- Chimera-users - RBVI Mailing Lists

selecting amino acids and labeling
by Gonzalez, Mireya 18 Apr '13

18 Apr '13

To whom it should concern I am working on some docking structures. Previously I used to have Quimera version 1.7 installed in my computer. Recently I downloaded the version 1.8 but I am having problems identifying the amino acids that are in contact with my compound using the cursor. This function is inactivated. Furthermore if I hold the key Ctrl for selecting them and labeling it is also not doing it at all. Any help with this issue will be greatly appreciated. Mireya Gonzalez

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question
by sunwei_223 18 Apr '13

18 Apr '13

Dear sir I have some question in using your excellent Chimera. How can i set 5 symmetry to a 3 symmetry map? thank you

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AutoDock Vina and hydrogens
by Elaine Meng 16 Apr '13

16 Apr '13

Hello, Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha": the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones. For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default. However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH. Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores. In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation. Recent fixes: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#bug_fixes> Download the daily build: <http://www.cgl.ucsf.edu/chimera/download.html#daily> Best, 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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Tube representation of the motion projections along the eigen vectors
by Prasanna Venkatesh 16 Apr '13

16 Apr '13

Dear all, I request you to give me the steps for "Tube representation of the motion projections along the eigen vectors" in Gromacs. Please give me step wise details with the input file types required. Thank you in advance. Prasanna.

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docking with flexible side-chains
by Thomas Evangelidis 16 Apr '13

16 Apr '13

Dear Chimera developers, Isn't docking with flexible side-chains supported in the AutoDock Vina GUI? I am surprised I didn't find any pertinent information about it in the documentation or the mailing list archives. thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Technical problem!
by Narges Mortezaei 16 Apr '13

16 Apr '13

Dear Sir/Madam We have confronted with kind of problem using chimera. We have constructed an structure of P-pili containing subunits and epitopes. A few cylinders that are representing arms of antibody have also been added to the model. The problem comes when we want to copy the cylinders to make more out of them. I do select corresponding cylinder, but when it comes to copy in Model Panel a copy option is not activated. I also tried "mcopy" command, but it did not work as well. Would you please give me some hints how to copy these kind of objects. Sincerely, Narges Mortezaei

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(no subject)
by Muhammad ALi 16 Apr '13

16 Apr '13

hi can we make a DNA model with chimera???

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pdb
by Muhammad ALi 16 Apr '13

16 Apr '13

when I download a ligand from PDB site it contains may ligand molecules ..and kindly tell me how to get a single ligand????

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Radial density plots
by Pranav Shah 15 Apr '13

15 Apr '13

Hi Tom, I am trying to plot a graph of average density as a function of radius in Chimera v1.7. I tried the code that you wrote for Padma in an earlier post. However, Chimera spits up this error "Accelerators file C:\Program Files\Chimera 1.7\share\Accelerators\radial_density.py has no register_accelerators() function." when I try to load the radial_density.py in the keyboard shortcuts menu. Could you tell me how this bug can be fixed? Awaiting your assistance, Warm regards, Pranav Shah Postgraduate student (Infection and Immunobiology), College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK.

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IDLE : code completion under MAC OS X
by Benjamin SCHWARZ 12 Apr '13

12 Apr '13

Hello, I started to develop simple python/chimera scripts. The manual is rather poor on these aspects (btw, is there a doxygen somewhere ?), and therefore the code completion in the chimera IDLE shell is particularly useful… Unfortunately, on my MAC (OS X), it appears to be messy : the TAB key triggers the usual "completion scrollable list window" on both my windows and linux (debian) machines, but not on my MAC. Note that I am still able to scroll through the "invisible" choices by pressing TAB and then using the up and down arrows, it is just that I cannot see the list, which is a bit annoying to have a clear view at once. I guess this has more something to do with the IDLE configuration than with chimera itself, but I don't know how to dig that up, so if you have any idea how to solve this I'd be pleased to read from it. --Ben

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Very similar structures
by Rebecca Swett 11 Apr '13

11 Apr '13

Hi guys, I have a question, I have two structures that are different by just a few atoms. Is there any way I could use the selection tools in chimera to find them and display them? -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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Re: [Chimera-users] Three suggestions
by Antoine Maillard 10 Apr '13

10 Apr '13

Dear Eric, Thank you for your replies and your quick implementation of an automated refresh for named selections! Concerning suggestion #1: changing Chain ID of a portion of a chain was meant to assist matchmaker in targeting the right domain and not let it take adventice (meaningless) pieces into account. I realize now that this could be quiet a challenge for Chimera to interpret in all the procedures already available... and will stick to the cut-into-domains-of-interest approach. About suggestion #2: the ~namesel command that you proposed would allow to edit the listing, which is sometimes useful, i.e. when you happen to get more and more named selections, sometimes similar in different models, and realize the names given were not specific enough. That would be nice! Suggestion #3: if this is a problem then leave it where it stands! (In case it is not: would it sound more reasonable to offer the window-size memorization as a tickable option? Could the window-location memorization and the tiling be combined when the "same" window is to be opened more than once?) All in all, suggestion #2 might make it: that's a big thank you already! Cheers, Antoine Antoine Maillard wrote: >> Dear Chimera developpers, >> >> Thank you so much for your work and your dedication! >> Having used Chimera quiet intensively recently, I have listed a few suggestions for your consideration. >> >> Suggestion #1: >> Tools > Structure Editing > Change Chain IDs: lacks a "restrict to current selection" button (would allow to name various domains of a single protein) > Are these domains disconnected from one another? Because I don't think there are many programs (including Chimera) that will like connected polypeptide chains that change chain IDs in the middle. If we're talking about disconnected domains then I can see the usefulness. Otherwise I would think that a named selection or and alias would be more appropriate -- and more descriptive. > >> Suggestion #2: >> Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability). >> - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened... > In the current daily build if a named selection becomes empty (which will happen during session close for example) it will delete itself. Does this meet the need you're describing? Otherwise I could implement ~namesel for deleting them even when they're not empty... > >> Suggestion #3: >> The 'window-size memory' feature that was devised by Eric for the File>Open window would be of interest to most windows: model panel / matchmaker / match / etc... Could you make it a general feature of the various windows in the GUI? > Well, due to the way the windowing library we use (Tk) works, it is quite a headache to impose an overall size on a window a priori. The File->Open thing works by imposing a size on the browser widget inside the window and the window adjusts to compensate. I wouldn't want to try to do this on a generic window basis. Nonetheless, for certain dialogs where it would be high value (i.e. that get a lot of use and that are resized initially a lot) I could see implementing it. The Model Panel comes to mind as you suggested. I'd listen to other suggestions... > >> (It would also be a plus if the preferred location of any of these windows could be memorized as well.) > This has been suggested and I have thought about it. The are several problems. One is that it doesn't work well with tiling. Say you bring up some dialogs that get tiled. Then you bring up a dialog whose placement is remembered, and it is right on top of the tiled dialogs. Or say you make the main Chimera window larger today that you did yesterday -- there's an excellent chance that the memorized positions will be on top of the larger window. Or you put the Chimera window on the right side of your display instead of the left side. Or you put it on a second monitor. I think you get the idea. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >> I trust your expert appreciation whether these suggestions are to be implemented sooner or later... or never :-( >> Thank you for your consideration and for your help! >> >> Antoine >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] Select incomplete sidechains
by Huang, Shengyou 10 Apr '13

10 Apr '13

Dear Chimera developers, Thank you for developing such a great and convenient software package. Is there a way to use commands to select/identify those incomplete sidechains of a protein? In addition, is it possible to do the DockPrep job using commands instead of menu? Thank you very much for your help! Shengyou Shengyou Huang, PhD Research Support Computing Division of Information Technology University of Missouri Email: huangshe(a)missouri.edu Phone: (573)882-3281

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Three suggestions
by Antoine Maillard 09 Apr '13

09 Apr '13

Dear Chimera developpers, Thank you so much for your work and your dedication! Having used Chimera quiet intensively recently, I have listed a few suggestions for your consideration. Suggestion #1: Tools > Structure Editing > Change Chain IDs: lacks a "restrict to current selection" button (would allow to name various domains of a single protein) Suggestion #2: Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability). - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened... Suggestion #3: The 'window-size memory' feature that was devised by Eric for the File>Open window would be of interest to most windows: model panel / matchmaker / match / etc... Could you make it a general feature of the various windows in the GUI? (It would also be a plus if the preferred location of any of these windows could be memorized as well.) I trust your expert appreciation whether these suggestions are to be implemented sooner or later... or never :-( Thank you for your consideration and for your help! Antoine

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Create custom macros / commands
by Thomas Hrabe 09 Apr '13

09 Apr '13

Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas ---------------------------------- Thomas Hrabe (Ph.D.) Sanford-Burnham Medical Research Institute 10901 Torrey Pines Road 92037, La Jolla, CA, USA

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Suggestion regarding
by Jean-Didier Maréchal 09 Apr '13

09 Apr '13

Dear all, in the fast access window, the last structure files and session are listed. Would it be possible to organize those files under a project name? I think that would be an interesting feature. Cheers, JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://g <http://asklipio.qf.uab.es>ent.uab.cat/jdidier<http://ent.uab.es/jdidier>

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computing dihedrals difference along simulation
by Ignacio Faustino 08 Apr '13

08 Apr '13

Dear Chimera users, I would like to know if there is a easy way to compute the difference between a couple of dihedrals a color a residue depending on the result. I guess I have to do some python scripting but just in case I want to ask. Regards, ************************************************************* Ignacio Faustino Plo, PhD student Institute for Research in Biomedicine (IRB Barcelona) Parc Cientific de Barcelona (PCB) C/ Baldiri i Reixac 10 08028 Barcelona - Spain email: ignacio.faustino(a)irbbarcelona.org *************************************************************

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Thumbnail images
by George Tzotzos 08 Apr '13

08 Apr '13

Is it possible to depict in Chimera a protein and/or ligand (any) in a water box. The reason I'm asking is because I want to show the thermodynamic cycle for calculating a binding free energy. The image should be high resolution for publication purposes. Many thanks in advance for any suggestions Regards George

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Command File
by Muhammad ALi 08 Apr '13

08 Apr '13

AOA Sir kindly tell me how to make a command file (containing required commands) for viewdock

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transfer positions to different sessions
by Dougherty, Matthew T 05 Apr '13

05 Apr '13

I am producing various animation movies. Each movie corresponding to a single session file. Each session has the same models in the same sequence on the model panel, although they may vary in terms of threshold, color, etc. Lets say I have positions P1,P2,...,Pn How can I transfer positions P3,P14-27 from session1.py to session2.py? thanks,

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Proxy / graphics issues related to Virtual Box?
by chris.wood＠stfc.ac.uk 05 Apr '13

05 Apr '13

Hello, Having fixed my main problem issue of getting Chimera to run on a Virtual Box (see my previous email), I've got two quick questions which may or may not be as a result of running Chimera on a Virtual Box: - When I have a structure open, I am unable to view any of the menus - when I click on a menu title, I can just see that the menus do open, but are below / behind the black canvas background (the closest analogy I can think of is that the z-index, the terminology used in CSS/HTML for determining which objects appear infront of other ones) appears to be incorrect - In Ubuntu (my virtual OS), when I try and fetch a structure from the EMDB, I get an error message that "Error fetching EMDB 1048: [Errno ftp error] proxy support for ftp protocol currently not implemented" - although I assume that this is normal behaviour when trying to download files across a proxy? o However, in Windows (my host OS) I get a different error when trying to fetch the same structure: error: [Errno 10061] No connection could be made because the target machine actively refused it File "C:\Program Files\Chimera 1.7\bin\lib\socket.py", line 571, in create_connection raise err See reply log for Python traceback. o When I use the "Check for updates" button in the Ubuntu version, it gives me a message that I am running chimera candidate 1.7, and that there is a newer version available, but when I click the same button in Windows, I get an error: "Unable to contact UCSF Computer Graphics Lab to check for new version. Either the network connection is down somewhere in between or an HTTP proxy needs to be configured with the Web Access preference." - although I do have the proxy server set in Network Places. Although these are relatively minor bugs, I thought you might like to be made aware of them (if you weren't already!), or that you might know how I could fix them, if they are problems to do with my setup! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk<mailto:chris.wood@stfc.ac.uk> www.ccpem.ac.uk<http://www.ccpem.ac.uk> Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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docking
by Muhammad ALi 04 Apr '13

04 Apr '13

AOA sir plz tell me how to download a receptor file and a ligand file in PDB , and from where????

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Re: [Chimera-users] Chimera on a virtualbox
by Greg Couch 04 Apr '13

04 Apr '13

(No real need to involve the list, we'll figure this out and report back) -------- Original Message -------- Subject: Re: [Chimera-users] Chimera on a virtualbox Date: Tue, 05 Feb 2013 17:22:51 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: chris.wood(a)stfc.ac.uk It appears as if you missed the: export LD_LIBRARY_PATH=$CHIMERA/lib before running gdb because the import of libgfxinfo.so failed. And there should be a space between "break" and "_exit" in the gdb command. -- Greg On 02/05/2013 04:38 PM, chris.wood(a)stfc.ac.uk wrote: > > Hi Greg, > > I know that doing anything with graphics within virtual machines is > not always a brilliant idea, but I have seen Chimera work in > VirtualBox and I wanted to get to the bottom of why mine doesn't... > > I've got the latest graphics driver on my host (and I run Chimera > successfully on it anyway). I've run the commands you suggested, with > the following output > > $ gdb $CHIMERA/bin/python2.7 > > GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04 > > Copyright (C) 2012 Free Software Foundation, Inc. > > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html> > > This is free software: you are free to change and redistribute it. > > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > > and "show warranty" for details. > > This GDB was configured as "x86_64-linux-gnu". > > For bug reporting instructions, please see: > > <http://bugs.launchpad.net/gdb-linaro/>... > > Reading symbols from /home/ccw/.local/chimera-1.7/bin/python2.7...done. > > (gdb) break_exit > > Undefined command: "break_exit". Try "help". > > (gdb) run $CHIMERA/share/__main__.py --debug > > Starting program: /home/ccw/.local/chimera-1.7/bin/python2.7 > $CHIMERA/share/__main__.py --debug > > [Thread debugging using libthread_db enabled] > > Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". > > Traceback (most recent call last): > > File "/home/ccw/.local/chimera-1.7/share/__main__.py", line 69, in > <module> > > value = chimeraInit.init(sys.argv) > > File "/home/ccw/.local/chimera-1.7/share/chimeraInit.py", line 594, > in init > > import chimera > > File "/home/ccw/.local/chimera-1.7/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: libgfxinfo.so: cannot open shared object file: No such > file or directory > > [Inferior 1 (process 4025) exited with code 01] > > (gdb) bt > > No stack. > > I guess the lack of libgfxinfo.so is fairly significant, and I assume > that the result from bt is all part of the problem? > > Thanks, > > Chris > > *From:*chimera-users-bounces@cgl.ucsf.edu > [mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Greg Couch > *Sent:* 05 February 2013 23:26 > *To:* Chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] Chimera on a virtualbox > > (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> <mailto:gregc@cgl.ucsf.edu> > > *To: *** > > > > chris.wood(a)stfc.ac.uk <mailto:chris.wood@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 > <mailto:chris.wood@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 <mailto:chris.wood@stfc.ac.uk> > www.ccpem.ac.uk <http://www.ccpem.ac.uk> > > > Tel: +44(0)1235 567864 > > Tel: +44(0)7909 586624 > Fax: +44(0)1235 567801 > > -- > Scanned by iCritical. > > > -- > Scanned by iCritical. > >

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Resolution
by Muhammad ALi 04 Apr '13

04 Apr '13

AoA I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me

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deleting entries from rapid access list (plain text format)
by Boaz Shaanan 02 Apr '13

02 Apr '13

Hi, Is there a way to delete entries from the rapid access list without having to edit the preferences file? If there isn't such a way, is it possible to request to add such feature? 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

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Weird looking stretch in ribbon presentation
by Boaz Shaanan 30 Mar '13

30 Mar '13

Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? 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

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distance label decimal places
by matheus froeyen 28 Mar '13

28 Mar '13

Hi, does someone know how I can control the number of decimal places shown in a distance label using the command line? thanks! mathy

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transparency command unrecognized
by Corey Fugate 28 Mar '13

28 Mar '13

I am following the Chimera Movie Making tutorial, but when I use the command "transp 80,r" the command line tells me, "Unrecognized command: "transp". I tried replacing "transp" with "transparency" and got the same result. Can someone explain to me why this isn't working? (I'm using build 1.5.3 on my MacBook. Thanks, Corey

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Reg: Hydrogen Bond Analysis
by Amit Jaiswal 27 Mar '13

27 Mar '13

Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. ~~~~~~~~~~~~~~~~~~~~~~~~~

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sphere representation for specific atoms
by Xiongzhuo Gao 27 Mar '13

27 Mar '13

Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen

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need help
by Hira Saleem 25 Mar '13

25 Mar '13

Respected fellows! i need help from you. actually i am working on my project and uses chimera for this . i have a problem because i have a huge data and i have to collect RMSD value of 10000 pdb ids in a 262 by 262 matrix. just wanted to know if there is another procedure to collect value instead of collecting manually. because it takes too much time and very hectic work. waiting for your precious suggestion and will be very thankful to you.

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torsion angles to x,y,z coordinate
by Chinh Su Tran To 23 Mar '13

23 Mar '13

Dear Chimera users, I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations) Is it possible to do that in Chimera? Please help. Thank you. Chinh

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3D projection of eigen vectors
by Prasanna Venkatesh 22 Mar '13

22 Mar '13

Dear support member, I would like to know the steps or command lines that I should follow to make 3D projection of eigen vectors like Tube representation or porcupine plots in Chimera. Thank you in advance. Regards, Prasanna Ph.D student Ajou university, South Korea

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internal coordinates (z-matrix) in chimera
by Chinh Su Tran To 21 Mar '13

21 Mar '13

Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. I have bunch of conformations, so I may not use the gui. Thank you. Chinh

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importing maps into chimera
by Arnaout, M. Amin,M.D. 21 Mar '13

21 Mar '13

What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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re
by Larry Simpson 21 Mar '13

21 Mar '13

Hi I have a strange problem with Chimera 1.7. My computer (Windows 7 64 bit) just had Microsoft updates last night and now Chimera does not see any drives but C and D. I usually use files on virtual drives E, etc. I tried rebooting, reinstalling Chimera but it is still the same problem. Any suggestions? Larry

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how to make super8.msf.
by han xiaodon 21 Mar '13

21 Mar '13

dear professor. would you share me how to make super8.msf.

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MSI Installer
by Yanni 20 Mar '13

20 Mar '13

Hello Do you have a chimera MSI installer available to download? Many thanks Yanni

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Re: [Chimera-users] show alpha-carbon as sphere in chimera
by Elaine Meng 19 Mar '13

19 Mar '13

On Mar 18, 2013, at 8:07 PM, Feixia wrote: > Hi Elaine, > Is there a way to show alpha-carbon only in Chimera as sphere? I can show beta-carbon, but always together with alpha-carbon. Alpha-carbon for some reason doesn't show by itself. Thanks a lot. > Best, > Feixia Hi Feixia, Maybe you are also displaying ribbon. By default when the ribbon is shown, the alpha-carbon will not show. You can allow showing both ribbon and alpha-carbon with command: ribbackbone <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> However, you can see the "real" position of the alpha-carbon is not exactly on the ribbon. Sometimes it will seem to float away, and the image might not look good. That is because the default ribbon is a smooth interpolation. Possible ways to handle this issue: (a) don't show ribbon (b) make the alpha-carbon sphere(s) big enough and/or change the viewing angle so it is not obviously floating away from the ribbon. Whether this is possible depends on which positions you are displaying and the specific backbone conformation in those areas. (c) change the ribbon from the default B-spline to cardinal spline, with or without some compromise smoothing, for example with commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> More discussion/explanation of this issue: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon…> 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

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Fwd: Re: Version 1.7 on linux
by Greg Couch 19 Mar '13

19 Mar '13

(Forgot to reply to list as well.) Hi Austin, What's your alias? chimera should *not* be on your PATH, it expects to find its version of various system libraries. Instead put a symbolic link to CHIMERA/bin/chimera in one of the directories on your PATH. Not sure what you mean about two threads, a screenshot would help. HTH, Greg On 03/19/2013 12:31 PM, Austin B. Yongye wrote: > Hello Chimera users, > I just installed version 1.7 on my centos v5.4 machine. When I launch > it using an alias, there is a splash across my entire screen and two > threads are shown on the bottom panel. This splash persists for long, > and I get the usual GUI only after switching between the two threads a > couple of times. When I proceed to open a structure, nothing shows up > on the GUI though it says a structure has been opened. > All these problems go away when I launch chimera directly from the > installation directory. > Any suggestions? Thanks. > Austin- > >

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How to change water molecule from triangle stick to folded line stick?
by 강현아 19 Mar '13

19 Mar '13

Hello, Chimera Users! I am just a beginner and haven’t learned much about Chimera. When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape. Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick) But, they are still triangle. It looks like there is H-H covalent bond in H2O. How can I remove this unwanted bond? Is there any other option for molecule shape? Like licorice… Please let me know how can I draw water with folded line stick shape, not triangle. Thanks in advance. Best regards, Hyeona Kang

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simple question
by Francesco Malatesta 19 Mar '13

19 Mar '13

Hello I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? thank you very much Francesco Malatesta

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Colors of van der Waals speheres
by Rosa Miralles 19 Mar '13

19 Mar '13

Hi, I would like to create an image with van der Waals radii colored in only one color instead of being colored as the corresponding atoms. Is it possible to choose the color of the van der Waals spheres? Thanks for your help, Rosa.

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Import Chimera Modules
by Jonathan Williams 18 Mar '13

18 Mar '13

Hello, I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html) and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: >>> import chimeraInit >>> chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/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: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. Any help or advice would be greatly appreciated, Jon Williams

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Transparent single atoms when rendering stereoimages
by Rebecca Swett 18 Mar '13

18 Mar '13

Hi, i'm rendering some peptides structures that have single magnesium and manganese atoms in frame, and when I save the images as a stereopair, the atoms render as transparent, with protein ribbon showing through. I've tried several different colors on this, I think it's just a bug. The tips of sidechains also are transparent where the atoms are showing. I"m using the windows 64 bit build, in 1.7, downloaded today. -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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define plane question
by Steven Waldauer 16 Mar '13

16 Mar '13

Hi Everyone, Hopefully this isn't a stupid question. I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined? For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation. Thanks, Steve

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chimera and modeller
by Tomek Wlodarski 15 Mar '13

15 Mar '13

Hi! I am trying to run Modeller from Chimera (Model/Refine Loops). I have downloaded the newest version of both, and I can run Modeller as a stand alone software via python. As a location of Modeller exe I put: /usr/lib/modeller9.11/bin/mod9.11 however when I try to run this it does nothing... Status is "completed" while State is "running" and Run time is (-). On the other hand I can run via Modeller server.. When I tried to run /usr/lib/modeller9.11/bin/mod9.11 I got: FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation Any ideas or suggestions? Thanks a lot! Best! tomek

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structure
by Gonzalez, Mireya 15 Mar '13

15 Mar '13

To whom it should concern I am using your chimera on a specific protein that has/display 8 chains (A,B,C,D,E,F,G,H) with the same sequence. I would like to know how to hide the chains so I can work with one chain at a time in order to see where exactly my compound is binding so I can get the amino acid domain. Any help with this matter will be greatly appreciated. Dr. Mireya Gonzalez-Begne Research Assistant Professor University of Rochester Center for Oral Biology 601 Elmwood Ave. Rochester, NY Telephone: (585)273-1424

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3 DAYS! autoPACK Visualization Challenge: HIV in Blood Plasma due March 18
by Graham Johnson (qb3＠UCSF) 15 Mar '13

15 Mar '13

Autodesk unites with UCSF and TSRI to challenge you to explore the mysterious world of HIV in vivo. We will provide competitors with a cellPACK model of HIV in blood plasma and a powerful open source app, called autoPACK. It is up to you to convey humanity's complex relationships with this virus, be they emotional, political, or intellectual. We need your help to excite general audiences with visuals that will help us spread interest in the search for a cure. We challenge you to use the animation tools available in Chimera, namely the new Animation GUI (Tools>Utilities>Animation), to create a movie and submit it to the challenge. You may submit to any of the following categories: • Open Video: (grand prize $2,500 cash) competing against professional animators who are 3 months in • Open Image: (grand prize $1,500 cash) competing against professional artists who are 3 months in • Newly opened, 3 day long, Molecular-Viewer-Only: ($250, 3D print of HIV model, and AMD graphics card) competing strictly against other Chimera or PMV users only. Critical details on the following pages will help you get started immediately: 1) General challenge site: http://www.autopack.org/cellpackchallenge2012 2) Overview, installation, and animation instructions for Chimera-autoPACK: http://www.autopack.org/documentation/tutorials/molecular-viewers 3) Official autoPACK Visualization Challenge website to register and enter for free: http://autopack.cgsociety.org 4) Full prize details: http://autopack.cgsociety.org/autopack/prizes Please let me know if you have any questions and good luck! Graham Graham Johnson PhD qb3@UCSF Fellow UCSF Lab: http://mesoscope.org Medical Illustration: http://grahamj.com Enter the autoPACK Visualization Challenge! Ends March 18 http://autopack.cgsociety.org

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Reduce mesh density?
by Maja Divjak 13 Mar '13

13 Mar '13

Hello Chimera, I would like to export some protein models in obj format and I was wondering if there is some way of reducing the mesh complexity when I do that please? I am using the models for animations in Maya and when I use the mesh reduce feature in Maya, Im getting some rather odd results, so was wondering if I can actually simplify the models first in Chimera? Thank you for your time, Maja Divjak Walter and Eliza Hall Institute, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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Re: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it?
by Elaine Meng 11 Mar '13

11 Mar '13

Hi Boaz, Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS). Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits. After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example. Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog. That option was just provided for convenience because people often like to evaluate pocket hydrophobicity. 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 Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote: > Hi, > I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane? > Thanks for your input. > Boaz

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ViewDock: flexible receptor residues in different chains
by Jérôme Hénin 11 Mar '13

11 Mar '13

Hi everyone, When viewing Autodock Vina results in ViewDock, I hit a problem that I think is due to insufficient parsing of the PDBQT file. I have flexible receptor residues in two identical chains, say, Leu15 in chain A and Leu15 in chain B - these sidechains are part of the PDBQT file. However, ViewDock apparently ignores chain identifiers in that file, so it is unable to distinguish between these two residues, and it creates mangled bonds linking them while some other bonds are missing. I don't know how much work it would be to parse chain identifiers from the PDBQT file, I would have a go at it if I was more of a Python person, but I really am not. Best, Jerome

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Re: [Chimera-users] internal coordinates (z-matrix) in chimera (Chinh Su Tran To)
by Visvaldas K. 08 Mar '13

08 Mar '13

Dear Chinh, I am not sure if you can do multiple (batch) conversions in chimera, but the tool you seek could be openbabel, using command line or openbabel gui. On the command line you can issue, for one molecule (it's for Linux): babel my.mol my.gzmat This creates Gaussian style Bond-Angle-Torsion a.k.a. Z-matrix coordinates. For batch processing, you can use: babel *.mol -ozmat -m Best regards, Vis

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comparing angles in 28 structures
by Elaine Meng 08 Mar '13

08 Mar '13

Hi Paola, Other than measuring the angle in each one, the only other idea I have is to open the 28 structures as a single trajectory in the MD Movie tool. You can only do that if each file has the same atoms with the same names. Then you can plot the angle across the 28 "frames" in the trajectory. However, if the structures do not have the exactly the same atoms, I don't know any other method than opening and measuring each one individually. There are several trajectory input options including multiple PDB files, although in that case you would need to give the files names including numbers and ending in ".pdb". The MD Movie tool including input options is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h…> After you open the trajectory, you can use the MD Movie controller to "play" through the 28 frames. You can plot values such as the angle of interest, see the MD Movie menu: Analysis.... Plot <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#p…> 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. this is a "user" question, so chimera-users(a)cgl.ucsf.edu (CC'd here) is a better place to send it than chimera-dev, which is for programming questions On Feb 21, 2013, at 12:30 PM, Paola Peshkepija wrote: > Good afternoon, > I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. > Thank you in advance for your help! > Paola

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Chimera Tutorial in Boston area
by Scooter Morris 06 Mar '13

06 Mar '13

Hi all, I'll be teaching a Chimera tutorial scheduled as part of the VizBI conference <http://vizbi.org/2013/> in Cambridge, MA. See the Program <http://vizbi.org/2013/Program/> for information about what we'll be covering, or just bring your favorite structure and we'll explore some of Chimera's new features. -- scooter

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Re: [Chimera-users] How to fork/specify a web browser
by Greg Couch 06 Mar '13

06 Mar '13

Forgot to include list in reply. -------- Original Message -------- Subject: Re: [Chimera-users] How to fork/specify a web browser Date: Wed, 6 Mar 2013 09:23:11 -0800 From: gregc(a)cgl.ucsf.edu To: Yasha Karant <ykarant(a)csusb.edu> > For certain of the tutorials, help files, etc., Chimera linux displays a > comment to use a web browser in order to use a URL file://foobar . > How does one configure Chimera to automatically use a specified browser > to diplay the URL generated by Chimera? I have not been able to find a > preferences setting for this, nor an answer on the web or in the Chimera > manuals/help. I have not perused the source code for Chimera to find a > solution. > > Yasha Karant > Chimera uses Python 2.7's webbrowser module to open files in a web browser. For Linux, if you are using a GNOME or KDE desktop environment, then it will use the default browser that is configured for that environment. Otherwise, it looks for firefox (and derivatives), kfm, konqueror, galeon, epiphany, skipstone, opera, mosaic, and grail(!). You can override the the search order with the BROWSER environment variable. You may have noticed that Google's chrome is not on that list. Chrome support is included in Python 3's webbrowser module. But, that support would only be needed if you are not using a GNOME or KDE desktop environment. I will look into how much work it would be to backport Python 3's webbrowser module to Chimera. HTH, Greg

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How to fork/specify a web browser
by Yasha Karant 05 Mar '13

05 Mar '13

For certain of the tutorials, help files, etc., Chimera linux displays a comment to use a web browser in order to use a URL file://foobar . How does one configure Chimera to automatically use a specified browser to diplay the URL generated by Chimera? I have not been able to find a preferences setting for this, nor an answer on the web or in the Chimera manuals/help. I have not perused the source code for Chimera to find a solution. Yasha Karant

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Guessing net charge
by Miro Moman 05 Mar '13

05 Mar '13

Hello, When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Best regards, Miro Moman -- http://www.e-moman.eu

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Re: [Chimera-users] [chimera-dev] 2-D projection of volume in Chimera
by Tom Goddard 04 Mar '13

04 Mar '13

Hi Jesus, There is a tricky way to do a projection of a map in Chimera. You can use the map binning capability. For example, if map #0 has 144 planes along the z axis I can add all those planes with vop bin #0 binsize 1,1,144 This can be done with a dialog instead of a command using Tools / Volume Data / Volume Filter, filter type bin and type in the bin size as 1 1 144. You also want a view along an axis other than x, y or z it sounds like. To do that you would resample the map on a new rotated grid so that the z axis is along the desired projection axis. The following video shows how to use the Chimera volume dialog subregion selection capability to do that http://www.cgl.ucsf.edu/chimera/videodoc/rotatedbox/ Tom -------- Original Message -------- Subject: Re: [chimera-dev] 2-D projection of volume in Chimera From: Elaine Meng To: Jesus Montoya Date: 3/4/13 11:59 AM > Hi Jesus, > Sorry, I don't think there is a way, currently. Here is the most recent information I could find on that topic: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005124.html> > > Regards, > 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. For future questions, you may want to send to chimera-users(a)cgl.ucsf.edu (chimera-dev is mainly for programming questions). > > On Feb 26, 2013, at 5:28 PM, Jesus Montoya wrote: > >> Hi, >> >> Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? >> >> For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). >> Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. >> >> While a "solid" representation of the volume is similar, it is not exactly what I need... >> >> Thanks! >> >>

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Thank You
by Noel Pace 04 Mar '13

04 Mar '13

thank you to all of you who helped me in compiling a DEMO which I will be using for my dissertation project. I will be making this DEMO public once it has been tested and modified accordingly. Noel Pace Malta

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Question about using the volume command
by Henning Stahlberg 04 Mar '13

04 Mar '13

Hi, The command volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be <data-value,brightness-level>". What am I doing wrong? Thanks for any suggestions, Henning.

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Work with Volumetric Data
by esserlo＠helix.nih.gov 28 Feb '13

28 Feb '13

Hi, I am using Chimera to render electron density in gaussian cube files and it works well. I am wondering though whether it is possible to integrate the e-density inside the current volume as defined by the closed surface. If there are people with expertise in this field of volumetric data (processing), I would be interested in obtaining C or C++ libraries that provide functions to calculate volume, surface areas etc. Thanks, Lothar

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vop morph map color
by Steve Reichow 28 Feb '13

28 Feb '13

Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1: vop morph #0,1 The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following: vop morph #0,1 volume #2 color khaki This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks! I am using Chimera Version 1.6 Mac OSX -- ~~~~~~~~~~~~~~~~~~~~~~ *Steve Reichow *Email: slreichow(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~

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Re: [Chimera-users] Question about using the volume command
by Elaine Meng 28 Feb '13

28 Feb '13

Hi Henning, Best to share with the list (cc'd here)... One problem with the solid level is that the second number should be between 0 and 1. However, even when I tried that, I got the same error, so I'm guessing that is a bug. The second issue may also be a bug: I don't know why the style does not change directly between surface and mesh. I'll try a simple test case and submit a bug report for that one too. Sorry for the problems, 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 Feb 28, 2013, at 12:38 PM, Henning Stahlberg wrote: > Hi Elaine, > > Yes, you are right with the solid level option. > But I still don't understand this. > This here doesn't have any effect, I give the command on the command line: > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > No change of display. > > This leads to an error message in the log window: > volume #5 level 2.30,2.6 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > TypeError: 'NoneType' object is not iterable > File "/Applications/Chimera.app/Contents/Resources/share/VolumeViewer/solid.py", line 213, in update_coloring > cmap, cmap_range = self.colormap() > > (I just submitted a bug report on the above.) > > > And this gives an error message after the "solid" command, but after that the other commands appear to work: > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > Solid level must be <data-value,brightness-level>; no change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > The display changes to surface view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > The display changes to mesh view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > The display changes to surface view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > The display changes to mesh view. > > Do you have an example how to change the display from "mesh" to "surface"? > > Thanks for your help so far, > > Henning. >

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Question about using the volume command
by Henning Stahlberg 28 Feb '13

28 Feb '13

Hi, The command volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be <data-value,brightness-level>". What am I doing wrong? Thanks for any suggestions, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62

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Problem with coloring blobs
by Terry Lang 25 Feb '13

25 Feb '13

Hey Guys, I am trying to compare a before-and-after active site. I have the CASTp pockets for each active site (2PXR pocket id 17 and 3H47 pocket id 18). However, both pocket representations have little hang-overs that are not part of the continuous pocket; I'd really just like to show the continuous pocket. I am trying to mask the overhangs and am failing. I tried coloring them white but they block the pocket. I then tried setting them to be transparent but now you can see through the entire blob (I sense a bug there). I can't figure out how to delete just a part of the blob. Other suggestions? Thanks! Terry

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Help with energy minimization
by Kirsten Reimer 25 Feb '13

25 Feb '13

Hi there, I've been using Chimera for several weeks now and I'm having some trouble with the energy minimization tool. I'm attempting to model a small RNA structure, and I keep getting the same error (using all default settings). To be honest I don't know enough about the program to feel comfortable changing the settings. I've attached the .pdb file that I'm using as well as the error message. Is there some way I could get help with this? Thank you! Kirsten Reimer [cid:f40e0cbe-7688-410c-a025-32c781322ff6@unbc.ca] University of Northern British Columbia

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Error on Ubuntu 12.04 in VirtualBox uder Win7 with Nvidia Graphic Card
by Lingyu 25 Feb '13

25 Feb '13

Hi all, I have tried to open Chimera on Ubuntu 12.04 LTS system, which is installed under Win7 system through VirtualBox. The graphic card is from Nvidia company. And I've got below error: abc@ubuntu:~$ chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x480006c Serial number of failed request: 1444 Current serial number in output stream: 1450 Then I tried "chimera --debug-opengl", after I disable all OpenGL features, still it didn't work. Here is the OpenGL information generated by "Chimera Debug Graphics Driver" interface: OpenGL information: Vendor: VMware, Inc. Renderer: Gallium 0.4 on llvmpipe(LLVM 0x300) Version: 2.1 Mesa 8.0.2 OS: Linux 3.2.0-23-generic x86_64 I have seen a previous post "answerpot.com/showthread.php?4472311-Chimera+on+a+virtualbox", which asked a similar question. Can this problem be solved? Thanks in advance! Lingyu

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question about stereo pairs
by Kristin Parent 25 Feb '13

25 Feb '13

To whom it may concern, When creating a stereo image in chimera using the camera view options, what is the default degree of rotation between the left and right image? Can this be changed? Thank you in advance. Kristin -- Kristin N. Parent, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology Michigan State University 603 Wilson Road Room 519 Biochemistry Building East Lansing, MI 48824 Office phone: (517) 432-8434

3 2

Chimera Troubleshoot start-up
by Anthony Vu 25 Feb '13

25 Feb '13

Dear Sir or Madam, I am a undergraduate student at the University of Houston, pursuing a major in Chemistry. The biochemistry class of this major requires to use the Software name Chimera for writing the assigned term paper due at the end of April. However, this will be the very first time to use it. And I do not know how to use it properly, Can you help me in this troubleshoot? Is there any active tutorial in this software? Anthony Vu P.S. Please respond to this email immediately!

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session file/HID
by Dougherty, Matthew T 25 Feb '13

25 Feb '13

I am developing some USB HID midware code utilizing keyboard shortcuts. This is being done using controllermate to generate an organized system of text strings across devices, and corresponding additions in standard_accelerators.py One thing I need to write is an automated method that will increment keyframe names to be used for savepos. On a more general level, how do I create variables in standard_accelerators.py that willbe saved in the session file, so I can retrieve them at a later session? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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spectrum prediction
by francesco oteri 24 Feb '13

24 Feb '13

Dear chimera users, I have been studying the association between a protein and an electrode by MD simulation. In particular I am interested in the relative orientation in respect to the surface. I only have the PM-IRRAS spectrum of the complex. I am wondering if someone knows a method or a software that simulate the PM-IRRAS spectrum or the infrared spectrum of a protein. Thank you in advance, Francesco

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NVIDIA graphics cards: thanks
by compchem compchems 23 Feb '13

23 Feb '13

Greg, Lionel, thank you very much for your kindly help. Your answers are just what I was looking for. My best wishes to you. Dmitry.

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nvidia graphics cards
by compchem compchems 22 Feb '13

22 Feb '13

Hi, What nvidia graphics cards are recommended to work with UCSF Chimera under Debian Linux? What are better - quadro series or geforce? Unfortunately I have seen only special topics about, for example, 3d graphics. So I don't have holistic view of the subject. Many thanks in advance. Dmitry.

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robust molecular surface calculation
by Francois Berenger 21 Feb '13

21 Feb '13

Hello, Is there any plan to plug some alternative molecular surface calculation algorithm into chimera? I have seen some interesting articles about isosurface and gaussian density functions: "Yu, Z., Jacobson, M. P. and Friesner, R. A. (2006), What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J. Comput. Chem., 27: 72–89. doi: 10.1002/jcc.20307" "What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules DOI: 10.1002/jcc.20307" http://onlinelibrary.wiley.com/doi/10.1002/jcc.20307/abstract The algorithm looks simple, robust and even parallelizable. I kind of guess that's the algorithm used in MOE when I look at their triangulation. Regards, Francois.

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A way to extract mesh data?
by Hyeong-Tae Jou 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to extract mesh data when drawing volume data. Thanks for your help in advance. Regards, Hyeong-Tae Jou ----------------------- Korea Institute of Ocean Science and Technology

2 2

Center
by Sebastian Mock 20 Feb '13

20 Feb '13

Hi, is it possible to center a molecule absolute? I have to molcules and want to center one in the absolute center of the other one. Or e.g. center both in coordinate system on 0.0,0.0,0.0 The "center" command only centers the camera. But I need to move the molecules, not the camera view. Greets Sebastian

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New user-visualizing coulombic
by Minor, Armond 20 Feb '13

20 Feb '13

Hello, I am just starting out using the program for a project with my Biochemistry professor. We are trying to develop a simple procedure to visualize the Coulombic surface of short DNA sequences. I have very little experience working with Chimera and do not know if I am going about it in correct way that will yield meaningful data. I have tried following the instruction but must of them seem to be for people who are more familiar with the programs than I am. Basically what I have tried is opening a pdb file, running PDB2PQR, opening the pqr file then running APBS on that. I am not sure what to do with the .dx file that comes out and how to use it to color the surface. If I use it to color the Electrostatic potential map I get a range of values that seem to be not what my professor is expecting. If I instead use the coulombic surface tool I get values like she expects but I am not sure if these are connected to the .dx file or just the pdb2pqr file. Any help would be greatly appreciated thank you. Armond Minor Student, Biochemistry, SUNY Oneonta

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Draw schemas with Chimera ?
by Benjamin SCHWARZ 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to draw "simplified schemas", such as those that can be found in biology publications where a protein complex is represented by a superimposition of ellipses, each ellipse representing a different protein in the complex, and their 2D placement reflects their known interactions in the complex (cf, for instance http://www.erasmusmc.nl/proteomics1/files/PBAP.jpg) This question triggered several interrogations : 1.) Is it possible in Chimera to draw 2D ellipses that would always reorient towards the screen as the scene rotates the same way the labels do 2.) Is it possible to draw ellipsoids ? 3.) Is it possible to save a picture in SVG format ? Thanks for your help, and thanks once more for the wonderful tool you provide us --Ben

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Drug-Protein Interaction
by kanika sharma 20 Feb '13

20 Feb '13

Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*

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2. Unit of electrostatic surface coloring within Chimera
by Boaz Shaanan 19 Feb '13

19 Feb '13

Hi Florian, The units for the electrostatic surface generated by APSB (andDelphi) are kT/e, which is what Chimera uses for determining the threshold when colouring the electrostatic surface. I'm quite sure that's the case. Cheers, 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: Tuesday, February 19, 2013 7:53 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 118, Issue 20 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. Algorithm for areaSAS calculations (Korbus, Michael) 2. Unit of electrostatic surface coloring within Chimera (Florian.Capito(a)external.merckgroup.com) 3. Drug-Protein Interaction (kanika sharma) 4. Re: New user-visualizing coulombic (Elaine Meng) 5. Re: session file/HID (Tom Goddard) 6. Re: questions about modeller and task panel (Elaine Meng) 7. Re: Drug-Protein Interaction (Elaine Meng) 8. Re: Algorithm for areaSAS calculations (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Feb 2013 10:27:44 +0100 From: "Korbus, Michael" <michael.korbus(a)h-da.de> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Algorithm for areaSAS calculations Message-ID: <0781A55E8298FD4CBCAAA70C4AF2EDB6350489B0BA(a)Virgon.h-da.local> Content-Type: text/plain; charset="us-ascii" Dear Ladies and Gentlemen, I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm? Thank you for your help. Sincerely, Michael Korbus Michael Korbus Dipl.-Ing. Biotechnologie (FH) Hochschule Darmstadt University of Applied Sciences Fachbereich Chemie u. Biotechnologie Schnittspahnstr. 12 D-64287 Darmstadt Tel +49/6151/16-8630 Fax +49/6151/16-8404 ------------------------------ Message: 2 Date: Mon, 18 Feb 2013 14:09:24 +0100 From: Florian.Capito(a)external.merckgroup.com To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Unit of electrostatic surface coloring within Chimera Message-ID: <OF57DE4D54.6BC4EDF1-ONC1257B16.004734C6-C1257B16.004845D9(a)merck.de> Content-Type: text/plain; charset=ISO-8859-1 To whom it may concern, I am using Chimera to color surfaces of proteins according to electrostatic potential files calculated by APBS. Now, in Chimera, there is the option to select a threshold, e.g. at which value the surface should be colored in red and at which value it is colored in blue. Now i would like to know in which unit this threshold works? Is it kcal (mol?e)-1? While this has been described for the Coloumbic surface coloring within Chimera Help, I could not find any explanation for this in the help menu, when loading external APBS potential files into Chimera. Thank You very much for Your time and help!!! Mit freundlichen Gr?ssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito(a)external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de Pflichtangaben finden Sie unter http://mandatories.merck.de Mandatory information can be found at http://mandatories.merck.de This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. ------------------------------ Message: 3 Date: Mon, 18 Feb 2013 12:24:37 +0100 From: kanika sharma <ksharma997(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Drug-Protein Interaction Message-ID: <CAAo-yeL3vs_KH76GdFQT0iP39-K2zcYRuBvmUG8pgfTxt8ivAQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*

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Unit of electrostatic surface coloring within Chimera
by Florian.Capito＠external.merckgroup.com 19 Feb '13

19 Feb '13

To whom it may concern, I am using Chimera to color surfaces of proteins according to electrostatic potential files calculated by APBS. Now, in Chimera, there is the option to select a threshold, e.g. at which value the surface should be colored in red and at which value it is colored in blue. Now i would like to know in which unit this threshold works? Is it kcal (mol·e)-1? While this has been described for the Coloumbic surface coloring within Chimera Help, I could not find any explanation for this in the help menu, when loading external APBS potential files into Chimera. Thank You very much for Your time and help!!! Mit freundlichen Grüssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito(a)external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de Pflichtangaben finden Sie unter http://mandatories.merck.de Mandatory information can be found at http://mandatories.merck.de This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

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meaning of evidence in PDB/UniProt Info
by Luis M. Sánchez 19 Feb '13

19 Feb '13

In PDB/UniProt Info some features have a line with a numeric value for evidence. For example: N-linked (GlcNAc...) (complex) evidence=1 2 3 7 8 9 10 12 What do those numbers means? Thanks for a great program and best regards -- Luis M. Sánchez

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Algorithm for areaSAS calculations
by Korbus, Michael 19 Feb '13

19 Feb '13

Dear Ladies and Gentlemen, I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm? Thank you for your help. Sincerely, Michael Korbus Michael Korbus Dipl.-Ing. Biotechnologie (FH) Hochschule Darmstadt University of Applied Sciences Fachbereich Chemie u. Biotechnologie Schnittspahnstr. 12 D-64287 Darmstadt Tel +49/6151/16-8630 Fax +49/6151/16-8404

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questions about modeller and task panel
by Smith, Susan Margaret Ellen 19 Feb '13

19 Feb '13

Hello, I am trying to use Chimera as an interface to a local installation of Modeller on my Mac. I have two questions: 1) When I open the task panel, I can see the current tasks and the completed tasks (nice visual cuing), but I do not see any way to kill a job. How can I select a job and how can I stop it? 2) When I run the tutorial example for Modeller, I get the following message, which seems like it is telling me that something is wrong (although the job appears to still be running in the task panel). I have re-installed the Modeller package, but I don't know what 'environment variable' was not set ... It seems like the program doesn't know where to put the output, although I specified a path for the temporary output. Can you help with this? Thanks, Susan Target seq: oprd_human Template structures: 4DKL (#0)Run locally, the Modeller binary location: /Library/modeller-9.11/bin/mod9.11_mac10v4 Now, modeller is running locally... MODELLER process output ----------------------- FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation ----------------------- MODELLER process errors ----------------------- ----------------------- Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 166, in statusCB self.finished() File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 201, in finished self._after(self._aborted) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 635, in _collectResultsCB OKModels = self._showingOKmodels(self.pathTemp) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 646, in _showingOKmodels modelsInfoFile = osOpen(os.path.join(outputPath, "ok_models.dat")) File "/Applications/Chimera.app/Contents/Resources/share/OpenSave/__init__.py", line 324, in osOpen raise UserError(val) UserError: [Errno 2] No such file or directory: '/Users/dlambe/Desktop/ok_models.dat' ________________________________ 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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Mirror
by Sebastian Mock 19 Feb '13

19 Feb '13

Hi everyone, is it possible, when I docked two enzymes and want to dock a second one (e.g. multienzymes complex with one sort of the first and two of the second enzyme) on the opposite site in the same orientation, to just mirror the coordinates and angles? Greets Sebastian

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Sequence
by Sebastian Mock 18 Feb '13

18 Feb '13

Hi all, how can I save a docking result as one sequence/chain only? I have a dimer docked to a tetramer and I want this to be the new Receptor in the Docking Process. Therefore, I need the two enzymes in only one sequence, as it were just one molecule. Any ideas? Removing the "ter" commands in the pdb file, did not change anything. Greets Sebastian

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Re: [Chimera-users] two questions: link card in pdb and bond commans
by Elaine Meng 17 Feb '13

17 Feb '13

Hi Boaz, (1) Chimera does connect atoms for which there are LINK records, but it may be considered a metal-coordination bond and just get a dashed line pseudobond. However, there are examples where it is a regular covalent bond. I was just using build 38277 from Feb 13, but I don't think anything related to this has changed recently. Example of where it becomes a metal coordination bond: 4HHB.pdb:LINK NE2 HIS A 87 FE HEM A 142 1555 1555 2.14 Example of where it is a regular covalent bond: 1HZH.pdb:LINK O2 MAN H 482 C1 NAG H 483 1555 1555 1.38 Maybe there is something incorrect about the LINK record. I don't remember the details of when you would use LINK records as opposed to CONECT or SSBOND, but they are all described at the wwPDB site: <http://www.wwpdb.org/documentation/format33/v3.3.html> (2) Maybe I'm misunderstanding the question, but you could use command alias ^dobond bond sel ... which would make "dobond" appear in an Aliases menu, and this menu entry would work when you have two atoms selected. Also, there is a corresponding GUI, Tools... Structure Editing... Build Structure, the "Adjust Bonds" section. 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 Feb 16, 2013, at 12:05 PM, Boaz Shaanan wrote: > Hi, > 1) I thought Chimera connects two atoms that are marked as linked by the LINK card in the pdb header, is that not the case? It certainly does not work in build 38218 from 5 February (linux x86-64). I'm not sure whether it's my ignorance or a bug hence I'm sending it to the list. > > 2) The 'bond' command (for making a bond between two atoms in the same model) only works in command line? If so, will it be difficult to add it to the pull-downs similar to the distance panel (for 2-clicks lazy people like myself)? > Cheers, > Boaz

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Re: [Chimera-users] Modification of COX Demo
by Noel Pace 14 Feb '13

14 Feb '13

Dear Elaine, Thank you very much for the quick reply I am really happy about the news. How should I refer ucsf chimera in my dissertation? Thanks, Noel

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Re: [Chimera-users] moving to coordinates
by Sebastian Mock 13 Feb '13

13 Feb '13

Hi Conrad, first you have to convert the mentioned angles to degree. They are represented as rad here. (first 3 values in the translation file) The formula for this would be rad*180/pi. We don't know why, but for the y angle you have to switch the algebraic sign. Simply multiplied by -1. We just did the conversions in Excel. The rotation in PatchDock is in XYZ notation, first rotation, than translation (this would be the order you also have to use by appling the coordinates) Then we just loaded the receptor as well as the ligand, apply the changes you want (e.g. color active sites etc.) save it into a session file and wrote a little chimera command file containing the following: close session open Z:\Sebastian\2013\Liganden\ohne Liganden\PatchDock\2+3\reference.py cofr 0.0,0.0,0.0 cofr fixed turn x -28.32 models 1 turn y -42.12 models 1 turn z 128.78 models 1 move x 33.96 models 1 move y 68.95 models 1 move z 212.57 models 1 now you can just edit the turn and move values, open the command file and Chimera will perform the orientation. Greets Sebastian 2013/2/12 Conrad Huang <conrad(a)cgl.ucsf.edu> > Hi, Sebastian. > > Just out of curiosity, what is your solution? Thanks. > > Conrad > > > On 2/12/2013 6:00 AM, Sebastian Mock wrote: > >> Hi again, >> >> we figured it out by ourselves. No need to investigate this further! >> >> Thanks anyway! :-) >> >> Sebastian >> >> 2013/2/11 Conrad Huang <conrad(a)cgl.ucsf.edu <mailto:conrad@cgl.ucsf.edu>> >> >> >> Can you please send me the receptor and ligand PDB files as well? >> Perhaps we can cobble together something. >> >> Conrad >> >> >> On 2/7/13 1:13 AM, Sebastian Mock wrote: >> >> Hi, >> >> I am using Patchdock Algorithm to dock two Enzymes. >> >> I get the pdb's and can load them into Chimera without having >> problems. >> >> Because Patchdock only performs a jigsaw puzzle with the two >> molecules, >> I have to look at all the solutions it gave me and judge them by >> some >> criteria. >> This is very time consuming, as I have to match every single >> solution >> with the appropriate molecules in chimera and I get tons of >> solutions. >> I found the following two lists with imo coordinates of the >> dockings. Is >> it possible to load these into Chimera or at least to enter the >> coordinates, so that chimera moves the >> docking partner and I can just look at it and discard or accept? >> >> These are the example lists >> http://bioinfo3d.cs.tau.ac.il/**__PatchDock/runs/1_Hexokinase_** >> __combined.pdb_2_G6PIsomerase_**__combined.pdb_37_58_16_6_1_** >> 113/__trans.txt<http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_…> >> <http://bioinfo3d.cs.tau.ac.**il/PatchDock/runs/1_** >> Hexokinase_combined.pdb_2_**G6PIsomerase_combined.pdb_37_** >> 58_16_6_1_113/trans.txt<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> > >> http://bioinfo3d.cs.tau.ac.il/**__PatchDock/runs/1_Hexokinase_** >> __combined.pdb_2_G6PIsomerase_**__combined.pdb_37_58_16_6_1_** >> 113/__docking.res<http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_…> >> >> <http://bioinfo3d.cs.tau.ac.**il/PatchDock/runs/1_** >> Hexokinase_combined.pdb_2_**G6PIsomerase_combined.pdb_37_** >> 58_16_6_1_113/docking.res<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> > >> >> Thanks in advance >> Sebastian >> >> >> ______________________________**___________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.**ucsf.edu<Chimera-users(a)cgl.ucsf.edu> >> > >> http://plato.cgl.ucsf.edu/__**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/__mailman/listinfo/chimera-users> >> <http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> **> >> >> >>

1 0

how to reduce EM map resolution (Chimera 1.6.2)
by Sergey Ryazantsev 12 Feb '13

12 Feb '13

Hello I have low-resolution (~15A) model of decorated F-actin. I want to localize the "decoration" element by subtracting normal F-actin model obtained from Cryo-EM (EMD-5168) from my decorated model. The problem is that EMD-5168 has a higher resolution and "vop" command did not work. Even if it would work, it would be difficult to interpret the result of such subtraction. I think, both maps should be at approximately the same resolution. I know how to create low-resolution map from PDB, but I could not find any solution how to lower the resolution of the EMD-5168.map Any help would be greatly appreciated. Many thanks in advance. Sergey -- ____________________________________________________________________ Sergey Ryazantsev Ph. D. Electron Microscopy Laboratory (EMi) Department of Biological Chemistry, David Geffen School of Medicine University of California, Los Angeles. Phone: (310) 825-1144 (office) mailto:sryazant@ucla.edu

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Re: [Chimera-users] moving to coordinates
by Sebastian Mock 12 Feb '13

12 Feb '13

Hi again, we figured it out by ourselves. No need to investigate this further! Thanks anyway! :-) Sebastian 2013/2/11 Conrad Huang <conrad(a)cgl.ucsf.edu> > Can you please send me the receptor and ligand PDB files as well? Perhaps > we can cobble together something. > > Conrad > > > On 2/7/13 1:13 AM, Sebastian Mock wrote: > >> Hi, >> >> I am using Patchdock Algorithm to dock two Enzymes. >> >> I get the pdb's and can load them into Chimera without having problems. >> >> Because Patchdock only performs a jigsaw puzzle with the two molecules, >> I have to look at all the solutions it gave me and judge them by some >> criteria. >> This is very time consuming, as I have to match every single solution >> with the appropriate molecules in chimera and I get tons of solutions. >> I found the following two lists with imo coordinates of the dockings. Is >> it possible to load these into Chimera or at least to enter the >> coordinates, so that chimera moves the >> docking partner and I can just look at it and discard or accept? >> >> These are the example lists >> http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** >> combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**trans.txt<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** >> combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**docking.res<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> >> Thanks in advance >> Sebastian >> >> >> ______________________________**_________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >>

1 0

Installing Chimera on Mac
by Corey Fugate 11 Feb '13

11 Feb '13

Hi, I'm trying to run Chimera on my Mac. I put it in the Applications folder, but when I open the program a dialogue appears that says, "Cannot find writable directory for saving preferences file". How can I fix this? Thanks, Corey

2 1

moving to coordinates
by Sebastian Mock 07 Feb '13

07 Feb '13

Hi, I am using Patchdock Algorithm to dock two Enzymes. I get the pdb's and can load them into Chimera without having problems. Because Patchdock only performs a jigsaw puzzle with the two molecules, I have to look at all the solutions it gave me and judge them by some criteria. This is very time consuming, as I have to match every single solution with the appropriate molecules in chimera and I get tons of solutions. I found the following two lists with imo coordinates of the dockings. Is it possible to load these into Chimera or at least to enter the coordinates, so that chimera moves the docking partner and I can just look at it and discard or accept? These are the example lists http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6… http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6… Thanks in advance Sebastian

2 1

suggestion: savepos
by Dougherty, Matthew T 06 Feb '13

06 Feb '13

It would be helpful to have the option in preferences to prevent the overwrite of keyframes. Something that would check to see if it exists, and then give an error if it does. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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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 05 Feb '13

05 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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