- Chimera-users - RBVI Mailing Lists

color a residue
by Xuehong Liu 05 Sep '06

05 Sep '06

Hi, I chose the target as "selected residues", then selected the residue I want to put certain color on, but only a bond color was changed when I did that. However, if I did not select a residue, then the color option will change the color for the whole helix selected. thank Xuehong Xuehong Liu, Ph.D Research Assistant Professor Department of Physiology/Pharmacology Oregon Health & Science University 3181 SW Sam Jackson Park Rd. L334 Portland, OR 97239 phone: (503) 494-3230 fax: (503) 494-4352

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PDB Coordinates
by Albion Baucom 01 Sep '06

01 Sep '06

I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from. Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation? I am using beta version 1 build 2199 01/24/2006 on a linux platform. Thanks Albion

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how to save a copy of the reply log via command line
by Cathy Lawson 01 Sep '06

01 Sep '06

Hi, I'd like to issue a command-line command within a python script read into chimera to save a copy of the reply log. I tried googling the chimera site but didn't find the answer--what would be the command to do this? thanks, Cathy

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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 19 Aug '06

19 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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