- Chimera-users - RBVI Mailing Lists

Numbering the amino acid sequence
by Francesco Pietra 28 Apr '08

28 Apr '08

A referee is asking me to number the amino acid sequence involved in docking a ligand with a protein. Not satisfied by having a side table with a guideline. Is it possible to add that numbering in a least-intruding way? The figure exported in standard graphic formats from Chimera is already extremely crowded. Therefore, is any possibility of adding the numbering outside the protein with some kind of pointers? I can't do with colors alone: I already used different colors for different helices. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

3 2

Re: [Chimera-users] Chimera - Matchmaker tool
by Elaine Meng 28 Apr '08

28 Apr '08

On Apr 27, 2008, at 10:16 AM, Sujata wrote: > Hi, > I am using Chimera for awhile now to analysis modeled structures > and I love it, way better for visualizing than a lot of other > softwares and very user freindly. > I do have a question about Matchmaker- is there a way that I can > get the total number of atom-pairs in the 'matchlist' it generates > in Matchmaker? Or in other words, I want to know the final > percentage of atom-pairs that Chimera gives me after pruning the > long atom pairs that do not exceed 2 Angstroms to compute the RMSD. > > Thank you very much. > Sujata Sovani > Hi Sujata, Thanks, tell your friends! 8-) The final match RMSD and number of alpha-carbon pairs are reported in the Reply Log (under Favorites). They are also shown in the status line at the bottom of the Chimera window, but only temporarily. If you also show the sequence alignment from MatchMaker, these residue pairs used in the final fit iteration are shown in boxes with orange- red outline and light orange interior. I am not sure which percentage you wanted; one possibility is to divide by the total number of residues in a structure. You can also find out how many pairs were pruned by doing another match with the same parameters except without iteration. That does not change the sequence alignment, only the fitting. If you already showed the sequence alignment from matchmaker, you wouldn't have to rerun matchmaker, only choose Structure... Match from the sequence alignment window and apply it with all its options turned off. I hope this helps, 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

1 0

Independent model rotation
by Eduardo Sanz Garcia 26 Apr '08

26 Apr '08

I have a little request (I don't know if it would be feasible). I always work with several models at the same time. I would like to set the the default center of rotation as "independent". It seems that the "Save" button in the following panel (attached image) should do it, but it is not. Is there a way to implement this option? Thank you very much.

2 1

questions on find hbond, find clashes/contact
by Harinathachari Bahudhanapati 25 Apr '08

25 Apr '08

Dear chimera support, I am a huge fan of chimera and I have so say I spend a lot of time on chimera these days, as a part of writing for my dissertation. I have a few questions and I sincerely you to request to help me out. 1. About findHbond: I never seem to get this one right. I model Enzyme-inhibitor complexes on patchdock. The inhibitor templates are either pdbs from rcsb or modelled on swissmodel. I am not able to locate or find any hbonds newly formed in the docked models, when I search for intermodel hbonds (I am looking for protein-protein interactions). Are there any special criteria or am I missing some thing? I want something similar to that of the output of HBPLUS (I never seem to get this working either - very frustrating) 2. About find clashes: What are the ideal parameters for clashes and contacts. I tried several things, they give me several no of overlaps for several different parameters. Are these vanderwaals interactions? because some times I see more than 40 interactions between two residues -i.e., between the atoms of Enzyme and inhibitor? How reliable are these interactions (I need to publish my data) This tool does not seem to work unless I add hydrogens to both the chains. 3. It would be great, if there was a energy minimization tool in chimera because I introduce mutations. Please kindly suggest me if there are any easy to use tools for this. I tried COOT and swisspdbviewer, but not really that user-friendly. I read all the newsletter e-mails from CHIMERA users-list everyday. Thanks to Elaine, tom, eric and conrad. You guys rock.. sincerely Hari hbahudha(a)fau.edu

2 1

correlation plot
by bala 25 Apr '08

25 Apr '08

Dear chimera friends, I have a simulated trajectory of a RNA molecule. I want to make a correlation plot based on residue fluctuation. I am new to scritping in python. Can anybody please give me some suggestions or any sample script for such analysis if possible. Regards, Bala

2 1

PDF Chimera documentation
by Elaine Meng 25 Apr '08

25 Apr '08

Hi everybody, For those of you who have asked about a PDF version of the documentation: we just made PDFs of the User's Guide and Programmer's Guide for the last production release (1.2470 Nov 2007). These are linked near the bottom of http://www.cgl.ucsf.edu/chimera/docindex.html (the page you get from clicking "Documentation" in the lefthand column of the Chimera home page). ** HOWEVER, these files have several limitations: - large size (User's Guide >600 pages, Programmer's Guide >2600 pages!) - suboptimal page ordering due to the nonlinear nature of the documentation - some redundancies, i.e., pages occurring more than once in the PDF document Because of these limitations, we recommend using the documentation in HTML form where possible, and printing from your Web browser to obtain hard copies of specific parts as needed. Also, the HTML documentation is updated constantly, whereas the PDF files may not be updated very often. Best, 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

1 0

Benchmark scores
by Sacha De Carlo 25 Apr '08

25 Apr '08

System : DELL Inspiron 530s, WinXP, 3Gb @ 800MHz Graphics : Radeon HD 2400 Pro 256Mb DDR3, driver version 6.14.0010.6764 Proc: Intel Dual E2160(a)1.8GHz Test date: 2008/4/25 Benchmark scores surface 648 mesh 554 contour 168 solid 248 recolor 115 Molecule Benchmark scores 1F4H (33805): 93.0 171.0 8.0 7.0 173.0 14.0 30.0

1 0

Tile 3D EM maps
by Eduardo Sanz-Garcia 24 Apr '08

24 Apr '08

I found that "tile" only works with atomic coordinate models. Is there a way to "tile" 3D EM maps? Thank you

2 1

Morph surfaces
by Thomas Goddard 24 Apr '08

24 Apr '08

Hi Craig, You can make a low resolution surface from atomic coordinates using the new molmap Chimera command (added in January 2008). You can create such a surface for each frame of your morph using the MD Movie dialog menu entry Per-Frame / Define Script. If your morph is model #2 the script would look like: molmap #2 8.5 where 8.5 is the desired resolution in Angstroms. To produce a smoother surface, to color it (transparent red), and to set the volume step size (the surface is a contour surface of a map computed from the molecule) the script would look like molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1 The color spec is red,green,blue,opacity. The molmap command replaces a previous map for the molecule by default so the surfaces will not accumulate. More details on the molmap command are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html You'll need a Chimera daily build to use this command: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Craig Yoshioka wrote: > Hi Dr. Goddard, > > I'm Craig, a graduate student in Clint and Bridget's lab at Scripps. I > am trying to use Chimera to put together an animation movie. I have > fitted a couple of crystal structures into different EM maps and have > used the Morph Conformations to interpolate between them (excellent > btw). I want to do the animation using surfaces though, and have not > found a satisfactory way to do so. The surfacing command under the > actions menu seems to fail half the time, but provides far too detailed > a surface for this animation anyways. I really like the flexibility of > the surfacing used by the multi-scale model window (letting you set the > "resolution", etc.) but this surface does not update with the morph > conformations animation. I have taken to saving the morph conformations > pdb to the disk as all frames, and reopening it to get access to all the > intermediate PDBs. I then using multi-scale surfacing on this to > generate a large series of surfaces, and I generate the animation by > switching them on and off in series. This is, of course, very time > consuming. Is there a way for me to switch the algorithm used by the > surfacing in the actions menu to use the multi-scale models surfacing > instead? That way the animation would be much easier. > > thanks for your help, > > -Craig > >

4 4

chimera on OS X 10.5
by Mark Moll 23 Apr '08

23 Apr '08

When I run Chimera on OS X 10.5 "Leopard", I get a ton of the following errors in /var/log/system.log: The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__ () to debug. I first reported on this on November 2, 2007, but with the latest daily build this still happens. I removed all extensions, but that doesn't seem to make a difference. My own extension becomes painfully slow, because Chimera is constantly writing the above error message. I never get the error above with the version of python that comes with Leopard or with the version of python2.5 in MacPorts. Would it be possible to build Chimera's version of Python similar to these other versions of Python? Or does the problem lie elsewhere? -- Mark

3 2