- Chimera-users - RBVI Mailing Lists

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

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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

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Chimera crashes at launch
by Gökhan Tolun 14 Jan '13

14 Jan '13

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

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heptamer
by Hossein Lanjanian 14 Jan '13

14 Jan '13

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

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How to install ?
by pythonchemia Gazeta.pl 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

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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

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Place markers
by Kim Fong 09 Jan '13

09 Jan '13

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

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crosslinks
by Trisha Davis 09 Jan '13

09 Jan '13

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

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Color surfaces
by Hernando J Sosa 08 Jan '13

08 Jan '13

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

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Chimera 1.7 for mac
by Pat Heath 08 Jan '13

08 Jan '13

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

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

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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

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average pdb
by edu troche 07 Jan '13

07 Jan '13

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

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

07 Jan '13

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

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Announcement: Release of DOCK 6.6
by Scott Brozell 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

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

03 Jan '13

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

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Circular DNA minimization
by Damien Larivière 03 Jan '13

03 Jan '13

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.

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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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