- Chimera-users - RBVI Mailing Lists

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 30 Jan '13

30 Jan '13

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

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

30 Jan '13

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

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

30 Jan '13

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

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Selection and deleting
by Zhixue Zhu 29 Jan '13

29 Jan '13

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

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

24 Jan '13

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

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

24 Jan '13

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

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Chimera 1.7 release candidate
by Elaine Meng 23 Jan '13

23 Jan '13

Hello, A Chimera production release candidate (version 1.7) is available; please try it and report any problems: <http://www.cgl.ucsf.edu/chimera/download.html> New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, and interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. See the release notes for details: <http://www.cgl.ucsf.edu/chimera/1.7/docs/relnotes/1.7.html> Mac PowerPC and OS X 10.5 are no longer supported. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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

23 Jan '13

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

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selection using mouse
by francesco oteri 22 Jan '13

22 Jan '13

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

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

18 Jan '13

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

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colour with coulombic potential
by giulia zanetti 18 Jan '13

18 Jan '13

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

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

17 Jan '13

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

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copy file command
by Rachel Kramer Green 17 Jan '13

17 Jan '13

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

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

17 Jan '13

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

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