July 2010 - Chimera-users - RBVI Mailing Lists

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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(no subject)
by Maria Ingrid Liebl 06 Jul '10

06 Jul '10

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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movie panel
by Susan Tsutakawa 02 Jul '10

02 Jul '10

Dear Users List, I apologize for these novice questions. I looked in the archives and could not find it. How do I get a MD molecular movement panel if I accidentally close it or I start a new session? I made a morph and I can see it on the model panel. Another very novice question is how do I delete a pdb in my model panel. Thank you in advance. Sincerely, Susan

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Chimera Installation - NOVELL SUSE Enterprise Linux Desktop 11 (64bit)
by Madhumita Pattanayak 01 Jul '10

01 Jul '10

Request you let me know, whether the following specification will support the installation of Chimera: Operating System Novell SUSE Enterprise Linux 11 (64 bit) Processor Intel® Core?2 Duo Processor E8400 Chipset Intel® Q43 Express Memory (RAM) 4 GB PC-3-10600 (1333 MHz) DDR3 SDRAM Memory Graphics ATI Radeon HD 3470 256MB Appreciate an early reply in this regard. Many thanks for your help. Regards, Madhumita Senior Research Fellow CCMB, Hyderabad India "The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium."

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Chimera-users July 2010