- Chimera-users - RBVI Mailing Lists

Amira map file reader
by Tom Goddard 06 Feb '13

06 Feb '13

I made Chimera able to read Amira map files, file suffix ".am", also known as AmiraMesh files, with format described here http://www.mpi-inf.mpg.de/~weinkauf/notes/amiramesh.html Chimera only reads scalar (not vector) files. This is in the current Chimera daily build. http://www.cgl.ucsf.edu/chimera/download.html#daily Tom

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Mirror
by Sebastian Mock 06 Feb '13

06 Feb '13

Hi, is there any possibility to mirror / copy a molecule. E.g. you have two docked molecules. If I want the docking partner to be mirrored to the other side of the receptor molecule in the same exact location, but mirrored. Thanks in advance Sebastian

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(no subject)
by rashmi gupta 06 Feb '13

06 Feb '13

Sir I want to know that if i had modeled a protein structure and want to categorize it into different chain or domain then how would i do this through chimera? Plz give the solution of question -- Rashmi Research scholar IMS, BHU

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Re: [Chimera-users] Chimera on a virtualbox
by Greg Couch 06 Feb '13

06 Feb '13

(Forgot to send reply to whole list) -------- Original Message -------- Subject: Re: [Chimera-users] Chimera on a virtualbox Date: Tue, 05 Feb 2013 13:51:47 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: chris.wood(a)stfc.ac.uk Hi Chris, So what are you trying to do with Chimera inside a virtual machine? Presumably, you're not trying to use it graphically because virtualized graphics performance is usually abysmal. Chimera benefits immensely from direct access to the graphics hardware. So that leaves using Chimera as a server, and for that the headless version of Chimera is usually better -- the headless version uses a software implementation of OpenGL and thus avoids any driver issues. That said, this bug is still likely to be related to OpenGL support in VirtualBox. Make sure the computer that VirtualBox is running on has an up-to-date OpenGL graphics driver. It doesn't matter what VirtualBox does if the underlying system has a bad graphics driver. To confirm that the bug is in the graphics driver, get a backtrace of where the error occurs by using gdb as follows in a Terminal window (and assuming there is a symbolic link to the chimera binary on your path): % export CHIMERA=`chimera --root` % export LD_LIBRARY_PATH=$CHIMERA/lib % gdb $CHIMERA/bin/python2.7 (gdb) break_exit (gdb) run $CHIMERA/share/__main__.py --debug (gdb) bt The '%' and '(gdb)' parts are the shell and gdb prompts, respectively. The output from the bt command will probably be in Chimera's molecular drawing code (as opposed to drawing the UI). If you need help interpreting the chimera backtrace, you can send it to me. HTH, Greg On 02/05/2013 12:48 PM, chris.wood(a)stfc.ac.uk wrote: > > Hello all, > > I'm trying to run Chimera on VirtualBox. The installation completes > fine, but when I try and run the program (|cd| to the bin directory > and run |./chimera|) I see > > X Error of failed request: BadDrawable (invalid Pixmap or Window > parameter) > > Major opcode of failed request: 72 (X_PutImage) > > Resource id in failed request: 0x480006a > > Serial number of failed request: 1382 > > Current serial number in output stream: 1388 > > I've tried enabling / disabling hardware virtualization & 3D > acceleration, but to no avail. Although people do seem to have > problems with chimera on a virtualbox, it normally seems to be a > problem with OpenGL, which this doesn't seem to be. > > Has anyone seen this error before? Is there anything else I'm missing? > I can't even work out if it's a hardware, VirtualBox, or OS problem... > > ** > > *System:* > > VirtualBox 4.2.4 > Guest additions 4.2.4 > > Guest OS: Ubuntu 12.04 > Host OS: Windows 7 professional > > Thanks in advance! > > Chris > > ------------------- > > Dr Chris Wood > > STFC Rutherford Appleton Laboratory > > Didcot > > OX11 0QX > > chris.wood(a)stfc.ac.uk > www.ccpem.ac.uk > > > Tel: +44(0)1235 567864 > > Tel: +44(0)7909 586624 > Fax: +44(0)1235 567801 > > > -- > Scanned by iCritical. >

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color spill
by Yadong Yu 05 Feb '13

05 Feb '13

Hi there, I have a color spill problem when drawing a few figures of a hexamer. The coordinates of 6 protomers were saved into a PDB file. I wanted to color chain A red and the rest gray, so I selected chain A and colored it with red. The red color strangely spilled to an N-terminal segment of the next chain. I think there is some problem with the format of my PDB file, but don't know exactly what is wrong. Here's the end of A and begin of B where spill happend: ATOM 2657 C ASP A 418 74.297 91.204 65.520 1.00 0.00 P1 C ATOM 2658 OT1 ASP A 418 73.965 91.654 66.693 0.00 0.00 P1 O ATOM 2659 OT2 ASP A 418 73.731 91.612 64.449 0.00 0.00 P1 O ATOM 2660 N ASP A 418 74.565 88.894 65.731 1.00 0.00 P1 N ATOM 2661 CA ASP A 418 75.338 90.111 65.514 1.00 0.00 P1 C ATOM 2662 CB ASP A 418 76.099 90.113 64.183 1.00 0.00 P1 C ATOM 2663 CG ASP A 418 77.091 91.332 64.042 1.00 0.00 P1 C ATOM 2664 OD1 ASP A 418 76.837 92.210 63.175 1.00 0.00 P1 O ATOM 2665 OD2 ASP A 418 78.018 91.382 64.875 1.00 0.00 P1 O ATOM 2666 N LEU B 87 68.825 113.707 134.628 1.00 0.00 P2 N ATOM 2667 CA LEU B 87 68.215 113.786 133.272 1.00 0.00 P2 C ATOM 2668 CB LEU B 87 67.055 114.822 133.239 1.00 0.00 P2 C ATOM 2669 CG LEU B 87 66.068 114.738 134.402 1.00 0.00 P2 C ATOM 2670 CD1 LEU B 87 65.132 115.985 134.379 1.00 0.00 P2 C ATOM 2671 CD2 LEU B 87 65.430 113.355 134.203 1.00 0.00 P2 C ATOM 2672 C LEU B 87 69.159 114.128 132.171 1.00 0.00 P2 C ATOM 2673 O LEU B 87 69.384 113.413 131.199 1.00 0.00 P2 O Any suggestion? Thank you! Yadong

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Modeller
by Hernando J Sosa 05 Feb '13

05 Feb '13

Hi, I am trying t use modeller within chimera but it always end with an error: .... Kind, OS, HostName, Kernel, Processor: 4, Linux watson.cgl.ucsf.edu 2.6.32-279.14.1.el6.x86_64 x86_64 Date and time of compilation : 2012/08/29 11:36:00 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2013/02/05 13:11:37 check_lice_E> Invalid license key: Go to http://salilab.org/modeller/ to get a license key, and then set the 'license' variable to it in the file /usr/lib/modeller9.11/modlib//modeller/config.py I have installed modeller in my computer and have a license to it. I also verified that the license number was set in the config.py file. So I am not sure what the problem could be ?? System details: Chimera v. 1.7 Modeller v. 9.11 OS: Windows 7 64bits Thanks, Hernando

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Chimera on a virtualbox
by chris.wood＠stfc.ac.uk 05 Feb '13

05 Feb '13

Hello all, I'm trying to run Chimera on VirtualBox. The installation completes fine, but when I try and run the program (cd to the bin directory and run ./chimera) I see X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x480006a Serial number of failed request: 1382 Current serial number in output stream: 1388 I've tried enabling / disabling hardware virtualization & 3D acceleration, but to no avail. Although people do seem to have problems with chimera on a virtualbox, it normally seems to be a problem with OpenGL, which this doesn't seem to be. Has anyone seen this error before? Is there anything else I'm missing? I can't even work out if it's a hardware, VirtualBox, or OS problem... System: VirtualBox 4.2.4 Guest additions 4.2.4 Guest OS: Ubuntu 12.04 Host OS: Windows 7 professional Thanks in advance! Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 -- Scanned by iCritical.

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MatchMaker
by Mock, Sebastian 05 Feb '13

05 Feb '13

Hi, I am facing a problem with Matching! Is there any possibility to match two structures, without losing the coordinates of e.g. a dimer unit. In this case, I want to match a homo-dimer to another similar structure. When I match all of the above mentioned dimers (chains), Chimera will match it all at the same place, so I will have two identical positions. In this case I am losing the steric information about the assembly of the homo-dimer. Is there any method, to treat the dimer as one molecule, which cannot be splitted and can be matched on another structure without losing the biological assembly? It is hard to explain, I hope you get me. Thanks in advance Sebastian

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Modification of COX Demo
by Noel Pace 05 Feb '13

05 Feb '13

To whom it may concern, I am a university student in his final year following a course in Pharmacy at the University of Malta. Currently, under the supervision of my tutor, I am working on a dissertation entitled " The Development of Computational Chemistry Practicals". During my research I came across your software UCSF Chimera and found out the DEMO section. I would like to make use of the editing function to edit the COX demo present with the software to represent Beta-Receptors instead. I will write down that the demo has been based on the COX demo present. Is the above request possible? I really find your software to be suited for my needs and would be honored to have your support in the fulfillment of my dissertation. I thank you in advance Noel Pace M. Pharm Student (Malta)

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Blast protein
by Bobo Dang 05 Feb '13

05 Feb '13

Hi guys, I was trying to build homology model using chimera. The uniprot ID of the molecule I want to build is Q9X2V8, when I was trying to blast to find the homologs which have structures. It returns "no BLAST matches found". Does this mean there is no Q9X2V8 homolog from PDB? how does Chimera judge one molecule could match (could be the homolog)? thanks bobo

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pseudo bond reader in command line
by M. Elizabeth Stroupe 04 Feb '13

04 Feb '13

Hi, I am trying to make a figure with pseudo bonds - the figure is fairly complicated and it will be a frame in a movie of related shots, so I need to call the pseudo bonds in from the command line. How do I read in a text file that defines the pseudo bonds (as if from the pseudo bond reader) and then alter their attributes (to make them into dotted rather solid lines)? Thanks much, Beth

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Add hydrogens to DNA
by sette＠uniroma2.it 02 Feb '13

02 Feb '13

Hi, I used the addH to add hydrogens to a DNA pdb file generated with 3DNA but most of the atoms are not protonated. Is addH used for DNA or just for proteins? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Re: [Chimera-users] Problem with Chimera 1.7 on Linux OS
by Greg Couch 01 Feb '13

01 Feb '13

Those errors are coming from Chimera asking the graphics driver about multisampled visuals. You might be able to avoid the problem by starting up chimera with the --debug-opengl flag and turning off multisampling. But the fact that you are getting an error means that you need to update the graphics driver on your Linux production computer. For Linux computers, we recommend installing the proprietary NVIDIA or AMD graphics driver depending on which brand of graphics hardware you have. If you have Intel graphics, the only easy way to get updates is to update to a newer version of Linux. If you are running Chimera inside a virtual machine, then updating the graphics driver means updating the virtual machine software, but chimera would perform better without that intervening layer. Also note that on some newer versions of Linux, eg., Ubuntu 12.10, the default setup interferes with OpenGL applications, in particular, opening the SideView tool causes Chimera to crash. The workaround is to switch to a non-compositing window manager like xfce. HTH, Greg On Fri, 1 Feb 2013, Stephen P. Molnar wrote: > I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit > Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it > onto my Linux production computer. The installer ran smoothly without > generating any warnings or errors. > > > > However, when I run the executable I get the following messages: > > > > computation@debian:~/Apps/chimera/bin$ ./chimera > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring > > OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your > SPU > > > > I have the win version open in MS Win 7 on the same computer as I compose > this message. > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy > set > > Foundation for Chemistry Stochastic and > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Problem with Chimera 1.7 on Linux OS
by Stephen P. Molnar 01 Feb '13

01 Feb '13

I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it onto my Linux production computer. The installer ran smoothly without generating any warnings or errors. However, when I run the executable I get the following messages: computation@debian:~/Apps/chimera/bin$ ./chimera OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU I have the win version open in MS Win 7 on the same computer as I compose this message. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1

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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 31 Jan '13

31 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 31 Jan '13

31 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 25 Jan '13

25 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 15 Jan '13

15 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

2 2

Re: [Chimera-users] em fit refinement
by Feixia 15 Jan '13

15 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 15 Jan '13

15 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

2 2

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

2 1

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

2 1

How to install ?
by pythonchemia Gazeta.pl 11 Jan '13

11 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

5 5

Showing Binding surface
by Bobo Dang 11 Jan '13

11 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

3 8

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

3 2

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

2 1

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>

2 3

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 08 Jan '13

08 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

1 0

Front End for NAMD?
by Rudy J. Richardson 08 Jan '13

08 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 08 Jan '13

08 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

3 4

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

2 1

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

2 1

Announcement: Release of DOCK 6.6
by Scott Brozell 05 Jan '13

05 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

1 0

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

2 1

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

2 2

GLYCAM force fields and Chimera
by john Kerk 28 Dec '12

28 Dec '12

Dear Users I want to assign the partial charges of a glucose molecule using chimera-1.7 but I can not find this force field in Add charge suite although the GLYCAM force field files are existing under amber12. can I get help wishing merry Christmas , John

3 2

a PyMol file into Chimera
by Anindito Sen 21 Dec '12

21 Dec '12

Dear All, Questions of the following type/s may have been answered many times before but will be of help if you can reply (again). I have a PyMol file with file extension 'pse' . I want to Visualize it Chimera. Is there any trick to do that ? Best Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

2 1

More on initial energy value from Chimera
by Thomas Sturgill 20 Dec '12

20 Dec '12

Elaine has explained that the initial energy is a total energy and not a free energy. Understood. I want to verify that a negative energy is "better" than a positive energy, and a more negative energy is "better" still. This is what I assume now, but I had an angst that the energy value is somehow based on absolute value, so the "best" minimized energy is zero. Humor my question, because I have to be 100% certain. No need to go into caveats about the ability of Chimera minimization to make models worse, and how difficult the energy parameter is to interpret. Tom. Thomas W. Sturgill, M.D.-Ph.D. Biozentrum, University of Basel Department of Biochemistry/Hall Lab Klingelbergstrasse 70 CH4056 Basel, Switzerland TEL: (+41 61) 267 2172 FAX: (+41 61 267 2149 Visiting Professor U. of Virginia, Pharmacology Charlottesville, VA 22908 USA FAX: (434) 924-5207

2 1

Display at low definition
by Damien Larivière 20 Dec '12

20 Dec '12

Dear all, I have a basic question: In the image below, on the left, the definition of the atoms is quite good, they are perfect spheres. On the right, they are not anymore. I probably activated something in Chimera, but I'm not able to remember. May you tell me what to do to get a good definition again? Many thanks for your help, Damien

3 3

RNA structure creation plugin
by Eric Pettersen 19 Dec '12

19 Dec '12

Hi All, Dr. Fabrice Jossinet from the University of Strasbourg recently released Assemble2, a Chimera plugin for designing RNA structures in 2D and then generating the corresponding 3D structure. If you're an RNA person, maybe you'd like to try it out and offer feedback. Here's the Assemble2 web site: http://bioinformatics.org/assemble/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Adjust bond angle doesn't seem to work
by oxi 19 Dec '12

19 Dec '12

Hi, I'm new to Chimera Using 1.7 candidate build 37955 When I select two adjacent bonds and adjust their relative angle in Tools->Build Structure->Adjust bond angles, nothing seems to actually change in the graphic view I tried selecting the 3 atoms involved afterwards and measure the angle, and it still reports the original angle, so I don't think it's a graphic glitch but the angle isn't actually being changed. Is this a bug or am I doing it wrong? Thanks

2 3

rotation axis display
by Hernando J Sosa 19 Dec '12

19 Dec '12

Hi, Is there a way to display an axis line? I would like to display the rotation and translation axis as given in the reply log after a fit in map operation. Thanks Hernando

2 2

selected molecule
by krit tantanarat 18 Dec '12

18 Dec '12

Dear all I am using MAC and try to select the atom by using Control + left click no mouse but it did not work. How to picking atom from screen using MAC ? Thanks, Krit

2 1

problems with mounted filesystems on MacOS
by Mario Dejung 17 Dec '12

17 Dec '12

Hi everybody, I have a problem with Chimera on my Mac computer. I have a mounted filesystem on my computer, but sometimes (Wifi switched of for example), the path is no longer available and my Chimera crashes, if I try to open a file, because this mounted path is the last one Chimera is trying to open, but the path is no longer available… So Chimera is no longer responding and I have to force quit. The next problem is, when I restart Chimera, it is still trying to open something from the last path… And crashes again. The only thing that works is, I have to double click a map or a pdb or something, but then, when I try to open something with the menu, Chimera is no longer responding. Hope someone has some suggestions and can help me. Thanks in advance Mario

2 1

Electric field lines?
by Hurt, Darrell (NIH/NIAID) [E] 17 Dec '12

17 Dec '12

Hi Chimera team, Is it possible to visualize electric field lines in Chimera from, for example, an APBS run? If so, how do I do it? I've scanned through the documentation, but didn't find anything… Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

4 6

mouse does not report potential values after change of surface transprency
by Boaz Shaanan 15 Dec '12

15 Dec '12

Hi, When I colour a surface according to the potential (read from a delphi or apbs map) and change the surface transparency (in order to show some residues below the surface), the mouse no longer reports the potential values as I walk over the surface. I have to re-colour the surface in order to get back this functionality but the surface is opaque now. Is that how it's supposed to be? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Friday, December 14, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 116, Issue 19 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: mask command (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Dec 2012 16:15:56 -0800 From: Tom Goddard <goddard(a)sonic.net> To: Xiangan Liu <xiangan.liu(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] mask command Message-ID: <50CA6FBC.6020202(a)sonic.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Xiangan, The mask command is working fine in my tests. It only sets the map values to zero outside the surface. The values inside the surface are identical to the original map. If that is not the case for you than use menu Help / Report a Bug... and provide the exact mask command you used and explain how you know that the new masked map values are different from the original map. This sounds like the right approach to segmenting a subunit. If instead you had a fit atomic model you could use Color Zone and the Split button on that dialog. Tom > Hi Tom, > I am trying to use your MASK command to extract some interested > volumes from a density map based on another reference density map. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html > > I followed your guide line from the link above, but the extracted > density is not the same as the original density. > Is there anything I should pay special attention? > It looks like the command was created many years ago, is it still good > for the latest chimera version? > > Do I have any other way to segment map based on a known subunit > density map, something similar to color zone? > > Thanks, > > Xiangan Liu > > ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 116, Issue 19 **********************************************

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Re: [Chimera-users] mask command
by Tom Goddard 14 Dec '12

14 Dec '12

Hi Xiangan, The mask command is working fine in my tests. It only sets the map values to zero outside the surface. The values inside the surface are identical to the original map. If that is not the case for you than use menu Help / Report a Bug... and provide the exact mask command you used and explain how you know that the new masked map values are different from the original map. This sounds like the right approach to segmenting a subunit. If instead you had a fit atomic model you could use Color Zone and the Split button on that dialog. Tom > Hi Tom, > I am trying to use your MASK command to extract some interested > volumes from a density map based on another reference density map. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html > > I followed your guide line from the link above, but the extracted > density is not the same as the original density. > Is there anything I should pay special attention? > It looks like the command was created many years ago, is it still good > for the latest chimera version? > > Do I have any other way to segment map based on a known subunit > density map, something similar to color zone? > > Thanks, > > Xiangan Liu > >

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Mac Retina display
by Tom Goddard 14 Dec '12

14 Dec '12

A few weeks ago I added support in Chimera for retina displays (2880x1800 pixels) on Macbook Pro laptops. The recent Chimera builds use the full resolution and produce beautifully smooth edges and text. Older versions of Chimera will use only half the retina screen resolution 1440x900, which is comparable to non-retina displays (~120 dots per inch). The attached image compares the old (left) and new (right) graphics and text in a direct screen snapshot magnified by 2x. The improvement is in Chimera daily builds and the Chimera 1.7 release candidate. Tom

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Saving trajectories in one pdb file
by Daniel Gurnon 13 Dec '12

13 Dec '12

Hi all, I'm using Chimera to prepare multi-model pdbs for use in ePMV. I've run into two issues: 1) When saving a portion of a trajectory in one pdb file, frame numbers are used as model numbers. But only 4 digits are supported. Above 9999, the model number becomes ****. Could you enable 7 digits? I'm taking frames from the end of a long trajectory. 2) I was hoping that I could retain the effect of "hold selection steady" by saving as a pdb with transformed coordinates, but this isn't the case. Is there a way to make this work? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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morphing model extrapolation
by Gajewski, Stefan 12 Dec '12

12 Dec '12

Hi! I have two .pdb files on hand. Both are in between two biologically relevant conformations. When I create a morph between them, I can see them permuting between the two crystal structures but only half way to the two relevant conformations. The morphing model should generate a trajectory between the two coordinate sets. Is it possible to let the morphing model generate more coordinate files/frames beyond the target structure? Let's say 120 frames morph A to B and compute 60-100 more frames beyond B based on the previous trajectories? Thanks, Stefan ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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Measure symmetry helix
by Mariam Shirdel 12 Dec '12

12 Dec '12

Hi! I'm trying to measure the symmetry of an EM density map to fit a pdb to it and make several copies. When I run the commands in the command line: me sym #0 min 0.89 helix 8.97,-111.86, the result I get is Symmetry EMnew.spi: Helix C5, rise 8.97, angle -111.9, center 39 39 38, n 30. The problem is that when I run sym #1 group #0 update true, I get a pentagon base which goes through the whole helix. I just want the measure symmetry to give me Helix, without the C5. What are the commands to achieve this? I tried: sym #1 group c5*h,8.97,-111.86, but it didn't work, and I don't think that's the correct way for me to do it. Does anyone know what to do? Best regards, Mariam Shirdel

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Question about displaying x-ray ribbon.
by Jianfeng Lin 11 Dec '12

11 Dec '12

Hi Chimera Team, Is it possible to make the ribbon of PDB crystal structure plumper in Chimera. I wonder it because the ribbon of interested crystal structure looks slim (in flat, edged, or rounded mode), and leaves much empty space when I fit it into my low resolution cryo-ET volume. Thank you very much in advance! Jianfeng -- Postdoc at Nicastro Lab Biology Department Brandeis University 415 South Street, Waltham, MA 02453, USA Tel. 001-781-736-2439

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model loop in chimera
by Mikolajek H. 11 Dec '12

11 Dec '12

Hi, I am trying to model a protein in chimera using the model loop command. I get this error: Modeller temporary directory: c:\users\admini~1\appdata\local\temp\modellerjtn4xd Unable to run modeller: [Error 2] The system cannot find the file specified Do you know where I am going wrong? Best wishes Halina

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surface calculation
by Anton Vila Sanjurjo 11 Dec '12

11 Dec '12

Hi, I have seen posts regarding this problem before. Here is the log I got after attempting to render a surface representation of the 50S ribosomal subunit (rcsb ID: 3CPW). #0, chain 0: 23S ribosomal rna #0, chain 1: L35E #0, chain 2: 50S ribosomal protein L44E #0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3' #0, chain 9: 5S ribosomal rna #0, chain A: 50S ribosomal protein L2P #0, chain B: 50S ribosomal protein L3P #0, chain C: 50S ribosomal protein L4P #0, chain D: 50S ribosomal protein L5P #0, chain E: 50S ribosomal protein L6P #0, chain F: 50S ribosomal protein L7AE #0, chain G: HS6 #0, chain H: 50S ribosomal protein L10E #0, chain I: 50S ribosomal protein L13P #0, chain J: HMAL13 #0, chain K: 50S ribosomal protein L15P #0, chain L: 50S ribosomal protein L15E #0, chain M: 50S ribosomal protein LC12 #0, chain N: 50S ribosomal protein L18E #0, chain O: 50S ribosomal protein L19E #0, chain P: 50S ribosomal protein L21E #0, chain Q: HL31 #0, chain R: 50S ribosomal protein L23P #0, chain S: 50S ribosomal protein L24P #0, chain T: 50S ribosomal protein L24E #0, chain U: HL21/HL22 #0, chain V: 50S ribosomal protein L30P #0, chain W: 50S ribosomal protein L31E #0, chain X: 50S ribosomal protein L32E #0, chain Y: HL5 #0, chain Z: 50S ribosomal protein L37E C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 989.35 Total solvent accessible surface area = 1473.85 In this case, I am not interested in splitting the file into its individual chains. I have also unsuccessfully played with the probe-radius and vertex parameters. I should mention that I was able to get this to work with previous versions of Chimera (1.5.something) and that small proteins can be successfully rendered with the latest versions. best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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placing models on the same plane
by Bala subramanian 10 Dec '12

10 Dec '12

Friends, I open two pdb files. When i visualize them, one model is far away from the viewer and another is closer. I want to put both models on the same plane in order to make a figure. Is there any way to do this without doing a fitting. Thanks, Bala -- C. Balasubramanian

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Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes
by Elaine Meng 10 Dec '12

10 Dec '12

Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use. A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.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 P.S. better to send questions about using Chimera to chimera-users(a)cgl.ucsf.edu (CC'd on this message), not chimera-dev(a)cgl.ucsf.edu which is meant for programmers On Dec 2, 2012, at 10:21 PM, tao zhao wrote: > Hello, > I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. > It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next. > > Could you please give me some instruction? > Thank you very much. > > Tao Zhao > Northwest A&F University,Yangling, China

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Re: [Chimera-users] Disulfide bonds
by Elaine Meng 06 Dec '12

06 Dec '12

On Dec 5, 2012, at 1:20 AM, Moritz Bitzhenner wrote: > Hi Elaine, > You are a lifesaver. Thank you very much, it all worked perfectly. Now I have a nice colourful ribbon structure protein with disulfide bonds. The middle of the bond is coloured in yellow, the rest of the sidechain is coloured in light grey. Can I change the colour of the grey sidechain without changing the colour of the AA in the ribbon structure? But it´s not that important. > > I also created a movie of the rotating protein. (Command line: roll). Can I decrease the speed of the rotation? > > With best regards from Germany and many thanks for your help. > Moritz Hi Moritz, Greetings to you in Germany! You can specify that coloring should apply only to atoms/bonds (not ribbons, surfaces, etc.) using the Color Actions dialog. Menu: Actions... Color... all options, and then in that dialog see the "Coloring applies to" section. The same thing can be done in the command line, for example: color goldenrod,a :cys ...means to make atoms-only of Cys residues the color named goldenrod. Each command has a manual page, which you can see with the "help" command (e.g. commands "help roll" "help color") so I recommend looking at those for more details such as how to control the speed of roll. See also the general information on making movies: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.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 P.S. best to send to chimera-users(a)cgl.ucsf.edu so that others can benefit

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Disulfide bonds
by Moritz Bitzhenner 04 Dec '12

04 Dec '12

Dear Chimera Users I am fairly new to the program and I have a particular problem with the display of disulfide bonds. I have an amino acid sequence, I created a pdb-file with Expasys Swiss Model Workspace. I opened the pdb file with Chimera and coloured the ribbon structue (it looks amazing), I even did a movie of my rotating protein. But I cannot display the three disulfide bonds. Is my pdb file lacking the CONECT information? How can I include them? With Swiss PDB Viewer (Deepviewer) I can show the bonds, but somehow I cannot transfer the information to the pdb file and Chimera. I also tried manually bonding the closest cysteins by selecting Cystein residues and "bond" in the command line. How do I select the two single atoms that I want to connect? I read through former similar questions in the list server but nothing helped so far. If you can find any time helping my case, it would be greatly appreciated. With best regards from Germany, Moritz Here is the AA sequence: GEIDNNQCQICELLVKDIIEGLTANQSVEVIEHGLNLICDHIPLHVRVCKQFVDSNFQKIVQFIENHDDPQEICEKCGVC

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stick representation after selection / DNA helical axis
by Damien Larivière 03 Dec '12

03 Dec '12

Dear all, I used the command sel @N1 @N3 to select the N1 and N3 atoms of a nucleic acid structure (like 1bna). when I do "show only" in Actions / Atoms&Bonds, a specific representation is displayed as in the image below: sticks connect N1 atoms of one strand and N3 atoms of the other strand. May you tell me the meaning of this representation and how can I modify it (I mean, how to change the type of atoms to be connected)? In fact, I would like to visually apprehend the helical axis. Is there a way to calculate and display this axis in Chimera? Many thanks for your help Damien

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Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
by Francois Berenger 30 Nov '12

30 Nov '12

-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger(a)RIKEN.JP> Reply-To: Francois Berenger <berenger(a)RIKEN.JP> To: CCP4BB(a)JISCMAIL.AC.UK Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.

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(no subject)
by Richard Sibout 28 Nov '12

28 Nov '12

Dear users of Chimera, I can't find the definition of ACT, DTV, EDO...in the residue (non standard) section. Can someone help me to find these definitions ? Thanks Richard

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Help... Report a Bug
by amna khan 27 Nov '12

27 Nov '12

hi, when i minimize my structure it gives the following error for my pdb file. that prolone residues is missing and about integral charges. please help me to remove this error #0, chain D: dna (5'- D(*ap*gp*ap*tp*gp*gp*gp*gp*ap*ap*tp*cp*cp*cp*cp*tp*A P*gp*A)-3') #0, chain P: nuclear factor κ-B (nf-kb) Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 321 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added No incomplete side chains Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 188 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added Charge model: AMBER ff99SB Total charge for #0: -15.624 The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_3 and H_2 No incomplete side chains Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 188 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added Charge model: AMBER ff99SB Total charge for #0: -15.624 The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3 regards amna khan

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stupid problem
by Hartzell Jr., Criss 27 Nov '12

27 Nov '12

Until recently, FAVORITES > SEQUENCES only opened a new window showing the sequence. Since I upgraded to version 1.6.2, this not only opens the sequence window, it also automatically adds a new model for each sequence to the model panel and opens a new instance of the structure in the graphics window. How do I stop this? I just want the sequence window. Thanks. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Cluster list
by Rebecca Swett 26 Nov '12

26 Nov '12

Is there any way to get a list of all the members of each cluster when using the tool Ensemble Cluster? Basically i'm looking to run the clustering bit, and then write a list -cluster 1 members:1-3,4-8, etc. for all clusters produced. Anyone out there have any suggestions? Thanks for anything you've got. I think I could get it by manually going through: choosing a cluster, selecting it, and then using the write list function with a custom identifier, but i've got a lot of these to handle. -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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how to add misiing proline between H2 and H3
by amna khan 26 Nov '12

26 Nov '12

hi, i am new to chimera when i minimize my pdb structure, it gives the following error The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3 i am not able to minimze the strcuture due ti this error , please help me how to remve this error regards

2 1

Mutation of residue
by Tijesunimi Odebode 26 Nov '12

26 Nov '12

Hello all, I am new to Chimera and I am trying to change a serine in the sequence of my protein to a leucine. Is there a way of doing that in Chimera? Thanks in advance for the help. TJ

2 2

Quadro versus GTX graphic cards
by Oliver Koch 24 Nov '12

24 Nov '12

Dear Chimera users, I want to buy new computer for my lab and I'm not sure which graphic cards I should buy. Is it really necessary to invest in expensive nvidia quadro graphic cards in comparsion to the nvidia gtx consumer cards? My private desktop computer has a GTX570 and everything is working fine. I searched the internet and talked to a lot of people, but nobody could say if you really recognize the difference in your daily work. The background: I want to use the computer for modelling (Chimera, Moe, ...) with two screens and stereoview using nvidia 3d vision. The OS will be linux (presumably scientific linux). I would be very happy if you can share your opinion. Many thanks Oliver -- Dr. Oliver Koch Junior Research Group Leader "Medicinal Chemistry" Chemical Biology Faculty of Chemistry Technische Universität Dortmund Otto-Hahn-Straße 6 44227 Dortmund EMail: Oliver.Koch(a)tu-dortmund.de

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Movie with multiple models
by Benefield, Desiree A. 20 Nov '12

20 Nov '12

Hello again, I have a 3D reconstruction volume file. I'd like to show the initial model as a solid surface, then as a mesh surface, and then as the mesh surface with crystal structures. Can you recommend the best way to approach this? Specifically, I am uncertain as to what command will help me accomplish this and/or if I need different chimera files for each form of the model... Very sorry to keep bothering you. I appreciate the advice. Desiree

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Coulombic coloring
by Mock, Sebastian 20 Nov '12

20 Nov '12

Hi Chimera Team, is it possible to color the active site of an enzyme let's say green after the coulombic coloring, without losing the last-mentioned? The coulombic coloring disappears when I try to color specific positions in the structure to green. Thanks in advance Sebastian

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Question about tilting a structure in a movie
by Benefield, Desiree A. 20 Nov '12

20 Nov '12

Hello all, I am a new Chimera user and interested in using the program to create a movie of one of my molecular structures. I have been using some basic commands (turn, rock, etc.) but I would also like to be able to tilt my molecule. For example: tilt forward 45 degrees and tilt back to the original position. I can get the model to tilt by using the command line: turn x 1 45 however, I can't figure out how to make the model return to its original position smoothly. I can use the reset command but that looks a little disjointed. Any advice or suggestions would be greatly appreciated. Thanks, Desiree

2 2

coil representation thickness
by Evan Kantrowitz 20 Nov '12

20 Nov '12

Hi, I am trying to setup a python script to display a series of similar structures. I would like each shown as just a thin coil like licorice but much thinner. I can get the representation I want by using custom scaling in the Ribbon Style Editor and setting everything to 0.1. Is there a command line command to set the thickness of licorice. Else, how can I do give the scaling commands used in the Ribbon Style Editor from the command line or what python command(s) will do it. Thanks in advance. Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Problems installing and running chimera on opensuse 12.1
by Visvaldas K. 20 Nov '12

20 Nov '12

Hi all, I'm having problems after the opensuse (gnome desktop) upgrade to the 12.1 version. I can go on for hours how great this new gnome desktop is *NOT*, but that's not the main issue here. During installation, the messages are as follows: Downloads% ./chimera-alpha-linux_x86_64$1$.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/visvaldas/Downloads' inflating: chimera_install_vautEs/installer inflating: chimera_install_vautEs/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-2012-11-14 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/visvaldas/.local/UCSF-Chimera64-2012-11-14' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yesyes Traceback (most recent call last): File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_vautEs' Installation is done; press return. This was using the November 14 version of Chimera. libbz2 error happens also during the run (I don't care much about icon problem). visvaldas% ~/.local/UCSF-Chimera64-2012-11-14/bin/chimera 1HVR.pdb Traceback (most recent call last): File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory Thank you for your attention, and many thanks. Vis

3 4

Nutate or lemniscate program to scenes/animation?
by Hurt, Darrell (NIH/NIAID) [E] 19 Nov '12

19 Nov '12

Hi Chimera folks! I love, love, love the new scene-based animation! I know that it is still under development, but it is fantastic! And the "Animation" utility panel is easy to use and understand. I love the "Rock" and "Roll" "Actions" available in the Animation panel. That goes a long way to making movie-making a point-and-click affair! I would like to suggest or propose one more "Action" in addition to "Rock" and "Roll". It is "nutate" or "lemniscate". It is basically a "rock" in both the X and Y planes at the same time. I think that it can be coded relatively simply with a cosine function about the X axis concomitant to the sine function about the Y axis that is driving the current "Rock". You can see an example of what I'm talking about here: http://youtu.be/55_cmJLe3Is Also, if I could, I would also suggest or propose that the "Rock" and "Nutate/Lemniscate" have a single parameter to control the "width" of the rock or nutation/lemniscation — maybe choices of 15, 30, 45, and 60 degrees or a free-form entry. Thanks for everything you do! Best wishes, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

3 3

Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram
by Tom Goddard 16 Nov '12

16 Nov '12

Hi Daniel, Probably you can modify your script and make Chimera open the copies much faster. The python script should also achieve that. The trick with your command script is that between each command Chimera draws a frame and may update the volume dialog histograms. One way to avoid this is put all the commands on one line separated by semicolons. Maybe another better method is have one open command and one transform setting command open template.em template.em template.em ... (repeat for as many copies as you need) matrixset transforms.txt I believe the matrixset command can have the positions for as many models as you want with the model id number specified before the transform. See the Chimera manual or try matrixget to write an example file with several models being displayed to see the precise format when you have multiple transforms. A Python script could be faster still because it wouldn't need to open the same map file over and over. It could create all the map copies from the first. As an example making 100 translated copies of an open 100**3 volume took 3 seconds with the following Python from VolumeViewer import active_volume v = active_volume() from chimera import Xform for i in range(100): c = v.copy() c.openState.localXform(Xform.translation(i*20,0,0)) c.show() Tom > Hi Tom, > > > Yes, both methods that you describe work nicely. In particular, I was > not aware of the possibility of changing the level of a set of models > with a single command line operation: that does help a lot. > > The only actual annoyance that remains in my implementation for the > manipulation of sets of volumes is the loading of the volumes?. I > suspect the way I do it is too rudimentary, as I just open Chimera > passing as argument a .cmd command file that loads the same file again > and again, placing it each time in a different location, i.e: > > open 0 template.em > matrixset transform_0.cmd > open 1 template.em > matrixset transform_1.cmd > > ? and so on for hundreds of models, so that the user basically sees > the Volume Viewer getting updated with a new model and then a new one > for several minutes. I guess with the .py script that you send me I > will be able to load the volumes in a less messy manner than this one. > > Thanks for all the info! > Daniel > > >> Hi Daniel, >> >> I see. You'd like to control the contour level, color, >> surface/mesh style, step size... of all the copies as if they were >> one model instead of 100 different models, each a copy of the same >> map. For making hundreds of copies of an atomic model, the >> multiscale dialog in Chimera does this using a single model. But >> that doesn't currently work with maps. One disadvantage of having a >> single model for all the copies of a map is that the maps will all >> have to have the same color, same step size, same contour level >> because all those properties are stored with the model. Maybe that >> restriction is fine for your use. I would like to make that possible >> by allowing Chimera to place identical copies of any type of model by >> just specifying the list of positioning matrices. The model would >> just remember the list of matrices for the different placements. >> >> For now using a hundred different models of the same map is >> workable. You can't adjust all of them at the same time with the >> volume dialog. But you can adjust one to figure out the contour >> level you like and then use one volume command to set the level for >> all the copies, for example, "volume #1-100 level 1.24 color yellow >> step 2". >> >> Another approach is to make a single map by adding your hundred >> placed copies on a single grid (e.g. the tomogram grid). Then you >> open that one map and all the copies appear. The drawback is that you >> may want finer grid spacing on the individual copies then you have >> with the tomogram, and that would make the map to large and slow to >> work with (and mostly empty). If you are interested in trying this >> approach though you can use a command like "vop add #1-100 onGrid #0" >> to produce such a map after placing the hundred separate models with >> your current script. Then save that new map and use it in the future >> instead of the 100 copies. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Using marker files to place oriented >> density maps inside a tomogram >> From: Daniel Castano Diez >> To: Tom Goddard >> Date: 11/15/12 7:12 AM >>> Hi Tom, >>> >>> thanks for the helpful explanation. The extension that you mention >>> you've been working on seems interesting. I guess that will allow >>> the user to change the isosurface level in one single model to >>> change it in all the models simultaneously, am I right? This would >>> solve another problem I'm having with my scripts, as they fed each >>> copy of the map into Chimera as a different model. So, I'm looking >>> forwards to trying it when it becomes available. >>> >>> best, >>> Daniel >>> >>> >>> >>>> Hi Daniel, >>>> >>>> You can use a Chimera marker file but that only knows how to place >>>> spheres. If you wanted to make use of the "map" and "matrix" >>>> attributes you added to the markers then that would require some >>>> extra Python script. That could be done -- it is just a different >>>> format of input from the script I sent you. >>>> >>>> If you can't display hundreds of copies of the map due to slow >>>> graphics then it doesn't matter how you input the data. Having >>>> hundreds of copies of the same map open doesn't load the map data >>>> more than once. So you shouldn't run out of memory. But the >>>> surface for each map might have a million triangles and it does >>>> make a separate surface copy for each copy you place in your >>>> tomogram. Of course you won't see the detail in a tiny map put >>>> into a tomogram so the solution would be to display a very coarse >>>> image of the map that is being placed many times in the tomogram. >>>> I've worked recently on making Chimera display multiple copies of >>>> identical objects without making copies of the surface in memory -- >>>> just reuse the same surface. But it is not in Chimera yet. And >>>> your graphics speed will still become unusable if you try to >>>> display too many copies with too much detail. So the main need is >>>> to show an appropriate low level of detail for all or most of your >>>> hundreds of copies. >>>> >>>> Tom >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: Re: [Chimera-users] Using marker files to place oriented >>>> density maps inside a tomogram >>>> From: Daniel Castano Diez >>>> To: Tom Goddard >>>> Date: 11/14/12 1:28 PM >>>>> Hi Tom, >>>>> >>>>> thanks for the answer. Actually I already wrote some scripts for >>>>> placing each different copy of the density map as an individual >>>>> model, but this is not practical for placing hundreds of copies >>>>> (as it's the case with tomograms). I will try your python script. >>>>> >>>>> >>>>> I was under the impression that a .cmm markerfile was a better >>>>> approach, as I though that one could define a marker with more >>>>> attributes as in the example: >>>>> >>>>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217"/> >>>>> >>>>> I mean, something like: >>>>> >>>>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" map >>>>> ="my_map.em" matrix = "my_matrix.txt" /> >>>>> >>>>> or similar with quaternions or euler angles... but I guess that >>>>> was wrong? That'll be a pitty, as I am interfacing Chimera with >>>>> the subtomogram averaging package Dynamo and the most stable way >>>>> seemes to be having Dynamo converting its "table" files (lists of >>>>> positions and angles) into .cmm files that could then be directly >>>>> fed into Chimera. >>>>> >>>>> Thanks! >>>>> >>>>> Daniel >>>>> >>>>> >>>>> >>>>> >>>>>> Hi Daniel, >>>>>> >>>>>> Take a look at the placem.py script which can place copies of >>>>>> maps or molecules at specified positions. >>>>>> >>>>>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >>>>>> >>>>>> It specifies the rotation as a quaternion which is close to a >>>>>> rotation axis and angle description. I could show you how to >>>>>> adapt it to use Euler angles or a 3x3 rotation matrix if you like. >>>>>> >>>>>> Tom >>>>>> >>>>>> >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'd like to use a Chimera marker file to place multiple copies >>>>>>> of a density map in different spatial positions inside a >>>>>>> tomogram. My input is thus a single map file a set of 3d >>>>>>> locations, each attached to an euler triplet (or a rotation matrix) >>>>>>> >>>>>>> With the documentation I could find >>>>>>> >>>>>>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… >>>>>>> it is explained how to place spheres without orientation in a >>>>>>> volume, but I was not able to figure out how to place a density >>>>>>> map at those locations, and also how to impart a different >>>>>>> orientation to the density map located at each position. >>>>>>> >>>>>>> My question is: where could I find a description of the marker >>>>>>> file syntax that describes this functionality? >>>>>>> >>>>>>> thanks, >>>>>>> Daniel >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------- >>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Chimera-users mailing list >>>>>>> Chimera-users(a)cgl.ucsf.edu >>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > >

2 1

delay updating to Ubuntu 12.10
by Greg Couch 16 Nov '12

16 Nov '12

Something happened in Ubuntu 12.10 that breaks Chimera's SideView tool, even if you have the proprietary graphics driver installed. So we recommend waiting until this bug is resolved. I plan to retest Ubuntu 12.10 every two or three weeks, but if anyone finds out that it is fixed earlier, please let me know. HTH, Greg

1 0

Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram
by Tom Goddard 15 Nov '12

15 Nov '12

Hi Daniel, I see. You'd like to control the contour level, color, surface/mesh style, step size... of all the copies as if they were one model instead of 100 different models, each a copy of the same map. For making hundreds of copies of an atomic model, the multiscale dialog in Chimera does this using a single model. But that doesn't currently work with maps. One disadvantage of having a single model for all the copies of a map is that the maps will all have to have the same color, same step size, same contour level because all those properties are stored with the model. Maybe that restriction is fine for your use. I would like to make that possible by allowing Chimera to place identical copies of any type of model by just specifying the list of positioning matrices. The model would just remember the list of matrices for the different placements. For now using a hundred different models of the same map is workable. You can't adjust all of them at the same time with the volume dialog. But you can adjust one to figure out the contour level you like and then use one volume command to set the level for all the copies, for example, "volume #1-100 level 1.24 color yellow step 2". Another approach is to make a single map by adding your hundred placed copies on a single grid (e.g. the tomogram grid). Then you open that one map and all the copies appear. The drawback is that you may want finer grid spacing on the individual copies then you have with the tomogram, and that would make the map to large and slow to work with (and mostly empty). If you are interested in trying this approach though you can use a command like "vop add #1-100 onGrid #0" to produce such a map after placing the hundred separate models with your current script. Then save that new map and use it in the future instead of the 100 copies. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram From: Daniel Castano Diez To: Tom Goddard Date: 11/15/12 7:12 AM > Hi Tom, > > thanks for the helpful explanation. The extension that you mention > you've been working on seems interesting. I guess that will allow the > user to change the isosurface level in one single model to change it > in all the models simultaneously, am I right? This would solve another > problem I'm having with my scripts, as they fed each copy of the map > into Chimera as a different model. So, I'm looking forwards to trying > it when it becomes available. > > best, > Daniel > > > >> Hi Daniel, >> >> You can use a Chimera marker file but that only knows how to place >> spheres. If you wanted to make use of the "map" and "matrix" >> attributes you added to the markers then that would require some >> extra Python script. That could be done -- it is just a different >> format of input from the script I sent you. >> >> If you can't display hundreds of copies of the map due to slow >> graphics then it doesn't matter how you input the data. Having >> hundreds of copies of the same map open doesn't load the map data >> more than once. So you shouldn't run out of memory. But the surface >> for each map might have a million triangles and it does make a >> separate surface copy for each copy you place in your tomogram. Of >> course you won't see the detail in a tiny map put into a tomogram so >> the solution would be to display a very coarse image of the map that >> is being placed many times in the tomogram. I've worked recently on >> making Chimera display multiple copies of identical objects without >> making copies of the surface in memory -- just reuse the same >> surface. But it is not in Chimera yet. And your graphics speed will >> still become unusable if you try to display too many copies with too >> much detail. So the main need is to show an appropriate low level of >> detail for all or most of your hundreds of copies. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Using marker files to place oriented >> density maps inside a tomogram >> From: Daniel Castano Diez >> To: Tom Goddard >> Date: 11/14/12 1:28 PM >>> Hi Tom, >>> >>> thanks for the answer. Actually I already wrote some scripts for >>> placing each different copy of the density map as an individual >>> model, but this is not practical for placing hundreds of copies (as >>> it's the case with tomograms). I will try your python script. >>> >>> >>> I was under the impression that a .cmm markerfile was a better >>> approach, as I though that one could define a marker with more >>> attributes as in the example: >>> >>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217"/> >>> >>> I mean, something like: >>> >>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" map ="my_map.em" >>> matrix = "my_matrix.txt" /> >>> >>> or similar with quaternions or euler angles... but I guess that was >>> wrong? That'll be a pitty, as I am interfacing Chimera with the >>> subtomogram averaging package Dynamo and the most stable way seemes >>> to be having Dynamo converting its "table" files (lists of positions >>> and angles) into .cmm files that could then be directly fed into >>> Chimera. >>> >>> Thanks! >>> >>> Daniel >>> >>> >>> >>> >>>> Hi Daniel, >>>> >>>> Take a look at the placem.py script which can place copies of maps >>>> or molecules at specified positions. >>>> >>>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >>>> >>>> It specifies the rotation as a quaternion which is close to a >>>> rotation axis and angle description. I could show you how to adapt >>>> it to use Euler angles or a 3x3 rotation matrix if you like. >>>> >>>> Tom >>>> >>>> >>>> >>>>> Hi, >>>>> >>>>> I'd like to use a Chimera marker file to place multiple copies of >>>>> a density map in different spatial positions inside a tomogram. My >>>>> input is thus a single map file a set of 3d locations, each >>>>> attached to an euler triplet (or a rotation matrix) >>>>> >>>>> With the documentation I could find >>>>> >>>>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… >>>>> it is explained how to place spheres without orientation in a >>>>> volume, but I was not able to figure out how to place a density >>>>> map at those locations, and also how to impart a different >>>>> orientation to the density map located at each position. >>>>> >>>>> My question is: where could I find a description of the marker >>>>> file syntax that describes this functionality? >>>>> >>>>> thanks, >>>>> Daniel >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>>> >>>> >>> >>> >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > >

1 0

Using marker files to place oriented density maps inside a tomogram
by Daniel Castano Diez 14 Nov '12

14 Nov '12

Hi, I'd like to use a Chimera marker file to place multiple copies of a density map in different spatial positions inside a tomogram. My input is thus a single map file a set of 3d locations, each attached to an euler triplet (or a rotation matrix) With the documentation I could find http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… it is explained how to place spheres without orientation in a volume, but I was not able to figure out how to place a density map at those locations, and also how to impart a different orientation to the density map located at each position. My question is: where could I find a description of the marker file syntax that describes this functionality? thanks, Daniel ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 3

Re: [Chimera-users] Fussy density around the particle
by Elaine Meng 14 Nov '12

14 Nov '12

On Nov 14, 2012, at 4:04 AM, Mohit Kumar wrote: > Hi Elaine, > Can you please tell me how to remove the fussy density from the plane of a > particle? > I went to Volume Viewer>Features>Planes>One to make a plane of the particle. > I can see a fussy density around the particle at the entire boundary. > How can I deactivate it ?? > Thanks in advance. > Best, > Mohit > Hi Mohit, Please send chimera questions to chimera-users(a)cgl.ucsf.edu rather than to me directly -- it allows other people to answer if I cannot, and allows other users to benefit from the information. In this case, I may not understand the question. You could (a) adjust the thresholds for density display using the Volume Viewer dialog <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> (b) filter your map using Volume Filter (in menu under Tools... Volume Data) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gauss…> (c) erase parts of a map using Volume Eraser (d) segment using Segment Map etc... see "volume tour" <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html> Best, Elaine

1 0

lib64bz2, question, running and installing chimera
by Sai Tong 14 Nov '12

14 Nov '12

I tried to install alpha version of chimera today in a linux machine running fedora core 14 chimera-alpha-linux_x86_64.bin after installation, running chimera gives the following Traceback (most recent call last): File "/opt/UCSF/Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/opt/UCSF/Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory The lib64 directory contains the following: lrwxrwxrwx. /lib64/libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. /lib64/libbz2.so.1.0.6 If I install the current production release version, running chimera from this production installation would be without problem. Should I temporarily link libbz2.so.1.0.6 to libbz2.so.1.0 in /lib64 in order to make the alpha version of chimera run?

2 1

Re: [Chimera-users] occupancy calculations
by Benjamin SCHWARZ 12 Nov '12

12 Nov '12

Hi Tom, Not sure I understand you well, my problem doesn't seem to be merely connected with threshold settings. Please have a look at the attached screenshot. I generated the red map with the occupancy tool, values range from 0 to 213. Then I saved it, changed the name, reopened it, and got that yellowish map with values from -128 to 127. It looks like a certain range of values was somehow shifted somewhere in the process… --Ben Le 10 nov. 2012 à 19:46, Tom Goddard a écrit : > Hi Ben, > > You have to set the contour level for the surface after you open the occupancy map. This is set with the volume dialog by moving the bar on the histogram or using the level entry field, or you can use the volume command (volume #0 level 0.123). The displayed level when you first created the map was apparently much lower than the level that is automatically chosen when you open the saved map file. > > Tom > > > On Nov 9, 2012, at 10:24 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Ben, >> The save and restore of the volume map isn't the part of Chimera I work on. I'm forwarding your message to Tom Goddard, who programs the vast majority of Chimera's volumetric capabilities, and hopefully he'll get back to you with a solution soon. >> >> --Eric >> >> Begin forwarded message: >> >>> From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> >>> Date: November 9, 2012 8:29:56 AM PST >>> To: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] occupancy calculations >>> >>> Hi Eric, >>> >>> Creation of the map works fine, but I have issues opening it when saved. You'll find attached a picture of the map as it is computed and rendered on my screen (good), ad of what happen to it when I save it and reload it from the file. Hopes this helps. >>> >>> <image--bug-visu---good.png> >>> >>> <image--bug-visu---bad.png> >>> >>> >>>> Hi Ben, >>>> I just added an option to MD Movie to allow atomic radii to be factored in. The two options (other than the previous behavior which is also available) is to increment all grid cells within the atomic radii uniformly, or to increment those closer to the atomic center more. The latter is a very simple scheme in that the "outermost" cells are incremented by 1, the next layer by 2, the next by 3, etc. with the center cell getting the highest increment. >>>> >>>> --Eric >>> >> --- Benjamin SCHWARZ Email : schwarz(a)igbmc.fr Voice : +33 (0)3 68 85 47 30 FAX : +33 (0)3 68 85 47 18 Biocomputing group -- Integrated Structural Biology -- IGBMC 1 rue Laurent Fries, BP 10142 F - 67404 Illkirch CEDEX FRANCE

2 1

save axes coordinates?
by esserlo＠helix.nih.gov 10 Nov '12

10 Nov '12

Hi, I'd like to write out the coordinates of helix axes and I know that this can be done in "Structure Measurements" gui window with "Save". However, I would like to be able to use a script. So how can I activate this "Save" function from a script (.com) ? Ah, there is one more thing, when I calculate the angle beween 2 helix axes the result is printed in the "Reply log" - useful but can I also automatically write this on out to keep a record? Thanks, Lothar P.S. I am currently using chimera-1.7-alpha 11/9/12 on 64 bit Linux.

2 1

icosahedral reconstruction volume color
by Reginald McNulty 09 Nov '12

09 Nov '12

Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie -- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Molecular Biology La Jolla, California 92037 Email: rmcnulty(a)scripps.edu

4 9

Re: [Chimera-users] Ubuntu 12.04 and Chimera 1.6.2
by Greg Couch 06 Nov '12

06 Nov '12

There are lots of things that could be wrong. To confirm that the X11/OpenGL GLX extension is missing, run the glxinfo program from the mesa-utils package (if you need to install mesa-utils, installing the associated dependencies might solve your problem) -- it should fail. Next examine /var/log/Xorg.0.log to see the error the X11 server has loading the GLX extension. Fix that error, restart the X11 server, and repeat until the glxinfo program works. Then Chimera should work too. Last bit of advice, a simple thing to try is to (re)install the graphics driver. If you have AMD/ATI or NVIDIA graphics, we strongly recommend that you install the proprietary driver that is installed with the Additional Drivers tool in the System Settings dialog. If you have Intel graphics and glxinfo works, but Chimera doesn't, then make sure you have all the Ubuntu patches installed. But even if you keep your system up-to-date, if you have Intel graphics, you should switch to newer versions of Ubuntu when they come out -- for instance, today, you should upgrade to 12.10, and I'd recommend 13.04 when it comes out, /ad infinitum/ or at least for the next 5 years, until the Intel graphics driver is much less buggy (it has drastically improved in the last couple of years, but there is much more being done). HTH, Greg On 11/06/2012 12:26 PM, sette(a)uniroma2.it wrote: > > Dear all, > > in Ubuntu 12.04, 32 bit, I have the following error message when > starting Chimera 1.6.2: > > "Error initializing OpenGL: X server is missing OpenGL GLX extension. > Couldn't configure togl widget". > > Do you know a solution for this problem? > > Thanks, > Marco > > > Dr.Marco Sette, Ph.D. > > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail: sette(a)uniroma2.it > e-mail: m77it(a)yahoo.it > Tel.: +39-0672594424 > Fax: +39-0672594328 > > www.rete29aprile.it > > > ---------------------------------------------------------------- > Invito da parte dell'Ateneo: > Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del > tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata > codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Re: [Chimera-users] Problem with RMSD calculation
by Eric Pettersen 06 Nov '12

06 Nov '12

On Nov 2, 2012, at 1:33 AM, Aditi Gangopadhyay wrote: > Dear Sir/Madam, > > I've been using Chimera for the calculation of RMSD of two ligands associated with a protein. (In my specific case, it is the same ligand, one being associated with the usual protein, and the other with the protein bound to a small molecule). However, I have had a problem with this, since the RMSD values are differing when I select my concerned ligand using GUI and when I select using the ctrl+drag way. I would be very grateful if you would kindly tell me where I'm going wrong in my selection or somewhere else. Thank you so much in advance for your help! > > Regards, > Aditi. > -- > Aditi Gangopadhyay > > Junior Research Fellow > DBT Centre for Bioinformatics > Presidency University > Kolkata, India Hi Adit, I'm assuming you are using the "match" or "rmsd" command to measure the RMSD. The problem with using a selection as an argument to the command is that the atoms are matched in the same order as they were selected. This is fine if you selected the atoms one by one (with shift-control-click), but a control-drag adds the atoms to the selection in an arbitrary order. Probably the easiest way to specify your ligand in the match command, assuming there is only one instance of the ligand in each model and the models are #0 and #1 (and the ligand name is, say, "XYZ"): rmsd #0:xyz #1:xyz --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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