August 2006 - Chimera-users - RBVI Mailing Lists

question about annealing residues in pdb file
by Shah, Sanket S 31 Aug '06

31 Aug '06

Hello, I have been using chimera extensively for pdb rendering and manipulation. I needed some information that i couldn't find in the archives. I am aware that chimera displays the pdb file according to the co-ordinates mentioned in the pdb file. However in my situation I have changed co-ordinates of some of the secondary structure elements like helices to do a better fit. and I have saved the new coordinates in the same pdb file. So now when i render this pdb file it shows me the structure with the modified orientation, however chimera displays a continuous model. In the sense, the breaks that I had introduced by changing the angles of some of the helices and thus making the linkage discontinuous are somehow annealed by chimera. So my question is what sort of algorithm chimera employs to seal breaks in the pdb structure. The same pdb strucutre when viewed in swiss model deepview software contains gaps/breaks at the junctions where the coordinates of the helices have been modified from the original ones. however no such breaks are seen when displayed through chimera. First I thought chimera does energy minimization to find out the best way to arrange the loops between the helices so as to create the best continuous structure. However it seems that chimera doesn't do energy minimization, yet it's able to display a complete structure. Could you please inform me about how this is accomplished. Thanks Sanket

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change chain id
by Yunierkis Perez Castillo 28 Aug '06

28 Aug '06

Hi all, I need to change the chain ID for a protein, that is, change the chain A to chain B. Can I do that with chimera? Thanks in advance Yunierkis

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addH/removeH for charged a.a.
by Dave Roe 26 Aug '06

26 Aug '06

Is there functionality that will - add a hydrogen (if needed) to all Lysines and Arginines to give the protonated form - remove a hydrogen (if needed) from Aspartic and Glutamic acids to give the deprotonated form? -- Dave Roe roex0050(a)umn.edu

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Volume color zones
by hsosa＠aecom.yu.edu 21 Aug '06

21 Aug '06

Is is possible to use different colors for different Volume zones ?. I have a volume (MRC format) and have defined two marker sets using the Volume-Path-Tracer. Then I select one of the path and colored the surface volume around using the Volume Color Zone utility. This work fine but then if I selected the other markers and do the same the volume close to the new markers get colored but anything else get uncolored, including the areas previously colored. Am I doing something wrong ?. Can I color several Volume zones independently ? Thanks Hernando --

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RealD (Stereographics) E2SGI emitter on Quadro 3450?
by Sabuj Pattanayek 18 Aug '06

18 Aug '06

Hi all, Anyone know if it's possible to use a RealD (Stereographics) E2SGI emitter on Quadro hardware? Thanks, Sabuj Pattanayek

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addH utility and PDB files
by Nihshanka Debroy 15 Aug '06

15 Aug '06

Hi, I have a couple of questions about the addH utility built into Chimera, and about PDB files in general. I used addH to protonate (add hydrogens) to PDB files. Does it use a force field of some kind in the process, like Amber or Charmm? It seems that depending on the force field used to protonate a PDB, the values for the partial charges and the van der waals radii are different. Specifically, I am using these charges and radii in the DelphiController. Another thing I've noticed is that when adding hydrogens, for the same amino acid, the hydrogens are sometimes different in name or number. For example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added for the gamma sulphur, balancing out charges completely. In other cases, the HG is not added, and so the amino acid ends up with a net negative charge. I was just wondering if this is supposed to happen. Here's another example. For Alanine, I was getting 1H, 2H and 3H attached to the nitrogen in some cases. In other cases, I just got "H" attached to the nitrogen. Does this mean those particular instances of ALA in the PDB had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a net negative charge on the ALA? Thanks for all the help and for this mailing list. It is a wonderful resource. Sincerely, Nihshanka Debroy

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Surfactant
by Annalisa Mercuri 14 Aug '06

14 Aug '06

Hallo everybody, I'm working with surfactants and emulsions. I'd like to use Chimera to reconstruct a micelle with my components, but I have no clue how to do that. Further my emulsion is made by a mixture of two surfactants. I would like to have a emulsion droplet image like the virus one. What do you suggest? Thank you for your help and advices Annalisa Mercuri MSc PhD Student School of Chemical Sciences and Pharmacy University of East Anglia Norwich Norfolk NR4 7TJ UK

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structure slice
by Raquel Hernandez 14 Aug '06

14 Aug '06

Hello chimera e-mail, I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks. Raquel Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047

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Fwd: Chimera and Macs
by Elaine Meng 14 Aug '06

14 Aug '06

Hello Mac users! When the Chimera window gets obscured by other windows on a Mac, clicking the X11 icon will bring it to the front (assuming you are using the recommended Mac/X11 version of Chimera). Begin forwarded message: > From: Kevin Dalby <dalby(a)mail.utexas.edu> > Date: August 13, 2006 11:54:43 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Chimera and Macs > > Hi Elaine > > I think we spoke briefly at the enzymes GRC. > > I am not a sophisticated chimera user. I use it on my mac while > working with another 10 programs . Usually i cant see the chimera > screen when i need it. Normally, when I want to get back to a > program that is hidden i go to the doc and just click on the > program icon and it comes to the front. This does not happen for > chimera. I know other spoilt mac users would enjoy a remedy. > > > best wishes > > Kevin > > > Kevin Dalby > Associate Professor of Medicinal Chemistry > University of Texas at Austin > tel 512-4719267 > fax 512-2322606 > > > > ----- 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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spaceball
by Mario Halic 09 Aug '06

09 Aug '06

hi!, can I use spaceball 5000 as input device in chimera? thanks, Mario

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Re: [Chimera-users] Electrostatic Potentials
by Thomas Goddard 08 Aug '06

08 Aug '06

Hi Nihshanka, Oops! My previous descriptions of how to determine electrostatic potential values at specific surface points assumed you were using the Surface Color tool to display the potential (menu entry Tools / Structure&Binding Analysis / Electrostatic Surface Coloring, or menu entry Tools / Volume Data / Surface Color). But you are using DelphiController and it has its own code for displaying potential values for which my previously described techniques will not work. To print the potential values at every surface point when the potential display was done with Delphi Controller you could put a print statement in chimera/share/DelphiViewer/MSMSTexturer.py at line 155, after the following lines of code else: # Point is outside of phi map. phivalue = 0 add the line print v_rs, phivalue Make sure the "print" line is indented the same as the "else:". This is going to print many thousands of lines in the Reply Log so be prepared to wait a bit. You could also use my previously described methods for showing potential values by using the Electrostatic Surface Coloring tool. Show a surface for your PDB model using Actions / Suface / show. Then in the Electrostatic Surface Coloring dialog press the "Open map data..." button and select the *.phi file generated by DelPhi (the one computed when running Delphi Controller). Then press the Color button on the surface color dialog. My previous code modification or the marker probe method could them be used. Tom

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Electrostatic Potentials
by Nihshanka Debroy 07 Aug '06

07 Aug '06

Hi everyone, I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes. Also, is there a way to get the actual potential values at each surface coordinate? Thanks a lot for the help. Sincerely, Nihshanka

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coloring carbon and deleting hydrogens
by Narender Singh Maan 04 Aug '06

04 Aug '06

Dear all, I am trying to show two residues of a protein structure with 50% surface transparency along with a stick model (rest of the protein is 0% surface transparent). Now in this i am having trouble in showing those stick residues in a different color (for e.g. the default for C atom is gray, which i want to show in green). Is there anyway in which i can do it?. also for those two residues i want to delete the hydrogens (only in stick, and not in surface representation)? any suggestions would be of great help. Thank you

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Coloring binding modes according to an energy term with ViewDock
by Vincent Zoete 04 Aug '06

04 Aug '06

Hi, Does it exist a way to color the different ligand positions obtained during a docking run, and displayed by the Viewdock module of chimera, as a function of a given energy term present in the columns of the viewdock table? If not, I think this could be an useful option to add to chimera. Also, it could be interesting to have the possibility to display the color scale as a function of the energy term together with the structures. If it cannot be done in the chimera display, it could be in the generated figures. Otherwise, congratulation for the great job the UCSF computer graphics lab is making with Chimera! Thank you for your time. Sincerely, Vincent

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Re: [Chimera-users] X3D to VRML conversion
by Thomas Goddard 01 Aug '06

01 Aug '06

> Date: Tue, 01 Aug 2006 12:27:52 -0700 > From: Ben Morris > > Hey Tom, > > Were you using the chimera VRML viewer when you tested the new x3d2vrml > output? I had the same exact problem in my testing of the code before > submitting it, and Conrad told me that the Chimera vrml viewer is less > than perfect when it comes to complex geometry (surfaces and ribbons). I > don't know if you were using Chimera, or even if it is the only problem, > but when I tested the code using a third party viewer, ribbons and > surfaces worked fine! > > ~Ben Hi Ben, Yeah, I tested Chimera VRML output by reading it back into Chimera. I agree that the fact that ribbons did not display properly could very well be a problem with the Chimera VRML renderer rather than the output. I just displayed a Chimera round ribbon (1a0m) using FreeWRL 1.15 on Linux and it displayed correctly. It gave about 30 warnings like the following which may or may not be important: WARNING -- node Normal may not be ok as a field of type normal (...called from VRML::Field::SFNode, 1363) It sounds like you are the one who have worked on the Chimera VRML output rather than Greg. Thanks for working on this. I think it will be useful to many people. Tom

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X3D to VRML conversion
by Nihshanka Debroy 01 Aug '06

01 Aug '06

Hi Dr. Meng, Thank you for your informative reply. That was very helpful. I was wondering if I could ask another quick question. I don't think that in Chimera, using the VRML format one can save non-surface information, like the backbone structure of a peptide (but one can display it). So I saved the information in X3D. And now, I'm trying to convert back to VRML format to be able to display it. I got completely lost when looking for some software to do this conversion. I tried using something called X3D to VRML97, but got a "segmentation fault" when I tried to open up the created VRML file. Has anyone faced this sort of an issue ? Thanks a lot, Nihshanka

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