- Chimera-users - RBVI Mailing Lists

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

4 3

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

2 1

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

2 1

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

1 0

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

2 1

about installation of Chimera in SUSE Linux 10.0 plateform
by Ching-Yi Hsieh 31 Jul '06

31 Jul '06

Hi, I have trouble to install Chimera in in SUSE Linux 10.0 plateform. Can you e-mail me the detail instruction about how to install soon??? Best, Dr. ChingYi Hsieh UCDavis Cancer Center

2 1

Chimera and DelphiController
by Nihshanka Debroy 31 Jul '06

31 Jul '06

Hi, My name is Nihshanka Debroy, and I am a graduate student at Duke University. I recently joined this mailing list. I was wondering if I could ask a couple of questions about the software. The first one is more related to Delphi. I have been using the Delphi Controller tool in Chimera, and I have been getting warnings that certain radii records are missing from my .siz file, and some residues have a net positive charge. I used the default files provided when installing Delphi. I was wondering if anyone has faced this problem before. Is there an online database where I could get the missing radii and charge values for atoms and residues ? Secondly, I am trying to generate the Connolly surface for certain proteins. What I have been doing so far is running Delphi Controller and assigning a probe radius of 1.4 Angstroms in the Parameter section. I just wanted to make sure that this is different from the molecular surface (MS) that is generated when simply choosing Actions->Surface->Show. Thank you for your time. Sincerely, Nihshanka

2 1

Segmentation Fault
by Donglu Xie 24 Jul '06

24 Jul '06

Hi All, Anybody has met this issue. When running chimera, it only shows "Segmentaion Fault", or " Segmentaion Fault (core dump)". No interface is shown. If you need more information about the system, please let me know. Any help is appreciated. Donglu Xie

2 2

Surface color key
by Alexander Rusnak 19 Jul '06

19 Jul '06

Hey Folks, I'm using Chimera to create a surface colored representation of a virus based on radius. That was not the hard part, my question is how do you make a key to show the scale of coloring. I cannot find that in the documentation, faq nor the server list. If it's there and I missed it sorry but you point it out to me and if it's not an option any suggestions on how to create one. Thanks. Alex

2 1

write out adjusted EM map?
by jbrown 19 Jul '06

19 Jul '06

Hi, I've recently used Chimera to manually fit several PDB subunits into my EM map. I am trying to figure out a way to write out the EM map in CCP4 format with the adjusted rotation/translations that I performed during my fit. Is there anyway to do this in Chimera (or are there any other programs you would suggest)? Also, any plans to include a means for writing out EM maps from Chimera in future versions? Thanks a lot, Jesse --------------------------- Jesse Brown Research Technician TSRI, Dept. of Cell Biology 858.784.8598 jbrown(a)scripps.edu

3 2