- Chimera-users - RBVI Mailing Lists

Error in viewing trajectories
by George Tzotzos 28 Nov '11

28 Nov '11

Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files. The error was "TypeError: Attempt to form duplicate covalent bond." I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour? Best regards George

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EM density fitting
by dhacademic 28 Nov '11

28 Nov '11

Hi, I have an EM density map of a protein, as well as several PDB structures, and want to find the most possible structure with the lowest fitting score. Can anyone tell me know how to calculate the fitting score between the EM-density map and a PDB structure in chimera? Many thanks! Best, Hao

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TypeError: Attempt to form duplicate covalent bond.
by George Tzotzos 27 Nov '11

27 Nov '11

Hi everybody, I'm trying to load a trajectory and I get the error message shown above. I'm attaching the error log in case it's of any help. The problem is that I'm able to load the trajectory in VMD without problems (prefer to work on Chimera, though). Any help on how to troubleshoot this would be most welcome. Have a good weekend George

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3D custom residue labels
by matheus froeyen 22 Nov '11

22 Nov '11

Hi I tried the command mode options to generate a custom hard coded 3D residue label: labelopt resinfo "ARG 167" rlabel offset 0.,0.,20. :151 however get an error in the labelopt command: "resinfo" keyword does not exist (although it is described in the chimera man pages) Then I tried to bypass this by using the atom labeling labelopt info "ARG 167" label offset 0.,0.,20. :151@CA but again no luck, then is displayed the label "none" in the 3D window the default residue labeling works however. How can I use custom labels without using the menus? I use chimera 1.5.3 build 33475 on mac osx. best regards mathy

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2dlabels with solid background
by Tom Goddard 21 Nov '11

21 Nov '11

Hi Gabe, Unfortunately there is no color key command. Here's another creative solution. Make the label background be another label using unicode squares. 2dlabels create b1 text '\u2588\u2588\u2588' color white xpos .5 ypos .7 size 64 This uses the square unicode character, hexadecimal 2588. This solution has the advantage that you can fade out this background together with the label. In order for the text label to appear on top of background label you have to create the text label after creating the background. I'd recommend making all the labels and backgrounds interactive with the 2dlabel dialog and saving them in a session which you use together with your movie script. The script will show and hide the labels that have already been made, sized, positioned. You can cut and paste the unicode square character, say from web page into the 2dlabel dialog. http://en.wikipedia.org/wiki/Box-drawing_characters This solution doesn't make it easy to make an outline around the background box. Elaine suggested that you just make another slightly bigger background in the outline color. That has the problem that the vertical outline edges are thicker than the horizontal ones if the the background is wider than it is tall. To get uniform thickness outline you could make two extra background boxes one square shorter than the normal background and slide them horizontally them to get vertical outline edges of equal thickness. Tom -------- Original Message -------- Subject: 2dlabels From: Gabriel Lander To: Tom Goddard Date: 11/19/11 6:59 PM > Hi Tom, > Again thanks for the volume tracer settings saver - it's been super helpful. > But now I have another question: > I'm currently making a movie that uses lots of labels, and for the most part the current 2dlabels create& acreate commands work really well. But for certain closeup views the text gets lost in the volume density, and I've been trying to figure out a way to get a box to show up behind the labels (like in the attached image). I've figured out I can get something like this if I use the "color key" option, and then offset the text to fit inside the box, but I can't find a "color key" chimera command that I can put it into my movie script. > I tried using the "shape rectangle" command, but it's a bit too tedious to position the rectangles exactly right for all the labels. > Any ideas? > -gabe >

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Calculating and showing the Mass center of Volume Segments
by Schmidt, Claudius 19 Nov '11

19 Nov '11

Hello, I got a volume map that I segmented in 4 parts. Now I wanted to measure how the parts are coordinated to each other. As the Axes/Planes/Centroids menu can only create planes by atoms I wanted to place atoms in the mass- center of each segment. Is there any way to realize that? Or do you have any other way to measure the angles. To explain what I'm trying to measure: Example you have 4 segments, I call them a b c d. I want to measure how the axis that is formed by a and b, forms an angle to c and d, or how ist he angle of the plane formed by a b and c compared to ab and d . All for segments are basically the same objects just turned and rotated. With best regards C. Schmidt

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D-Proline modeling in Chimera
by Raghavender Upadhyayula 18 Nov '11

18 Nov '11

I am using PyMol for modeling a peptide containing D-aminoacid (D-Proline) residue. I could invert the configuration arounf L-Proline to convert it to D-Proline. But, I want the "Phi" of the Proline to adopt a certain value. When i tried using the torsion command by selecting the bond N-CA of the D-Proline residue, there is no change at all. I want the Phi value to change from -60 deg to +60 deg and use this as the model for further analysis. Also, the "Psi" needs to fixed at 120 deg. Is it possible in any way to carry out the same steps and achieve the desired results in Chimera. Any suggestions on how to carry out this would be highly appreciated. -- U.S.Raghavender, PhD Postdoctoral Fellow SRI International 140 Research Drive Harrisonburg, VA 22802 540.438.6643

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Docking box
by George Tzotzos 18 Nov '11

18 Nov '11

Hi everybody, I'm visualising a cavity generated by CASTp. Ideally I'd like to draw and get the coordinates of a box around the cavity to use in docking simulations. Is this possible with Chimera? Your suggestions would be much appreciated. Regards George

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Structure superimposition - RMSD
by Suda Parimala Ravindran 17 Nov '11

17 Nov '11

**Hi all, I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help.. Thanks, -Suda

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Alignment
by bodvael email 15 Nov '11

15 Nov '11

Hi, I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don't know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example. Thanks, Bodvael

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van der Waals surface volume
by Jacob Alan Spooner 15 Nov '11

15 Nov '11

Hello chimera-users, I am wondering if and how I can get a volume for the van der Waals surface of my molecule. I know how to generate the vdw surface, and also how the volume and surface area for the solvent excluded surface, however the same method does not seem to work for the vdw surface as it does not show up in my model panel. I tried setting the probe radius of the MSMS to zero but it does not allow this so I am stumped on how I could obtain the volume of my vdw surface. Thanks in advance Jake Spooner

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Chimera issue
by Jason Mears 15 Nov '11

15 Nov '11

I installed Chimera on my linux machine, and there is an issue when I try to open a session (See attached img). It tells me that I need to update the graphics card, but my card is new and I would think is more than sufficient to run Chimera. Any suggestions? Thanks. - Jason -- Dr. Jason Mears Assistant Professor Department of Pharmacology 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

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custom label size
by Francesco Pietra 13 Nov '11

13 Nov '11

Hello: Is it possible to increase the letter size of custom labels? I would like to show the residue number only, saving as a stereo pair. As my stereo pair (a protein complex) works nicely for most people only at a reduced size of the figure (14x4 centimeters, or even smaller), larger letter-size is needed for the labels. thanks francesco pietra

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Visualising disulfide bonds
by George Tzotzos 12 Nov '11

12 Nov '11

Hi everybody, I'm trying to find a way to visualise disulfide bonds in AMBER trajectory files to no avail. Any help how to do so will be very much appreciated. Regards George

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Percent Identity for specified parts of a structure
by Victoria James 08 Nov '11

08 Nov '11

Hi there, I don't know if this command already exists, but I can't seem to find it in the Chimera tools or manual. I'd like to be able to calculate the percent identity of specified parts of 2 matched sequences - in my case the individual transmembrane helices of the structures. I wonder if a command already exists or if there is a way of doing this in Chimera without having to make new .pdb files of each of the areas of the proteins that I want to compare? I think it would be a useful command if it does not already exist. Thanks, Vicky

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rmsd
by sdimicco 08 Nov '11

08 Nov '11

Dear Chimera developers, is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? Thank you in advance. Simone

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.transparency in bild format
by Keren Lasker 05 Nov '11

05 Nov '11

hello: I am trying to use the transparency option in the bild format. it seems that: .transparency 0.3 .sphere 0 0 0 10 results in a sphere however .color 1 0 0 .transparency 0.3 .sphere 0 0 0 10 results in a black image, it only works if transparency is set to 0. any suggestions what i am doing wrong? thanks, keren.

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Adding sequences to an alignment
by Tom Goddard 02 Nov '11

02 Nov '11

Hi David, Here's the documentation on adding sequences to an alignment in Chimera http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… It says it uses the Needleman-Wunsch algorithm with parameters you specify unless you have the "Simply append..." option enabled in which case it puts the sequence at the bottom with no gaps if the sequence has exactly the same length as the existing alignment. I guess you don't have Simply Append enabled. Probably Needleman-Wunsch is simply failing to align your new sequence to the existing alignment so it ends up putting it to the right of the existing alignment my inserting a huge gap at the beginning. How similar is the sequence you are trying to add to the alignment sequences? I'm not the Chimera expert on this topic (Eric Pettersen and Elaine Meng are) so I've posted to the Chimera mailing list so they can give you a better answer. Tom > Hi Tom, > My name is David and I'm a postdoc in Jack Johnson lab at Scripps. I'm writing as I've a question concerning the use of Chimera. > I've superimposed two structures in Chimera and generated a structure-based sequence alignement. I have two set of sequences (2 families) with a group associated with one of the two structures (and thus its sequence) and the other group being linked to the second structure. > I tried to extend the structure based sequence-alignement by adding new sequences and adding the first 2 sequences exactly did that i wanted: aligning them to the corresponding reference whose structure is displayed. > However when I add the other group of sequence, it doesn't result in aligning to the other sequence and instead add it after the overall alignment. > I'm sure that I'm missing something obvious, could you please help me sorting that out? > Thanks a lot > Best wishes > David > > David Veesler > Research Associate > The structural Virology lab - Johnson's lab > Department of Molecular Biology > The Scripps Research Institute > 10550, N. Torrey Pines Road > La Jolla, California 92037, USA > > >

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Fwd: sphere viz in Chimera
by Elaine Meng 02 Nov '11

02 Nov '11

Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: January 8, 2008 10:09:06 AM PST To: Adam C Marko <adam.marko(a)ucsf.edu> Cc: Terry Lang <terry(a)lego.berkeley.edu>, sbrozell(a)scripps.edu, Eric Pettersen <pett(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> Subject: sphere viz in Chimera Hello, You guys will probably think I'm a nutjob (or prior suspicions may be confirmed), but Adam got me started thinking about how to improve sphere visualization in Chimera, and I wrote a short program akin to showsphere but that takes advantage of features in Chimera (attached at bottom - feel free to use, alter, redistribute, or ignore completely - I spot-checked the output but it's still caveat emptor). The old program showsphere was written in the time of Midas and shows the radii with a dot molecular surface. If you just show the PDB file with the sphere representation in Chimera, that doesn't include the radius information but just uses some default for carbon since the spheres are written as C atoms. The dot surface cannot be used for volume calculations in Chimera. Showsphere also made a separate file for each cluster. Chimera can show solid spheres, and an attribute assignment file can be used to set the radii from the SPHGEN output. Another difference from Midas is that you can read in multiple models from a single PDB file which are then separately displayable and specifiable. It was Adam's idea to take advantage of the controls in the Model Panel. So this new little program puts all the clusters (above a user-specified minimum size) into a single PDB file and creates an attribute assignment file for setting sphere radii in Chimera. The volume enclosed by a "molecular" surface around the cluster can be computed in Chimera. -- Example (using rec.sph, the SPHGEN output from the DOCK6 tutorial http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_… ): f77 chimerasphere.f -o csphere guanine.24% csphere enter name of sphere file: rec.sph rec.sph minimum size to include? 35 35 enter name of output PDB: recspheres.pdb recspheres.pdb enter name of radius assignment file: recspheres.rad recspheres.rad cluster # 1 contains 158 spheres cluster # 2 contains 80 spheres cluster # 3 contains 50 spheres cluster # 4 contains 46 spheres cluster # 5 contains 38 spheres -- then I started Chimera and used the following commands before saving screenshot below: open rec_noH.pdb (also from DOCK6 tutorial) open recspheres.pdb defattr recspheres.rad (to browse to this file instead, use "defattr browse" or Tools... Structure Analysis... Define Attribute. This step generates message "No attributes usable by Render dialog were defined" but that is nothing to worry about; just means "radius" is one of the attributes suppressed from appearing there) rep sphere #1 rainbow models #1 color purple #0 set bg_color white -- screenshot with Model Panel (Favorites... Model Panel) -- note you can toggle display of clusters individually using the Model Panel I originally had the program ask for a model number into which the sphere PDB file would be read, because the attribute assignment file must specify each sphere. For example, if you specified 2, you would have to "open 2 recspheres.pdb" and the assignment file would include specifications like #2.5:1017.het@c The current version doesn't ask and just uses specs like #.5:1017.het@c for which there is a [remote] possibility of matching something other than the sphere, but nonetheless it could happen. Lines for the alternative behavior are still in the file, just commented out. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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docking sphere visualization
by Trent E. Balius 02 Nov '11

02 Nov '11

Dear Chimera-user list, I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed. This might be a helpful new feature to be included in a future release of Chimera. Thank you, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/

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MD plotting
by Eric Pettersen 01 Nov '11

01 Nov '11

Hi all, For any of you using Chimera's MD Movie for trajectory playback, I just added the ability to plot atomic distances, angles, and dihedrals for your trajectory. You can click (or drag) on the plot to go to the corresponding frame. You create a plot by using the "Plot" submenu in MD Movie's Analysis menu. Most of the functionality is available in the current daily build, but tomorrow's build will have a couple of additional features: dumping plot values to a file, and showing the numeric value of the plot for the current frame in the list of plots (the value is blanked during playback since updating it slows down playback too much). Feedback welcome. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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alpha helix representation problem
by larif sofiene 29 Oct '11

29 Oct '11

greeting after a MD simulation of an in silico induced mutation A80P (located in an alpha helix) in a monomeric protein i get this strange alpha helix (a wire represented helix) http://imageshack.us/photo/my-images/573/alphahelix.jpg/ is it the induced mutation that break down the alpha 3 helix and disturb orientation of the helix axis or a problem with chimera not recognizing the helix (in sequence tool the helix is no more color filled as alpha helix after inducing mutation) thank you for this piece of art which is CHIMERA :)

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managing CONECT table
by Francesco Pietra 27 Oct '11

27 Oct '11

Hello: In preparing a model comprising various fragments I would like to suppress from the PDB CONECT table two connections to the central transition metal. I wonder whether there are rules for such manipulations. Chimera detects (as a bond) only one of these two connections. thanks francesco pietra

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Re: [Chimera-users] periodic box visualization
by Eric Pettersen 26 Oct '11

26 Oct '11

On Oct 26, 2011, at 4:52 AM, Giovanni Pavan wrote: > Dear all, > when a periodic system is visualized into Chimera (e.g., a periodic > waterbox), is it possible to visualize explicitly the borders of the > periodic box (defined for instance in the last line of coordinate/ > restart files in case of AMBER format structures)? > Last, is it also possible to see the periodic images of the original > box along X, Y & Z axes? How? > I thank you in advance for the support and I look forward to > receiving any feedback from you. Hi Giovanni, I'm sorry but neither of these is currently possible in Chimera. You'll have to use another visualization program (VMD?) if you need these capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic water box), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni Dr. Giovanni Maria Pavan SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI) Centro Galleria 2, Manno 6928, Switzerland. e-mail: giovanni.pavan(a)supsi.ch skype: giovanni_pavan phone: +41 58 666 65 60

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