- Chimera-users - RBVI Mailing Lists

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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