- Chimera-users - RBVI Mailing Lists

Q about opening two structures in the same window
by Farhana F Syed 06 Aug '09

06 Aug '09

Hello, I recently downloaded chimera and have been using to view my protein homology model - mainly to show the 2 residues that could be involved in binding to a molecule inside the cell. For that purpose, I need to be able to open the small molecule (citrate or phosphate) in the same window with protein; so I can show the small molecule binds to the specific amino acid residues. But even if I open the two together, how do I pick the small molecule and move it around where I need it? Please help. Thanks, Farhana

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loading atomic coordinates without drawing or calculating bonds
by Veysel Berk 05 Aug '09

05 Aug '09

Hello, I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms. Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations? Thanks in advance, Bests, Veysel Berk

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Re: [Chimera-users] movie making
by Eric Pettersen 05 Aug '09

05 Aug '09

On Aug 5, 2009, at 2:32 AM, Schulz-Gasch, Tanja wrote: > Dear Eric, > > your movie making recommendations were indeed very helpful. Thanks > again! Hi Tanja -- glad I could help! > I am currently preparing a show for visitors at Roche that are > interested in 3D modelling and I want to do this with > Chimera. I have alreday started scripting. However, I would like to > have breaks in the scripts in case that there are > questions. So my question is, is there a possibility to implement a > prompt in the Chimera script that waits only > the users presses 'return' or whatever and then Chimera is running > further through the script? The daily build has a few things that will help here. First, there is a "pause" command that will cause a script to pause until any key other than Escape or End is pressed. Those two keys will cause the script to abort instead of continuing. Secondly, even without an explicit "pause" command any script can be paused by hitting Shift-Escape. A second Shift-Escape will continue the script. Also, plain Escape (no Shift) will cause any script to abort. I hope the presentation goes well! --Eric Eric Pettersen UCSF Computer Graphics Lab

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Stereo 3D on 120 Hz displays
by Daniel Gurnon 04 Aug '09

04 Aug '09

Just wanted to let everyone know that its finally possible to view sequential stereo in Chimera with 120 Hz LCD displays. I just confirmed that it works with my system- here's what you'll need: An appropriate Quadro card (I have a FX 4500), with the recent 190-series driver A 120Hz 3D ready LCD screen (I have the samsung 2233RZ. The other choice is a Viewsonic model) The Nvidia 3Dvision glasses kit, which includes a USB IR emitter The latest beta driver for 3Dvision, version 1.10, found here: http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.html Note that this only works for Vista. The 3Dvision software is supposed to only support Geforce cards, but it worked for my quadro fx 4500. After installing the drivers and the hardware I opened the Nvidia control panel 3D settings and set the following options: Stereo-Display mode: "Generic active stereo (with NVIDIA IR emitter)" Stereo-enable: "Yes" Then restart your computer, and enable sequential stereo from within Chimera. The only issue so far is that the accessory software (photo viewer and 3D preview pack) that installs with the drivers won't load; instead you get a message saying your hardware isn't compatible. ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Minimize
by Alex Gawronski 04 Aug '09

04 Aug '09

Hello, I'm preparing proteins for Delphi analysis using Chimera's minimize function (from a script). However this process is very time consuming. Is using minimize necessary to get accurate results from Delphi? If not, what is necessary? I've played around with the "spec" and "freeze" parameters and they either seem to have no affect or throw an error (which I submitted as a bug). What do you suggest I do? Thanks, Alex Gawronski Carleton University

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Chimera pH
by Peter Baker 03 Aug '09

03 Aug '09

I am trying to generate models of my protein at different pH. Any suggestions as to run how to accomplish this? I do have PBD2PQR files for the different pH but I am not sure how to apply them. Thanks -pjb

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transparent ring fill, color by attribute
by Elaine Meng 03 Aug '09

03 Aug '09

On Aug 3, 2009, at 2:29 PM, Alexey V. Cherepanov wrote: > Dear Elaine, > > I have another question. On the structure, I color the atoms > according to > their attribute (in my case the chemical shift differences between the > solution and the solid state NMR). I show the residues as balls & > sticks and > fill the rings of riboses & bases. Can I show the filling (i) > semitransparent, and (ii) that it keeps the colors of the atoms > (e.g. if C1' > is blue, C2' is white and C3' is red in the ribose ring, then the > filling > should be blue close to C1, white close to C2' and red close to C3' > with the > gradient in between)? > > Many thanks in advance. > Warm regards, > > Alexey Dear Alexey, The answer to your question is mostly yes, except the color in the fill is not smoothly blended. Currently it shows a "pie slice" or wedge for each ring atom. Some tricky things: (1) the ring fill automatically matches the ring atoms, so that you cannot make the fill transparent unless the atoms are also transparent. However, you can get around that problem by opening another copy of the same structure in which the atoms/bonds are opaque. (2) the transparent ring fill must not be thick. Either it must be in the "thin" style, or if in the "thick" style, the atoms and bonds in that copy must be in the wire representation (which forces it to really be thin). Why? Because some mysterious extra bonds become visible through the transparent fill when it is thick. Example: - open your structure twice - assign your attribute (e.g. use bfactor column, or Add Charge, or Define Attribute to read your own arbitrary attribute values) --- for my example, I opened 6bna twice and will use bfactor -- - use one model to make the transparent rings and the other for whatever atom/bond display you want --- I used commands: delete solvent; rep stick -- - start Render by Attribute, move the color bars as you like; for each, click the square color well, and in the Color Editor turn on "Opacity" and adjust the "A" row (transparency). There is a "Keep opaque" option, and keep that turned on and only click Apply to test the coloring. When the coloring is how you like it, then in the "Models" list at the top of the dialog, only choose one of the models. Now do not move the coloring bars, only uncheck "Keep opaque" and click Apply again. You won't be able to see any change, but now the two models are colored the same except one has the transparency and the other does not. --- I made #0 my transparent model and #1 opaque. I colored blue->red- >yellow for increasing bfactor. - now, add thin ring fill to the transparent model, command: fill thin #0 Here is the documentation for the fillring command. Today it is only at my site (tomorrow it should show up on the "real" Chimera web site). <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/fillring.html> The fillring command (or "fill" for short) is brand new and a couple things still need fixing: - to turn off filling, use ~fill ("fill off" and "fill unfilled" are not working today) - saving a session with ring fill should be available in the next daily build Here is a picture of the result:

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Using Command Line
by cdlau＠ucsd.edu 30 Jul '09

30 Jul '09

Hi, I was wondering there was a command similar to the --geometry (feature in the system command line option (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#script)) but for the Command Line. I know there is a command "windowsize" in which the user can specify the dimensions of the chimera instance, however where the chimera instance is located cannot be specified with this command. I want to be able to use a feature similar to --geometry where I can specify X and Y offsets of the top left corner of the window from the top left corner of the screen. Thanks, Chris

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projection view for publication
by Tom Duncan 30 Jul '09

30 Jul '09

I have seen some good recent comments on settings for saving publication-quality images, but I wonder if there is a general preference (by users or or journals) for use of perspective versus orthographic projection when generating images for publication. Thanks, Tom Duncan ----------------------------------------------------- Thomas M. Duncan, Ph.D. Research Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY

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Re: [Chimera-users] domains as ellipsoids?
by Elaine Meng 30 Jul '09

30 Jul '09

On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote: > Hello Elaine, > I am writing to ask you the following: I need to define the > relative orientation of two domains of a protein, and I am not sure > about how to do it. I was thinking of approximating the domains as > ellipsoids and then calculate the angles between the axes of the > ellipsoids. I wonder if you have a better way to define the > orientation, or if Chimera can do things like calculate ellipsoids > axes and their orientation. > Regards > Stefano Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes> or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently. Please send chimera questions to chimera-users(a)cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Display all rotamers
by Eric Pettersen 29 Jul '09

29 Jul '09

In the daily build the Rotamers tool will now allow you to add multiple rotamers to a residue, using alt locs to distinguish them. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > On Dec 6, 2008, at 9:35 AM, daniel.hilger at lrz.uni-muenchen.de > wrote: > > > > I´m really sorry for my imprecise question. I will concretize it. I > > know > > the rotamer tool, but I don´t want to replace only one rotamer into > > another. I will have them all in the structure and in the according > > pdb-file. With the rotamer tool, it is only allowed to choose one > > rotamer > > out of the rotamer list before clicking "Apply". This is my problem, > > and I > > didn´t found an appropriate answer in the manual and help menu. > > Hi Daniel, > I'm sorry for misunderstanding - > > It's true that Apply only puts one copy in the structure, but if you > don't Apply and simply keep the Rotamer list dialog and choose all of > its lines, that displays all of the rotamers at the same time. Maybe > that would allow you to do what you want. The Rotamer list dialog > allows calculating clashes and H-bonds, plus selecting the rotamer > atoms so you can control their appearance with the Actions menu. > > The issue is that the structure can't have multiple indistinguishable > atoms (with the same name and residue number). We have talked about > allowing multiple rotamers to be applied to the structure by giving > them different "alternate location" ID codes, but that has not been > implemented yet. Also, some residues may have more rotamers than the > number of possible alternate location ID codes. Nevertheless we will > make sure it is on one of our requested features lists. > > So currently you can't save PDB with multiple rotamers, but you can > save/restore the session in the state where all of the rotamers are > displayed. > I hope this helps, > Elaine

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Convert the structure
by Abeer Shokeer 29 Jul '09

29 Jul '09

Hello I would like to convert the model structure that I have prepared 90 degree or in different position. Can I do that with Chimera? Thanks Abeer

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fusion proteins
by Brennal Pierre 28 Jul '09

28 Jul '09

Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren. _________________________________________________________________ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TXT_…

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FindClashes: iterative input feeding
by Anna Feldman-Salit 27 Jul '09

27 Jul '09

Dear Users and Developers, I'm interested in using a FindClashes option for a large set of files. It is about finding clashes between a small ligand and enzyme which are found at different conformational stages (more than 10000 each). How can one do it iteratively? I understand this is a scripting or could it be that such an application already exists? Thanks in advance. Regards, Anna

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Removing buried substructures
by Brian & Lanie Grech 27 Jul '09

27 Jul '09

Hi everyone The EM map I am currently working on contains hidden buried substructures and I want to remove these substructures from the map, leaving only the outer layer. Because the map I am working on is very complex, I am finding it difficult to remove the buried substructures using the Volume-eraser Tool. Consequently, I would greatly appreciate any advice on how to remove the buried substructures, without removing the outer layer. Thanks Brian

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wrl to spider or mrc format
by Pierre-Damien COUREUX 23 Jul '09

23 Jul '09

Hello everyone, I'm trying to use this skeleton hand (http://www.cc.gatech.edu/projects/large_models/hand.html) as a teaching tool in electron microscopy. I'm only able to open the file in the wrl format and I was wondering if there is an easy way in chimera to convert that file into a density spider or mrc format. So I can import it and make projections in spider for example. I tried to find on the web a free procedure to convert that wrl, without any success. If you have a clear protocol about how to do that, that would be great Thank you in advance for your help Pierre-Damien COUREUX

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Re: [Chimera-users] [chimera-dev] small suggestion regarding savepos
by Eric Pettersen 23 Jul '09

23 Jul '09

Hi JD, I think you're right: closing a session should clear saved positions. In tomorrow's build that's what will happen. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote: > Dear all, > > I see that when I close a session, the savepos list continues > containing the poses I defined for my anterior session. May be that > is something you want to have this way, but I was wondering if the > savepos (with an option for example) could list only the poses for > the working session. > > All the best, > JD > > > > > Dr. Jean-Didier Maréchal > Lecturer > Computational Biotechnological Chemistry @ Transmet > 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 > > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Matlab script for reading volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, The matlab script on the MRC file format specification web page at http://ami.scripps.edu/software/mrctools/mrc_specification.php was not written by us. But that appears not to be the script you are referring to since it merely reads MRC grid size and data values and does not read the origin, cell size, or cell angles. The Chimera code that reads an MRC map is in Python and included in the distributions: chimera/share/VolumeData/mrc/mrc_format.py It uses other Chimera modules (Matrix and VolumeData) so it can't be used on its own. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard Date: 7/23/09 8:22 AM > Dear Tom, > > It seems Voxel information in Volume Viewer is different from that by reading > .mrc map data. > > For example, > I opened "emd_1080.map" and saved it as "emd_1080.mrc". > > In volume viewer, > Origin index = 50, Voxel size = 2.7, Cell angles = 90. > > But if I use matlab script you linked, > Origin = -1022951423, Cell size = 1132920833, Cell angle = 1119092736 > > Could you let me know how to convert values from .mrc data to those shown in > volume viewer? > > Thank you. > > Best regards, > Do-Nyun Kim. > >> -------- Original Message -------- >> Subject: Re: [Chimera-users] save map as ascii >> From: Do-Nyun Kim >> To: Thomas Goddard >> Date: 7/21/09 7:24 AM >>> Dear Tom, >>> >>> Thank you for your nice reply. >>> Can I get some example code in python? >>> I don't need to write it down as text files, but I want to read values in >>> density map. >>> >>> Thank you for your help. >>> >>> Best regards, >>> Do-Nyun Kim. >>> >>> >>> Quoting Thomas Goddard <goddard(a)cgl.ucsf.edu>: >>> >>>> Hi Do-Nyun, >>>> >>>> Chimera does not write volume data in any ascii file format. >>>> Text formats are much slower to read the files are much larger so >>>> EM maps are almost always in binary. It is not hard to read the >>>> MRC/CCP4 binary formats. Here is the specification. >>>> >>>> http://ami.scripps.edu/software/mrctools/mrc_specification.php >>>> >>>> You can use some Python code in Chimera to dump maps as text files. >>>> If there is a strong reason for doing that let me know and I'll >>>> provide some example code. >>>> >>>> Tom >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [Chimera-users] save map as ascii >>>> From: Do-Nyun Kim >>>> To: chimera-users(a)cgl.ucsf.edu >>>> Date: 7/20/09 1:33 PM >>>> >>>>> Dear Chimera staff, >>>>> >>>>> I'm trying to get the map density data like voxel coordinates and >>>>> density values >>>>> at each voxel from .map files in EM database. >>>>> >>>>> Is there any way to get these data using Chimera? >>>>> >>>>> Or can I save it as an ascii file such that I can read it? All map >>>>> files seem to >>>>> be saved as binary files. >>>>> >>>>> Thank you for your consideration. >>>>> >>>>> Best regards, >>>>> Do-Nyun Kim. >>>>>

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Finding specific voxels in volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, Do you mean you want to find grid indices of volume data points inside a surface? or on (near) a surface? If it is a contour surface the problem is simpler since that just amounts to values above or near the contour level. Chimera doesn't have any capabilities to export lists of volume grid indices so this will require writing some code. It may be quite simple using a Python script in Chimera, but I'd have to know precisely what you need. Export Scene includes surfaces but not values at volume data grid points. The exported file is for graphical rendering -- it does not dump the underlying data. Please direct future questions to chimera-users(a)cgl.ucsf.edu instead of directly to me unless confidential information is included. This will allow others to benefit from the answer. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 7/23/09 7:37 AM > Dear Tom, > > So, now I can easily read and right maps, but I have one more question. > > When I "Export Scene" the surface mesh from a map, how are coordinates > determined? It seems the density map itself does not have coordinate > information. > What I actually want to know is coordinates of voxels in density map "in > current > scene" such that I can figure out which voxel of the density map contains a > point in the surface mesh. > > Thank you for your help. > > Best regards, > Do-Nyun Kim. > > > Quoting Tom Goddard >> Hi Do-Nyun, >> >> The interpolate.py script on the Chimera Python scripts web page >> >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts >> >> shows how to get volume data values interpolated at specific points in >> a volume data set. It uses trilinear interpolation from 8 nearest >> grid points. >> >> More details about the volume data objects are in the Python code >> distributed with Chimera: >> >> chimera/share/VolumeViewer/volume.py >> >> >> Tom

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hydrogen bonds
by Bala subramanian 22 Jul '09

22 Jul '09

Friends, I want to see the hydrogen bond between only side chains & only main chain. 1) I want to know if there is any easy way to do this in chimera 2) What is the default distance and angle used in chimera for calculating the hbond. I see that distance tolerance is 0.4 and angle tolerance is 20. Do these values mean default distance and angle. Thanks, Bala

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mmaker - superposing two structures based on a subset of a chain
by Andrea Rossi 21 Jul '09

21 Jul '09

Dear Chimera Team, I was wondering if it is possible to superpose two structures based on a subset of a chain (a domain for example). I tried the command: mmaker #0:1-100.H #2:1-100.h but Chimera doesn't seem to take into account the residue selection. Superposing according to a subset of a chain is particularly useful when the chain is formed by two or more domains and the domains are connected by a flexible linker (as in the case of antibodies). I can provide more specific examples if needed. Andrea

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save map as ascii
by Do-Nyun Kim 21 Jul '09

21 Jul '09

Dear Chimera staff, I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database. Is there any way to get these data using Chimera? Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files. Thank you for your consideration. Best regards, Do-Nyun Kim. -- Do-Nyun Kim, Ph.D. Laboratory for Computational Cell Biology & Biophysics Department of Biological Engineering Massachusetts Institute of Technology

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depth cueing
by Gabor Papai 21 Jul '09

21 Jul '09

Dear all, I am using Chimera alpha verion 1.4 (build 28110). Whenever I want to save an image on white background with white (or no color) depth cueing and I push the save as button (with supersample 3x3) the depth cueing changes to black. I can change it back to white, but it happens again when I try to save the image. How can I save image with white depth cueing? Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.fr

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icosahedral cage
by Kristin Parent 17 Jul '09

17 Jul '09

does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. 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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chimera crash in windows vista
by justin oppenheim 17 Jul '09

17 Jul '09

Hello: When I invoke chimera, it crashes with the message: "chimera failed abnormally; the exit code was 1. Use the --debug ...." Then when I execute the "chimera debug" from the list of all the installed progems, I get (in a prompt windows): Traceback (most recent call last): File "C:\Program Files\chimera\share\_main_.py, line 65, in (module) value=chimeraInit.init(sys.argv) File "C:\Program Files\chimera\share\chimeraInit.py", line 361 in init tkgui.initializeGUI(exitonquit,debug_opengl) TypeError:initializeGUI() takes exactly 1 argument (2 given) Return code: 1Press return or enter to to exit What can I do now. Please help! Thanks,JO

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