- Chimera-users - RBVI Mailing Lists

Chimera movie recorder
by Camilla 14 Sep '11

14 Sep '11

Hi, My name is Camilla and I'm an undergrad student at UNC-CH. I've been using Chimera to create models of fibrinogen polymerization. I discovered that I could make movies of my models to be able to see them from all views. However, my videos are very choppy and since I rotate the model by mouse, the movies are very poorly made. Is there a specific command I could use where I can get the model to rotate 360 degrees by itself to make this movie more smooth and to be able to still see the model all the way around one axis? Thank you, Camilla

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question regarding using molmap with symmetry option
by Janet Iwasa 14 Sep '11

14 Sep '11

Hello! I've been working with some virus models, and was hoping to use molmap with the symmetry option. The main reason I'm not using multiscale models is so that I can create a single surface for several of the different chains in the capsid. I've been having a little trouble getting this to work, and I'm not sure if I'm doing it correctly: molmap :.A-C 10 symmetry biomt Is this correct? Doing this gives me the error: "Keyword 'symmetry' doesn't match any known keywords" Advice? thanks, Janet

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uninstalling production release after installation of daily build (Windows)
by Boaz Shaanan 12 Sep '11

12 Sep '11

Hi, I noticed that after installing a daily build, the (very useful) uninstall feature disappeared from the pull-down of the production release (currently 1.5.3). I wonder how it can be removed once a new production release is available. I noticed that this cannot be done through the add-remove feature in the control panel either. BTW, I keep the daily build and production release in separate directories, to be on the safe side. 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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Re: [Chimera-users] structure editing query
by Bala subramanian 12 Sep '11

12 Sep '11

Thank you Elaine and Mary, Now i am able to do the modification now. It is wonderful to have an option to adjust the newly added bonds. Bala On Mon, Sep 12, 2011 at 7:11 AM, MARY VARUGHESE <maryvjes1985(a)yahoo.co.in>wrote: > hi, > consider creating bonds only after checking their valencies and bondtype > like single or double bond. > Hope this will help you. > > Mary > > --- On *Sat, 10/9/11, Bala subramanian <bala.biophysics(a)gmail.com>* wrote: > > > From: Bala subramanian <bala.biophysics(a)gmail.com> > Subject: [Chimera-users] structure editing query > To: "chimera-users BB" <chimera-users(a)cgl.ucsf.edu> > Date: Saturday, 10 September, 2011, 4:17 PM > > > Friends, > I am trying to modify the sugar of a nucleotide. I am interested in making > a linkage of two carbons in the sugar as in the attached pdb. I tried to use > the Build structure -> modify structure option but it does not work in the > sense that when i select carbon atom (c2') and tried to connect it to an > oxygen, chimera says that it is already bonded and hence some bonds to > create a new one. Is there any way to make such linkages as in the pdb ? > > Thanks, > Bala > > -----Inline Attachment Follows----- > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu<http://mc/compose?to=Chimera-users@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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НА: Re: problem in coloring a selected region
by Sp 12 Sep '11

12 Sep '11

Отправлено с моего коммуникатора HTC

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chimera rotation mode
by Jean-Francois Menetret 12 Sep '11

12 Sep '11

Hello, for some reason, the default rotation option in the viewing window always comes back to "independent" when I restore a session; how could I change the default to be "center of models" for example ? Jean-Francois

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atom order in RMSD calculations
by Elaine Meng 10 Sep '11

10 Sep '11

Hi Kristen, I'm CCing chimera-users since this is more of a user question than developer/programmer (chimera-dev) issue. The serial number is not the main factor in pairing the atoms. As mentioned in the "rmsd" documentation, <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> "If atom order is not specified... the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number." As for residues, if your models have multiple residues I believe they are compared in order. However, if your structures have exactly the same atom names and in the same order, I believe the rules above would pair the atoms in the epected order. The only other issue I can think of is that chemically symmetrical pairings are not tried, for example, if you had two phenyl rings or two carboxylates that exactly match in space but the atom names are in "flipped" positions, you would still get a higher RMSD. If it seems Chimera is not pairing the atoms as advertised, please use "Help... Report a Bug" in the Chimera menu and attach a session file with the two models, and give a short description and an email address if you'd like to hear back. There are a couple of ways to explicitly give the atom order, but if your structures have many atoms, they would be difficult/tedious: (a) interactively pick the atoms one by one from the graphics display in the correct order and then use the word "sel" to specify them in the command, as described in more detail in the documentation (link above) (b) specify all the atom names in order in the command 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 Sep 10, 2011, at 11:44 AM, Kristen Eisenberg wrote: > [chimera-dev] Calculating RMSD > > Hi, > I want to calculate the RMSD between two mol2 structures in place. The two > structures are different forms of the same structure. I haver modified the > mol2 so that the two of them have the same serialNumber in their respective > atoms. The problem is that when I use the command rmsd #model1 #model2, it > return an incorrect value of the rmsd, as the value showed is too high, > about 5, when it should be about 1 (the two structures are very similar). Is > there any way to calculate the RMSD value in place correctly or I am doing > anything wrong? > > Thanks for your help. > Kristen Eisenberg

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structure editing query
by Bala subramanian 10 Sep '11

10 Sep '11

Friends, I am trying to modify the sugar of a nucleotide. I am interested in making a linkage of two carbons in the sugar as in the attached pdb. I tried to use the Build structure -> modify structure option but it does not work in the sense that when i select carbon atom (c2') and tried to connect it to an oxygen, chimera says that it is already bonded and hence some bonds to create a new one. Is there any way to make such linkages as in the pdb ? Thanks, Bala

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path to an object displayed in a chimera session
by Jean-Francois Menetret 09 Sep '11

09 Sep '11

Hello, how can one find out the path to an object displayed in a chimera session ? Best wishes Jean-Francois

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structure analysis -> axes/planes/centroids
by Keren Lasker 08 Sep '11

08 Sep '11

Dear Chimera group: I have a quick question regarding low resolution representation of secondary structures. In the structure analysis -> axes/planes/centeroids tool there is an option of representing each helix as a axis. Is there a similar option for representing strands? thanks, Keren.

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help! questions about Join Models
by Joyce Yang 08 Sep '11

08 Sep '11

Hi, I am trying to understand what would exactly happen when join two peptide fragment together. My question is how Chimera manage to avoid any collision of atoms from two fragments. Is there any automatic minimization going on while using this Join Models function? Or it is actually possible to see overlapped coordinates of atoms in space after joining two fragments. Thank you very much. Joyce Yang

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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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Chimera daily-builds: session support for Animate extension
by Darren Weber 07 Sep '11

07 Sep '11

Hi, There is a recent addition to daily-builds to create a scene called 'session'. It can be seen in the Utilities > Animation dialog. The purpose of this scene is to enable easy, quick return to the saved session state after making a few changes, without reloading the session again. There are two potential problems with this new addition: 1. Some of the saved session data or properties may not be supported by the scene facility, yet. Elaine recently sent me an example session that is not yet supported by the scene facility; it contains a 'selection set' that raises an exception in the scene code. Similar problems may arise with other data models or properties. 2. Assuming everything in a session is supported by the scene facility, the 'session' scene should work. That is, it will work only while all the data that it refers to (e.g., models) are present. If changes result in removing any model data that is within the 'session' scene, the scene will contain 'orphaned' references and it will work only on the remaining model data (if any). When data is removed (closed), the scene facility will issue a prompt (warning) about how it will impact the functionality of the scene(s). This new feature to save/restore sessions is experimental in the daily-builds. For anyone using a daily-build for any mission-critical work, it may be handy to have a work around for the above problems. Try making the following changes to $CHIMERA_INSTALL_PATH/share/Animate/Session.py: 1. Comment out line 51 ("Animate.scenes.append('session')") and type 'pass' beneath it (using the same tabbed indentation). This will only disable the creation of a 'session' scene after restoring any session. All other session support remains enabled for scenes. 2. To completely disable all session support in the Animate extension, comment out all the statements that start with "chimera.triggers.addHandler". 3. If you have no need for anything in the Animate extension, completely remove it by deleting all of the content in $CHIMERA_INSTALL_PATH/share/Animate -- Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, (415) 488-5439 (google voice) http://www.cgl.ucsf.edu/chimera/

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Re: [Chimera-users] inter-atomic distances do not show in session after daily build upgrade
by Elaine Meng 07 Sep '11

07 Sep '11

Hi Boaz, Generally it is better to use "Help... Report a Bug" and attach the session so that we have the data, but in this case you don't need to do it -- I just reproduced the problem in my own little test session with one distance. I will report the bug and put you on the CC list. I almost always use daily builds too, but since they aren't tested, occasionally some bug will prevent you from doing what you want or need to do. Sometimes I save more than one daily build. Otherwise, I'm hoping you will be able to use the production release (version 1.5.3) until this is sorted out. If you saved the session in a newer version, however, I understand that may not work. I will put the bug at a high priority. Sorry about that, 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 Sep 3, 2011, at 11:53 AM, Boaz Shaanan wrote: > Hi, > I upgraded to the latest daily build and restored a session that had quite a few distances drawn. The dashed lines don't show while the table of distances is still there. Before the upgrade the session was restored several times and always showed the distances fine. Is there a way to resuscitate the display of distances? I sure hope so. > Cheers, > Boaz

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swapna: preserve option
by Bala subramanian 07 Sep '11

07 Sep '11

Friends, 1) I used swapna command with preserve true option but chimera complains it as mangled specifier. The preserve option is denoted in online documentation http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html 2) Just for a try i downloaded the 1VT7.pdb and changed the Guanine (first residue in chain A) to Adenine: swapna A :1.A but i found that added A is rotated. I mean the plane of A is not matching with that G (originally present in the structure). I am not sure if the preserve option is working. To be precise, i want added base to have the same plane as the original one. Thanks, Bala

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Cocoa-Togl
by Alexander Agathos 06 Sep '11

06 Sep '11

Hi, I have seen a patch concerning compiling Togl (a software component of Chimera) in Cocoa based TCL/TK http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/foreign/Togl/togl-coco… The problem is that I can't compile it because of the function in the patch : WindowRef r = TkMacOSXDrawableWindowRef(d); The function TkMacOSXDrawableWindowRef does not exist anymore. Is it possible to guide me on what I need to do? Cheers, Alexander.

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play movie forward then backward - script command?
by Gesa Volkers 01 Sep '11

01 Sep '11

Dear Chimera-Programmers, I like to create a movie in chimera by using a txt script and have some questions. I saw that it is possible to check the box "play forward then backward" in the movie recorder but it does not work when I check the box and then run my script to create the movie (maybe this is not suprising..). How can I include this command into my script commands? Another question. If I use the supersampling command, is it right to use the command as follows: movie record fformat png supersample 4 OR movie record fformat png supersample 4x4 Somehow I cannot see a difference in quality if I use the supersample command like this or if I do not use it at all, so I assume that something is wrong. Also the mp4-file size is always the same. And a third question: I liked to upgrade Chimera to the current version (I use 1.5 (build 31025) 2010-07-20). But after the upgrade all my old saved sessions did not work anymore. Is there a solution for this? Because that keeps me from upgrading.. Thank you in advance for your help! I use Chimera a lot and I am always surprised how helpful the tutorials are and how fast the programmers respond to the users. Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Numbering helices sequentially
by George Tzotzos 01 Sep '11

01 Sep '11

I've been looking in the archive for a procedure describing the sequential numbering (and differential colouring, if possible) of protein helices to no avail. I'd appreciate if anyone could suggest a relevant procedure. Thanks in advance George

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fit molecule with Laplacian filtered map
by Noboru I 31 Aug '11

31 Aug '11

Hello, This is my first time trying to apply the Laplacian filter to a cryo-EM map in Chimera before I perform the global search to fit my crystal structure. However, the resulting map looks like the original map blown up into million pieces with positive and negative density showing. I get the same effect even after I "smooth" the map with the Gaussian filter first. Could someone advise me on how I could use this Laplacian filtered map information to better fit my molecule into the original EM map? Thanks for your help in advance. Noboru

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chemdraw addins
by Bill Wuest 31 Aug '11

31 Aug '11

Hi, I am a big fan of your software and would like to use it in greater capacities (primarily for drug discovery). Is there a way to dock molecules (or better yet import chemdraw files) into chimera and then swap those structures in for ligands bound to crystal structures? I would like to model proposed compounds into a binding site of a protein and riboswitch both of which have the ligand bound in the crystal structure. Ideally I would like to import a chemdraw file which could be minimized by chimera and then be able to limit the docking to the ligand binding area and minimize again. That way I can see how the new analog changes the conformation of the protein. Any help would be greatly appreciated! If it would be easier to chat on the phone please feel free to call the number below. Have a great week! -Bill Wuest ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Bill Wuest Assistant Professor of Chemistry Temple University 130 Beury Hall, Office 448 1901 N. 13th St. Philadelphia, PA 19122 Phone: 215-204-7167 Email: wwuest(a)temple.edu

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(no subject)
by Fakron, Osama Mohamed 29 Aug '11

29 Aug '11

Hello My name is Osama M.Fakron , I am PhD student in Mechanical &Material School at Washington State University , I am working on reconstruct 3D image from SEM 2D images by EM3D software ,I am using Chimera for viewing my reconstructed images , I need some help in getting 3D position for any point in my reconstructed image , and also your supporting is appreciated. All the best for you Osama

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hardware stereo switching between distal and proximal when rotating
by frederick lee 29 Aug '11

29 Aug '11

dear chimera community, i have experienced this issue for some time now. i don't think this is happening with other software like pymol, dsvisualizer, MOE, etc given the same computer and hardware setup. somehow when viewing in hardware stereo mode (sequential stereo), the model will switch back and forth between proximal and distal views during rotations. is there a particular chimera setting that will prevent such from happening. thanks much. fred

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Entra nella mia rete su LinkedIn
by Chinmaya Joshi tramite LinkedIn 29 Aug '11

29 Aug '11

LinkedIn ------------ Chinmaya Joshi ha chiesto di aggiungerti ai suoi collegamenti su LinkedIn: ------------------------------------------ Vorrei aggiungerti alla mia rete professionale su LinkedIn. Accetta l'invito di Chinmaya Joshi http://www.linkedin.com/e/fihlc9-grxnbthx-1b/s9zCzPfFBIFwqUg8JgtGw69rcczGuT… Visualizza l'invito di Chinmaya Joshi http://www.linkedin.com/e/fihlc9-grxnbthx-1b/s9zCzPfFBIFwqUg8JgtGw69rcczGuT… ------------------------------------------ SAPEVI CHE LinkedIn può trovare le risposte alle tue domande più difficili? Pubblica le domande più impegnative su Risposte di LinkedIn e potrai avvalerti dell'esperienza dei migliori professionisti al mondo. http://www.linkedin.com/e/fihlc9-grxnbthx-1b/ask/inv-23/ -- (c) 2011, LinkedIn Corporation

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Re: [Chimera-users] electron density in Chimera
by Elaine Meng 27 Aug '11

27 Aug '11

On Aug 26, 2011, at 1:24 AM, Stefano Luciano Ciurli wrote: > Hello, > for a paper reporting a new structure, I would like to make a figure with Chimera, but I need a map that can be read. I have an mtz map that can be read with Coot, but I think I need to convert it to a format that Chimera can read. I cannot use the EDS server, because the file has not been released on the PDB. > How do I do that? > Stefano Hi Stefano, I didn't know anything about MTZ format, but found some explanation in the PHENIX mailing list that the program PHENIX can do the conversion: <http://phenix-online.org/pipermail/phenixbb/2011-March/016881.html> >From that message, "it's not a simple file format conversion. In this case MTZ file is supposed to contain Fourier map coefficients, and Xplor formatted file will contain Fourier image of electron density map (typically simply called "electron density map"). So this converson also involves a FT. " The PHENIX developers provide documentation and downloads for Linux and Mac. <http://www.phenix-online.org/version_docs/dev-713/phenix_documentation.html> Here's a list of the density formats that Chimera "knows": <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> Other Chimera developers or users may know more -- so it's generally better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (which I CC'd here) instead of to me directly. 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

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MatchMaker in version 1.5.3 (build 33475)
by John Rose 25 Aug '11

25 Aug '11

Hi, I have been using chimera since the late 1990s. In the previous versions I could use MatchMaker to superimpose two molecules and all the atoms were moved with the model. Noe I find that when I use MatchMaker the models are aligned BUT the non-reference structures shoe up in a licorice stick representatuin and I have not been able to either (1) generate a ribbon drawing of the non-reference structures or (2) get an all atom view of the non-reference structures. Am I missing something? The two structures are 1wdn and 1hpb. This happens on both the MAC and Linux platforms. This feature is important to several classes I teach so any help you can give me would be greatly appreciated. John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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