

03 Jan '13

Hi, Is it possible to set a dead-zone for the 3DConnexion Space Navigator in Chimera? I tried doing this using its OSX driver, but I cannot find such an option in its control panel. Thanks. Gökhan

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Circular DNA minimization
by Damien Larivière 03 Jan '13

03 Jan '13

Dear all, I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. The first phase, the Steepest Descent Steps, works fine. However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. I'm not versed in the art of minimization. Do you know the reason of this behavior? Thanks for your help, Damien ps: I'm working on Windows 7 with a core i5

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