April 2016 - Chimera-users - RBVI Mailing Lists

electron density map
by 陈柳青 28 Apr '16

28 Apr '16

Hi! I display the 2Fo-Fc map in chimera, but i wonder what the meaning of step 1, step2,etc in volume viewer. The other question is what the relationship between the level in chimera volume viewer and Coot map level ? Best regards -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Re: [Chimera-users] electron density map
by Oliver Clarke 28 Apr '16

28 Apr '16

Dear Liuqing, Step size refers to whether every point in the map is displayed (step 1), or every second point (step 2), or every fourth point (step 4) and so on - basically, the coarseness of the grid. Loading a map at a larger step size will have less detail, but will be faster to load and manipulate. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling) for details. The level in Chimera is the same as in coot in absolute terms (e-/Å^3) - it is just that in Coot, by default, maps are adjusted in steps of r.m.s. (often called “sigma”), whereas the default behaviour in Chimera is to deal directly with absolute electron density levels. You can mimic the Coot behaviour, however, by adjusting the volume level on the command line with the option sdlevel, for example “volume #1 sdlevel 1” will set the volume with id #1 to 2xr.m.s. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#level) for details. For convenience (really due to my forgetfulness), I use an alias to do this, as follows: "alias ^map_sig volume $1 sdlevel $2" so then one can use the command “map_sig #1 5” to adjust map #1 to 5xr.m.s., which should match the corresponding level in coot. If you want to mimic how maps look in coot, adjusting some of the mesh options is handy, as follows: "alias ^cootmode volume $1 capfaces false style mesh meshlighting false squaremesh false color "#08882eefa222" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron” Where “cofron" is an alias that mimics the centering and navigation behaviour of coot: "alias ^cofron set showcofr; cofr view; clip on” Cheers, Oli.

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Re: [Chimera-users] Viewing one biological unit of a model
by Derrick Lau 28 Apr '16

28 Apr '16

Hi Elaine, Very clear instructions. Thank you very much. Best regards, Derrick Lau PhD student University of New South Wales - Molecular Machines Group - (02) 9385 8639 *Cellular and Molecular Biology* 2016-04-26 8:09 GMT+10:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > Hi Derrick, > That PDB entry is an “NMR ensemble” including 100 different conformations > of the same thing. You can hide or delete any of those 100. To first see > what you have, show Model Panel from the Favorites menu. Initially all the > conformations are collapsed into a single line with ID “0.1 … 0.100” or > something like that. If you scroll down to click the “group/ungroup” > function in the right side of the Model Panel, that entry will expand out > (ungroup) to 100 entries. > > You could show any one by clicking to highlight only that line on the > left-hand side of the Model Panel, then clicking the “show only” button on > the right-hand side, for example. You can also toggle the Shown checkboxes > individually, or highlight multiple lines and “show only” those or “close” > (delete) them leaving only the others. > > Or you don’t have to use the Model Panel at all. For example, if the > structure was opened as model #0 and you wanted to hide all except the > first conformation, command: > > ~modeldisplay #0.2-100 > - OR - > ~modeldisplay #0.2-end > > …or even delete them > > close #0.2-end > > It might take a few seconds to execute the command. > > Note that a single NMR conformation is not necessarily a biological unit. > It is just one copy of the coordinate set. > 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 Apr 24, 2016, at 8:00 AM, Derrick Lau < > derrick.lau(a)student.unsw.edu.au> wrote: > > > > Dear Chimera, > > > > Hi. My name is Derrick. I have recently started learning to use Chimera > to look at the capsid structure of HIV. I would like some help in the > interface. One particular crystal model, the HIV-dimer model PDB 2M8L, > strangely loads a bunch of ribbon structures. Would you know the way of > switching off other biological unit so I can see one pair of dimer? > > > > I didn't have this problem with other capsid structures (like 3P05). > Your help is appreciated. Thank you in advance. > > > > Best regards, > > > > Derrick Lau > >

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Re: [Chimera-users] [chimera-dev] Labeling and coloring chains
by Elaine Meng 27 Apr '16

27 Apr '16

Hi Deniz, (1) It is easy to specify multiple chains in the command line. Show the command line from the Favorites menu. Example commands: color red,r :.A-D (meaning: color red ribbons-only in chains A-D in all models) color green,a #0:.B,.D (meaning: color green atoms-only in chains B and D of model #0) See manpages for color command and for command-line atom-residue-chain specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> … and you may want to try a “getting started” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> (2) For labeling the chains there are 2 general choices. A. For 3D labels that move along with the structure, there aren’t exactly chain labels, but you can choose to label one residue in each chain and then only show the chain ID and not the other residue information. For example, command “select :10” will select residue 10 in every chain that has a residue 10. Then you could use menu: Actions… Label… residue… custom, and in that dialog specify you want labels of the form: %(chain)s , Apply. Disadvantage is that they may be on top of things and hard to see. Advantage is they move around with the structure and will stay near that residue when you rotate and translate. B. you can arbitrarily add 2D labels that are just in the XY plane and do not move with the structure, containing whatever text and symbols you want. In menu, Tools… Depiction… 2D Labels. Click the Help button on that dialog to see its help. You can type in each label manually and move it around in the XY plane. You would want to get the final view for a figure or something close to it, before bothering to add 2D labels. There are examples of 2D labels in these tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html> C. Actually there is a 3rd related choice, just putting the mouse over an atom or residue will pop up temporary information that includes its chain ID, and sometimes that will suffice. As you can see, there are lots of tutorials and manual pages to explore. For future reference, chimera-users(a)cgl.ucsf.edu (CC’d here) is the address for Chimera usage questions. The chimera-dev list is more for programming-related questions. 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 Apr 27, 2016, at 12:48 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi, > I am very new to Chimera. If you have time, I would really appreciate your answers. > I am working with a structure that contains 80 chains. > 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. > How do I do this? > 2. Also, I would like to add labels to the individual chains I choose on the structure. > How do I do this? > Thank you, > Deniz

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Define plane or planes matched to hither or yon clip planes
by Oliver Clarke 27 Apr '16

27 Apr '16

Hi, I often encounter cases where I am showing a slab of density or model (or both), clipped using the global clip planes, and would like to show the viewer a thumbnail illustrating the position of these clip planes from an orientation orthogonal to the viewing direction (similar to what is shown in side view), to give context. Is there any way to define either two planes, one matched to the current yon and one matched to the global hither, or one thick plane with the thickness defined such that one side matches hither and the other yon? Alternatively I guess I can do this using the model-specific clip planes, but that's a little cumbersome to do when many models/maps are involved. Cheers, Oli

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how to change map origin in the map file
by 许靖蔚 27 Apr '16

27 Apr '16

Dear all: I recently have to match two maps and calculate the CC value between them. The origin of these two maps are different and the pixel value are also not the same. I could open these two maps in chimera and align them by map fitting. However, after I matched one of them to the other and saved the map, the re-opened map was still at the same position as the previous! So do you know how to same the map after fitting? Best wishes.

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HBond on every frames of a large trajectory
by Jérémie KNOOPS [531802] 26 Apr '16

26 Apr '16

Hi, What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow. Jérémie Knoops PhD Student Laboratory for Chemistry of Novel Materials<http://morris.umh.ac.be/default.aspx> University of Mons<http://portail.umons.ac.be/en2/> 20, Place du Parc B-7000 Mons (Belgium) Tel : +32(0)65 37 38 65<tel:%2B32%280%2965%2037%2038%2065>

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Save as GIF (animated or otherwise)
by Oliver Clarke 26 Apr '16

26 Apr '16

Hi, It would be very useful if Chimera (prob ChimeraX) was able to save either single frames, or, preferably, record movies in GIF format. This is not so much out of a desire to make animated gifs (although these can be handy for presentations and use on the web), but more because it makes it very easy to create labeled movies in vector graphics programs (one can edit a single frame in a vector graphics program and then insert it and alter the duration in for example GIMP or similar), which can then be easily converted back to mp4. Otherwise adding labels and custom annotations to movies is a pain for a novice like me, though if any one has any suggestions for recommended software I'd love to hear them! I've tried using iMovie and found it incredibly frustrating for the kinds of simple things like to do - adding labels, boxes, arrows etc to highlight specific domains during a morph, for example. At the moment I make a movie in chimera and convert it to a GIF using videoblend, edit in affinity designer and GIMP and then convert back to mp4 using online tools, but a more direct route would definitely be useful. Cheers, Oliver.

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need help to plot electrostatic surface charge distribution
by ashok rout 26 Apr '16

26 Apr '16

Hi, I have NMR structure of a protein. I want to plot electrostatic surface charge distribution. Can you please write me step by step commands how I can do it. I want to remove hydrogens first and then want to plot electrostatic surface charge distribution. Ashok -- thanks & regards, Ashok

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Information mathematical model
by VLADIMIR QUINTERO LEON 25 Apr '16

25 Apr '16

Hi, I'm doing a consultation on the mathematical model that works UCSF Chimera. I appreciate that you could provide that information. This query only has academic purposes. Excuse me, I don't speak English. Best regard, Vladimir Quintero León Departamento de Química Facultad de Ciencia y Tecnología Universidad Pedagógica Nacional Bogotá, Colombia.

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Chimera-users April 2016