- Chimera-users - RBVI Mailing Lists

Has the option provided by surfvalues.py script been incorporated into Chimera?
by Boaz Shaanan 21 Sep '11

21 Sep '11

Hi Tom, Here is the plain text version (I keep forgetting that the list has a problem with html formatted messages, but is it always the case? ): A while ago you wrote the very useful surfvalues.py script to show actual potential values while wandering with the mouse over the surface. I wonder whether it has been incorporated into the Chimera version by now. I couldn't figure out whether it has. 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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color surface by electrostatic potential from apbs dx file
by matheus froeyen 21 Sep '11

21 Sep '11

Hi I try to show the electrostatic potential calculated by apbs and written to a pot.dx file. This works fine when using the mouse / menus. However I try to do this also using the command line interface because I need to repeat it many times. $ chimera chimera.cmd $ cat chimera.cmd: open prod30.pdb ~ribbon : ~fillring : surface : open pot.dx ~scolor #0 scolor #0 volume #1 cmap rainbow scolor #0 volume #1 cmap -15,red:-5,yellow:0,green:5,cyan:15,blue I don't get an error but the surface is colored by volume data, not by electrostatic potential. Also the popup window "Surface Color" is not updated for the selected colors. In the surface color popup I need to select color surface "MSMS surface" again, change "volume data value" to "electrostatic potential" and then push the button "Color". Then I get what I want, but unfortunately using the mouse again. This should be done by the script too, I guess? I m using the last stable chimera 64 version for unix on redhat. best regards mathy

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Smoothing a trajectory
by Daniel Gurnon 20 Sep '11

20 Sep '11

Hi everyone, For the purpose of making educational content, I'm interested in smoothing out the often jumpy transitions from frame to frame in a MD trajectory. My approach was to write two python scripts (with critical help from Eric of course); one goes through the trajectory and saves pdbs of each desired frame, while the second opens these pdbs and creates a morph, interpolating from one pdb to the next. It seemed like I was almost there, and it looked great when I tried 50 frames.....but Chimera crashed when I tried morphing 200 frames, adding 3 frames of interpolation between each. Is there a better way to add transitions in between (ideally thousands of) frames of an MD trajectory? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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segmentation tool
by Jean-Francois Menetret 20 Sep '11

20 Sep '11

Hi, I am using the segmentation tool on a ~15A cryoEM map. I have noticed that the surface of the mrc maps saved from selected areas look pixelated. Any suggestions how to improve the quality of the segmented maps ? Best wishes Jean-François Ménétret

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mailling list hiccup
by Greg Couch 19 Sep '11

19 Sep '11

We had an internal problem with all of our email over the weekend. So if you sent email to chimera-users and it bounced, please resend it. It should work now. -- Greg

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Double coordinates for same residue
by Francesco Pietra 15 Sep '11

15 Sep '11

Hello: Surely a naive question: While beginning to treat a multichain, engineered protein - downloaded from PDB web (1.94 A resolution) - with Chimera, I noticed that many amino acids have such feature as GLU 252 below. Same for many SER, ILE, HIS (two imidazole rings for the same residue number) ATOM 2022 N GLU A 252 15.171 -45.532 45.115 1.00 26.12 N ATOM 2023 CA AGLU A 252 14.023 -44.631 45.214 0.50 26.30 C ATOM 2024 CA BGLU A 252 14.048 -44.592 45.252 0.50 26.30 C ATOM 2025 C GLU A 252 13.983 -43.654 44.050 1.00 25.90 C ATOM 2026 O GLU A 252 12.894 -43.403 43.470 1.00 25.36 O ATOM 2027 CB AGLU A 252 13.974 -43.909 46.559 0.50 26.93 C ATOM 2028 CB BGLU A 252 14.170 -43.759 46.533 0.50 26.77 C ATOM 2029 CG AGLU A 252 13.283 -44.741 47.629 0.50 29.02 C ATOM 2030 CG BGLU A 252 12.874 -43.673 47.313 0.50 29.14 C ATOM 2031 CD AGLU A 252 14.088 -45.948 48.051 0.50 33.10 C ATOM 2032 CD BGLU A 252 12.806 -44.716 48.426 0.50 31.91 C ATOM 2033 OE1AGLU A 252 13.481 -47.014 48.330 0.50 34.82 O ATOM 2034 OE1BGLU A 252 13.394 -44.454 49.504 0.50 31.18 O ATOM 2035 OE2AGLU A 252 15.333 -45.828 48.101 0.50 35.49 O ATOM 2036 OE2BGLU A 252 12.162 -45.782 48.231 0.50 33.14 O ATOM 2037 N GLU A 253 15.141 -43.133 43.683 1.00 24.58 N ATOM 2038 CA GLU A 253 15.225 -42.212 42.559 1.00 25.11 C ATOM 2039 C GLU A 253 14.838 -42.941 41.242 1.00 23.83 C ATOM 2040 O GLU A 253 14.142 -42.383 40.374 1.00 23.54 O ATOM 2041 CB GLU A 253 16.637 -41.603 42.476 1.00 26.18 C ATOM 2042 CG GLU A 253 17.033 -40.722 43.697 1.00 30.81 C ATOM 2043 CD GLU A 253 17.635 -41.491 44.915 1.00 36.16 C ATOM 2044 OE1 GLU A 253 17.540 -42.742 45.032 1.00 35.80 O ATOM 2045 OE2 GLU A 253 18.198 -40.809 45.801 1.00 40.87 O About the protein: SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA; SOURCE 3 ORGANISM_TAXID: 300; SOURCE 4 GENE: TMOA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P58KABE; The said residue are not among those not located in the experiment. I am interested in channels, pores and so on in the protein, so that the above issue is of most concern for me. Thanks for aid francesco pietra

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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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Followup to my last question on MatchMaker
by John Rose 25 Aug '11

25 Aug '11

It looks like there is something going on with PDB entry 1HPB that is causing the problem. 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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molecular surface isolated to chain
by Jeffrey Kentner 24 Aug '11

24 Aug '11

Hello, I am trying to create a nice aesthetic model of a protein binding to DNA. When I show molecular surface, the program doesn't seem to be able to differentiate between the DNA chain and the protein chain. I either end up with a surface on the DNA which is not fully closed, or if I extend the surface via the 'surface zone' it simply begins to cover the protein as well... I have consulted the documentation and can not find any description of how one would isolate the molecular surface to a particular chain. Is this not possible in Chimera? Cheerio, Jeffrey

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SSEHUnter and SSEBuilder questions
by Kristin Parent 24 Aug '11

24 Aug '11

Hello, I was hoping you could help me out. I am trying to locate secondary structure elements in an individual subunit of an icosahedral virus from a cryo-reconstruction. I have the entire virion in pif format and would like to use the density from a single subunit using SSEHUnter and SSEBuilder. I am not sure how best to get the volume data as a useable mrc input for this tool. I tried using the volume eraser to eliminate other areas in the map that are not the subunit I'd like. When I save the map and then the session, the subunit looks fine in the session, but if I open the subunit mrc file in a new session, I get what appears to be inverse density (the stuff I erased), and in the volume viewer, the density looks inverted. If I move the slide bar to the left, I end up with a solid cube. I am either doing something horribly wrong, or this is maybe not the best method for excising my subunit??? Please advise the best approach to creating a subunit mrc file that can be used by SSEHunter. Thanks in advance! Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

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(no subject)
by a kauz 24 Aug '11

24 Aug '11

I am currently trying to extract data (x,y,z coordinates) from a PDB file generated by Chimera (pdbrun command) The file looks like this: MODEL 1 HETATM 1 **** 1 7881.2318439.71911918.53 1.00 0.00 H HETATM 2 **** 2 7878.3608863.83911538.22 1.00 0.00 H HETATM 3 **** 3 7362.1978948.58411340.85 1.00 0.00 H HETATM 4 **** 4 8109.6319067.12510778.80 1.00 0.00 H HETATM 5 **** 5 8512.9689160.81011582.47 1.00 0.00 H HETATM 6 **** 6 8368.0819128.66911020.52 1.00 0.00 H HETATM 7 **** 7 7260.6139750.88411592.71 1.00 0.00 H HETATM 8 **** 8 5841.5699031.23313127.43 1.00 0.00 H HETATM 9 **** 9 6579.8098604.13912097.33 1.00 0.00 H HETATM 10 **** 10 7584.5978302.09511466.04 1.00 0.00 H HETATM 11 **** 11 8520.92710251.0411690.68 1.00 0.00 H HETATM 12 **** 12 9185.69810212.1111417.11 1.00 0.00 H (this is just an extract) How can I know how many decimal numbers each coordinate has? is there a way to set how many decimal numbers will be reported? or to put some kind of tab separation between the coordinates? thanks, Annamaria

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Re: [Chimera-users] creating a peptide bond between two fragments
by Eric Pettersen 23 Aug '11

23 Aug '11

On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: > Hi Folks, > I am trying to add a four amino acid segment to the N-terminus of > a protein in the pdb. I can generate the four residue stretch and > move its C-term close to the N-term of the structured protein. I > can then select the C' and N atoms, which are about 1.0 Angstrom > apart. At that point, I am stuck. Not sure how to add a bond and > then create a proper structure. I've played around with Join > Models, but no luck. Without a peptide bond recognized by Chimera, > ribbons are discontinuous. Any ideas? > Many thanks, > glenn There is now a section of the Join Models page specifically for joining two peptides, so this problem should be easy to solve in the future. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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a simple question about multiple sequence alignment
by Lan Hua 22 Aug '11

22 Aug '11

Hi all, I want to use chimera to create a multiple sequence alignment which will be used to build a model. From elsewhere, I know the pdb id of desirable templates, but I don't know how to create the alignment in the Chimera. Any inputs will be very much appreciated. Thank you! Best, Lan

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Fwd: Showing more than a single centroid trace
by Francesco Pietra 22 Aug '11

22 Aug '11

There is still a problem that had previously escaped my attention. I.e., after the centroid sequence is obtained for model 0 and residue 1, I run the movie for model 1 and residue 2. That's OK, however the second series of centroids starts with progressive number where the first one had ended plus one (if the first series was 1-250, the second series starts from 251). This means that the first part of centroids for model 1 (corresponding to the centroids for model 0, i.e., 250) is not shown. I used define centroid radius ... color ... #modelnumber:residuename & :residuenumber where the residuename is the same for the two series of centroids. Can the command be modified so that both complete series of centroids is shown? I am using chimera production version 1.5.3 (build 33475) 2011-05-24 17:23:26 GMT on Debian i386 (I found this more stable than on Debian amd64 with GTX-580 as the sole graphic cards) Thanks francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Thu, Aug 18, 2011 at 8:08 PM Subject: Re: [Chimera-users] Showing more than a single centroid trace To: Eric Pettersen <pett(a)cgl.ucsf.edu> On Thu, Aug 18, 2011 at 7:48 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Try selecting just the one ligand first with this: > sel #0:residuename & #0:residuenumber > then it and the environment around it with: > sel sel z<5 > --Eric That works fine, thank you very much francesco > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > On Aug 18, 2011, at 10:36 AM, Francesco Pietra wrote: > > On Thu, Aug 18, 2011 at 7:07 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > HI Francesco, > > Just put the model number wherever you need it, with no space before residue > name or number, maybe something like: > > sel #0:residuename & #0:residuenumber z<5 > > For me that works between the three ligands only. I.e, with a large > z<20, all the three residues are highlighted, while with z<3 only the > residue with the specified residue number is highlighted. The number > of atoms at the bottom line correspond. For example, with z<20, 6 > atoms, 3 bonds (three diatomic molecules) > > francesco > > > Elaine > > On Aug 18, 2011, at 9:46 AM, Francesco Pietra wrote: > > Hi Elaine: > > Thanks a lot. Could you also help me as how to find the environment of > > the moved ligand, when there are three of them with the same residue > > number? > > While define centroid works nicely with: > > define centroid radius# color # :residuename & :residuenumber > > sel #modelnumber :residuename & :residuenumber z<# > > does not. Could the command be modified to refer to only one of the > residues? > > Thanks > > francesco > > On Wed, Aug 17, 2011 at 7:34 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > If your movies are different model numbers, you can put model number before > residue name, for example: > > #0:hem > > You can see what models you have in the Model Panel (under Favorites in > menu). > > Elaine > > On Aug 17, 2011, at 7:11 AM, Francesco Pietra wrote: > > Hi Elaine; > > I selected with line command the molecule that was giving the centroid > > sequence. I was interested in the surroundings of that biatomic > > molecule at various frame numbers. What I said, is that this is > > possible only for the first movie. On subsequent movies, superimposed > > to the first one, the line command always refers to that molecule of > > the first movie. > > francesco > > On Tue, Aug 16, 2011 at 7:38 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > You cannot select centroid objects with a command -- they do not have > residue or atom names. You can only select them by clicking their lines in > the Axes/Planes/Centroids dialog, or by Ctrl-clicking on them in the Chimera > graphics window. > > Elaine > > On Aug 16, 2011, at 9:36 AM, Francesco Pietra wrote: > > Hi Elaine: > > I'll try your advice as soon as possible. However, turning mode1 out > > of view in model window while playing movie for model 1, the centroid > > for mode1 is still seen above model 0 and the trace for centroid for > > model 0 . What I could not do was to select the centroid for model 1, > > in order to highlight it. Command "sel :residuename" always selected > > the centroid for model 0. > > francesco > > On Tue, Aug 16, 2011 at 5:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > I'm not sure I understand what you are asking. Maybe you are saying that > when you hide a model, the centroid is also hidden? > > Instead of hiding the model with the Model Panel "Shown" checkbox or command > "~modeldisplay", which hides everything in the model, you can undisplay the > protein parts and leave the centroid displayed. For example, if I had > protein models #0 and #1 and also centroids for each of those, I could > undisplay the protein part only of #0: > > ~display #0 > > ~ribbon #0 > > ~surf #0 > > (commands to undisplay atoms/bonds, ribbon, and molecular surface of model > #0). Then, you would have the protein #1 plus the centroids of both #0 and > #1 displayed. 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 Aug 15, 2011, at 11:36 PM, Francesco Pietra wrote: > > Hello: > > I would like to show several centroid traces for model 0, 1, 2, .. > > Actually, it is the same model, differing, in the movies, for the > > protein fluctuations. > > What I did, was to superimpose movie for model 1 to the already done > > movie for model 0, hiding the protein for model 1 and choosing a > > different color for the centroid. Doing that, the instant position of > > the centroid can only be color-highlighted for model 0. > > I wonder whether there is a better procedure to show the various > > centroid traces above a single protein model. > > thanks > > francesco pietra > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > >

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register file extension .xmp for volume data
by Dieter Blaas 22 Aug '11

22 Aug '11

Hi, I routinely visualize spider format volume data that are output from Xmipp with the extension .xmp. This extension is not registered in Chimera and I have to scroll through the formats page each time to select 'spider volume data' or open the file with 'chimera spider:xxx.xmp'. Is there a way to make Chimera recognize this extension as 'spider format' automatically? There was an older Windows version that allowed to tell Chimera that all following data were of the same format as the first one but I have not seen this in any of the recent Linux versions. Thanks for hints, D. - ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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<no subject>
by Sacha De Carlo 22 Aug '11

22 Aug '11

unsuscribe

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Morph with Chimera: how to make visible connection/interaction in Morph
by WENHE ZHONG 19 Aug '11

19 Aug '11

Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe

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Showing more than a single centroid trace
by Francesco Pietra 18 Aug '11

18 Aug '11

Hello: I would like to show several centroid traces for model 0, 1, 2, .. Actually, it is the same model, differing, in the movies, for the protein fluctuations. What I did, was to superimpose movie for model 1 to the already done movie for model 0, hiding the protein for model 1 and choosing a different color for the centroid. Doing that, the instant position of the centroid can only be color-highlighted for model 0. I wonder whether there is a better procedure to show the various centroid traces above a single protein model. thanks francesco pietra

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XPLOR volumetric data not shown as a volume
by matthias.gutmann＠stfc.ac.uk 18 Aug '11

18 Aug '11

Dear all, having succeeded in writing an XPLOR data file and importing it into CHIMERA, I was expecting to see a cube like volume. Instead, I'm only seeing a thin plane. Is this to be expected? The header for the XPLOR file is as below: 1 SXD2001reciprocal_space_volume 301 0 300 301 0 300 301 0 300 30.10000 30.10000 30.10000 90.00000 90.00000 90.00000 ZYX 0 0.57280 0.05125 0.25826 0.23192 0.47232 0.40565 0.28667 0.06406 0.13678 0.22750 0.22332 0.11380 -0.02432 0.32358 0.22395 0.06303 0.22736 0.27504 0.30512 0.21062 0.26810 0.15033 0.25180 0.39434 0.85280 0.25197 0.07160 0.22430 0.28253 0.11386 0.34160 0.32177 -0.03150 0.22739 0.47072 -0.00241 0.26013 0.20844 0.20823 0.30089 0.40608 0.23863 -0.13479 0.28377 0.08277 0.25996 0.23550 0.09638 How can I get the entire volume to display as a volume rather than a single plane? Is the XPLOR format not a good one to use for this purpose? Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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Unrecognized command: "minimize"
by Viachaslau Bernat 18 Aug '11

18 Aug '11

Dear Chimera developers, I've got a problem with scripting in chimera. By analogy with your example I've written a python script for geometry optimization of small library of ligands. In GUI mode all commands run smoothly as I type them into chimera command line. Nevertheless, when I try to run a script containing the same commands I get the error `unrecognized command: "minimize"`, no matter if I run it from GUI interface menu or with --nogui parameter. Here is my testing script (test.py): import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/viachaslau/sybyl/sublib/") fn = "lib1.mol2" rc("open " + fn) rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format pdb 0 min/" + fn + ".pdb") rc("close all") rc("stop now") And here is the output from Python: ~/sublib> ~/chimera/bin/chimera --nogui test.py Executing test.py... Opening lib1.mol2... UNQ1 opened Traceback (most recent call last): File "/home/viachaslau/chimera/share/chimeraInit.py", line 677, in init chimera.openModels.open(a, prefixableType=1) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 973, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 8, in <module> rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "/home/viachaslau/chimera/share/chimera/__init__.py", line 2235, in runCommand makeCommand(*args, **kw) File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd MidasError: Unrecognized command: "miminize" Error while processing test.py: MidasError: Unrecognized command: "miminize" File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd See reply log for Python traceback. I run SUSE 11.3 as operating system and chimera is installed into ~/chimera/ I also tried to run commands row by row in IDLE window of chimera and found out that python suspends on runCommand("minimize ...") command -- Viachaslau Bernat, PhD-student Department Chemistry and Pharmacy Schuhstrasse 19, 91052 Erlangen -- Germany Phone: +49-9131-8522588 www.medchem.uni-erlangen.de

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delete volume densities
by Hernando J Sosa 17 Aug '11

17 Aug '11

A while ago I remember using a Chimera function to delete map densities that were outside a given distance from selected atoms in a structure. I can't seem to find this utility anymore. Can somebody please remind me where to find it. Is this utility still there in the new chimera versions? Thanks Hernando

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Re: [Chimera-users] suggested feature/model panel
by Eric Pettersen 17 Aug '11

17 Aug '11

On Jan 22, 2009, at 3:15 PM, Eric Pettersen wrote: > On Jan 21, 2009, at 5:05 PM, Matthew Dougherty wrote: > > > 1) ability to create folders in the model panel so models can be > > grouped > > 2) ability to have a model in multiple folders > > 3) ability to show/hide in a folder by a a single checkbox > > 4) ability to name the folder > > These are good suggestions, and we have discussed adding some kind of > grouping mechanism in Chimera given that there are a lot of situations > where you want to treat a set of models as a single entity (e.g. > multiple structures fit into a EM map). > > I think #2 and #3 are in conflict though. Really, I don't think you > want #2 -- it's too confusing. Say a model is in two groups: you > close one group -- what happens? You hide one group -- what happens? > You deactivate one group and move the other -- what happens? Perhaps > if you elaborated on the motivation for putting a model in multiple > groups then some other alternative could be devised that provides what > you need. > > I'll open a change-request in our Trac database for "grouping > mechanism" and include the above. I don't really want to promise a > timeline, but the issue is a concern of ours. Seems like I never opened that ticket, at least I can't find it searching the database. A year later I did open a very similar ticket (#8253) which has now been implemented. So the Model Panel now supports grouping (and ungrouping) models in the current daily build, which at least minimally satisfies points 1, 3, and 4 above. The groups can be named as you wish, and changing active/shown/color/etc. for a group changes the corresponding attribute of all the models in the group. Right now if multiple models are opened from a single data source they are automatically grouped. This comes into play most often when opening NMR ensembles. If anyone has any strong opinion as to whether this is a good default behavior or not, please speak up! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Calculation of Hydrophobicity
by Magnus Andersson 17 Aug '11

17 Aug '11

Hi, I'm a new user to Chimera and found it very useful really fast. I have a question however, is possible to make a calculation of the hydrophobicity of a surface or the electrostatic potential, not only show it visually? Best regards Magnus ------------------------------------------------------------ Magnus Andersson, PhD Assistant Professor Department of Physics Umeå University SE-901 87 Umeå, Sweden Phone: +46 90 786 63 36 Mobile: +46 706 460 602 Email: magnus.andersson(a)physics.umu.se<mailto:magnus.andersson@physics.umu.se> ------------------------------------------------------------

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Problem with volumetric data in XPLOR format
by matthias.gutmann＠stfc.ac.uk 17 Aug '11

17 Aug '11

Dear all, I'm trying to write volumetric data in XPLOR format in order to import it into Chimera for displaying. The volumetric data set is a general volume data set, not necessarily an electron density map. However, it keeps on failing as Chimera keeps on thinking there are only 262 data values, whilst expecting 90601 numbers (which is the correct number). I'm trying to write the XPLOR file in the format given on the CNS web page: Format of CNS maps The grid size of the map is determined by the GRID parameter in the FFT statement. The following lines show the beginning of a typical electron density map file: 2 !NTITLE REMARKS FILENAME="" REMARKS DATE:18-Jun-98 12:24:08 created by user: 30 4 12 15 5 10 16 2 12 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02 ZYX 0 -0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01 -0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00 -0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00 0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00 .... -9999 0.2044E-09 0.9999E+00 Is this correct or is Chimera expecting a different format? Looking forward to your replies! Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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suggestion
by Dougherty, Matthew T 16 Aug '11

16 Aug '11

It would be good to have a session description window that I could type text into. The typical method is to generate a session file name that is the description, but as the complexity of a session file increases it would helpful to be able to write a couple sentences/paragraph as to the subtle differences it has over a near identical session file. It would also allow me to pass messages/instructions in the session file to other users so they can properly implement the session file on their computer (e.g., "be sure to change the directory name and update your density files", "the related command files that work with this session file are ....") Later on such information could be extracted in mass from closed session files, allowing for searches using database-like queries. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

1 0

BIOMT
by Ludovic Autin 16 Aug '11

16 Aug '11

Hi there, I am wondering if its possible to access the matrices computed by the sym command and/or if its possible to save the multiscale structure as a PDB with the BIOMT fields instead of the full structure? thanks in advance Ludovic

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