- Chimera-users - RBVI Mailing Lists

alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Positions Available in Electron Crystallography of Membrane Proteins
by Iban Ubarretxena 14 Jul '10

14 Jul '10

Positions Available: Electron Crystallography of Membrane Proteins A number of different positions are available with the Transcontinental Electron Microscopy Initiative for Membrane Protein Structure (TEMIMPS;http://temimps.nysbc.org) TEMIMPS is a new center funded by the NIH Protein Structure Initiative and is composed of five research groups with combined expertise in membrane protein production, 2D crystallization, electron microscopy, image processing, and structure determination. Our center will focus on the development and implementation of high-throughput and high-resolution approaches to structure determination of membrane proteins using cryo-electron microscopy and 2D crystals. We are seeking highly motivated individuals with good communication skills and ability to interact with an interdisciplinary group ranging from biochemists to mathematicians. Individual positions will be available in New York, Cleveland, Seattle and Houston, working in the laboratories of Drs. David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel Penczek. These positions include a project manager, postdoctoral associates, software engineers and technical staff; up-to-date descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs . Further questions or applications should be sent to temimps(a)nysbc.org. Applications should include a cover letter, a curriculum vitae and contact information for three referees. Applications will be reviewed as they are received and will continue until the positions are filled. Iban Ubarretxena-Belandia, PhD Assistant Professor Dept. Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Bldg., Room 16-70E 1425 Madison Avenue, Box 1677 New York, NY 10029 Office: 212-659-5593 Fax: 212-849-2456 Email: iban.ubarretxena(a)mssm.edu WWW: http://www.mssm.edu/physbio/ This e-mail is confidential and may well also be legally privileged. If you have received it in error, you are on notice of its status. Please notify us immediately by reply e-mail and then delete this message from your system. Please do not copy it or use it for any purposes, or disclose its contents to any other person: to do so could be a breach of confidence. Thank you for your co-operation

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volume and area measurements
by Chinthaka Silva 13 Jul '10

13 Jul '10

Hi, Could you please tell me what is the difference between the values we get from the following two options? Volume Viewer: Tools --> Measure Volume and Area Tools --> Volume Mean, SD, RMS Is SD means standard deviation? What is RMS? In the 2nd option, we get 'Surface V and A'. What does 'Surface' mean in here? Thanks, Chinthaka.

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SAXS Profile
by yann sterckx 13 Jul '10

13 Jul '10

Dear all, I'm trying to run the SAXS Profile Option in Chimera, but it doesn't seem to work properly. Every time I try to run the option, I get the following error message. Error processing trigger "check for changes": HTTPError: HTTP Error 504: Gateway Time-out File "/Applications/Chimera.app/Contents/Resources/lib/python2.6/urllib2.py", line 516, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) See reply log for Python traceback. I work in Snow Leopard. Can anybody help me out? Thanks, Yann

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Fwd: request for stick and ball size in Atoms/Bonds menu
by Bala subramanian 12 Jul '10

12 Jul '10

Friends, I apologize that i sent the following mail wrongly to chimera-bugs. So i am fwdg it to the users list once again. ---------- Forwarded message ---------- From: Bala subramanian <bala.biophysics(a)gmail.com> Date: Mon, Jul 12, 2010 at 7:18 AM Subject: request for stick and ball size in Atoms/Bonds menu To: chimera-bugs(a)cgl.ucsf.edu Dear developers, Greetings. I downloaded a recent daily builds (July 8th) and I am quite happy to see the new additions on the Atoms/Bonds menu. I thank you all for your effort. I would like to request you for the addition the Stick and Ball size settings in the Atoms/Bonds menu. Because when i change the stick/Ball size from preference-New molecules option. I am not able to see the change for the molecule presently loaded in Chimera. It would be of great help to have this option in Atoms/Bonds menu itself. Regards, Bala

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Structural alignment of a protein-ligand complex with other ligands only
by N.R. Jena 09 Jul '10

09 Jul '10

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?

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Best density map contour level
by Thomas Goddard 08 Jul '10

08 Jul '10

Hi Maria, Unfortunately I don't think your procedure for setting the contour level will work very well. The problem is that the isosurface is not just the outside surface of the capsid. Usually the virus genome has lower density then the protein capsid so there contour surface may show the virus as hollow, or maybe layers of RNA/DNA will appear. So the expected volume is not going to be the volume of a solid ball. There are no well accepted standards for how to set the contour level when showing EM maps. On the other hand there probably is no "right" answer. A good level for looking at the protein capsid will be different from a good level for looking at the genome packing. If a capsid feature of an icosahedral virus does not appear at all 60-fold symmetric locations then symmetry averaged maps will show lower density and you will need a lower contour level to see such features. In practice I believe people analyzing map primarily choose the contour level by eye that best suits their analysis. Tom > Hi Tom, > > Thank you very much for your help. > I'll measure the radius of my 2 d images afterwards I'll use the radius to calculate the volume of my virus and finally > set the contour level so that this volume is enclosed. > > Thanks a lot, > Maria > > >> Hi Maria, >> >> Chimera shows the volume data as an "isosurface" meaning all points >> on the surface are at a specific map value. That map value is called >> "level" in the volume viewer dialog. The values in a map (volume data >> file) determined by electron microscopy are often not normalized in any >> way -- useful values could be 10000 or 0.1 depending on the map. For >> x-ray maps it is common to normalize so that standard deviation over the >> unit cell is 1.0. In EM there no unit cell so the standard deviation >> would depend on how big a box surrounded the virus density -- so this is >> not as useful a normalization. There is no standard accepted EM map >> normalization that I know of. If you knew the expected volume occupied >> by the structure you could set a contour level so that the surface >> encloses that volume. Here's an explanation of how to do that in Chimera >> >> >> http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… >> >> More often you just visually choose a level that you believe gives a >> surface matching the envelope of the proteins in the structure. The map >> mean, standard deviation and root mean square value can be calculated >> with menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> Tom >> >> >> >>> Dear Chimera users, >>> >>> I'm using Chimera to inspect my calculated density maps of viruses. In >>> order to compare different tree d reconstructions I would like to know >>> what the 'Level' value in Volume Viewer dialog means. At present I'm using >>> the level value 1 but I'm not sure if this is correct. >>> >>> Could you please give me some advice how to define the right contouring >>> threshold to present my data in order to inspect it? >>> >>> Thank you for your help, >>> >>> Maria L. >>> >>

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Alternative to the model panel
by Varela, Lawrence Rocco 07 Jul '10

07 Jul '10

Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more). I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets. Is there an alternative to using the model panel? Like for example writing to file all the info that displays in the model panel including most importantly the model ids? Thanks in advanced, --Rocco

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structural alignment
by Bala subramanian 07 Jul '10

07 Jul '10

Friends, I have 10 conformations of the same RNA molecule obtained from 5 separate MD simulations. Now to compare the conformations, I want to make a structural alignment of these conformations and make an alignment map ( something like multiple seq. alignment for protein ) so as to show residues (or residue positions) that higher flexibility among these ten conformations. What is the best way to do it in Chimera. Thanks, Bala

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Parameters choice for match->align and quality assessment
by compchem compchems 06 Jul '10

06 Jul '10

Dear Chimera developers, great thanks to you for possibility to work with your very useful program. I am new in structural alignment studies and have some questions about parameters in match->align. My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues. First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case. Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me. Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure). I am sorry for long letter and thanks for your attention to my problem. D. Yegorov.

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