- Chimera-users - RBVI Mailing Lists

Alignment
by bodvael email 16 Nov '11

16 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 16 Nov '11

16 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 16 Nov '11

16 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 06 Nov '11

06 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 03 Nov '11

03 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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