Hi all, I am new of chimera and I am trying to display the NOEs that I have used in my calculations along with the structured I have obtained. With my big surprise I have discovered that in a previous version of the program (MIDAS) this was possible (by the command NOESHOW), but it seems that this features is not supported in this version of the program. Do you have any clue in how to resolve this? Is there a workaround or I have to use another program? If this is the case, which program (sometimes I need to display an Amber restraint file or a Discover restraint file). Thanks in advance for your help
Hi Randazzo, Sorry about the slow reply, I had to dig up my old Midas manual and read about NOESHOW. Currently there is nothing in Chimera that (like NOESHOW) reads constraints/restraints from files and displays them on structures. We have discussed adding similar capabilities, but it has not been done. Related things you can do now in Chimera are: - measure and display distances <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
- measure angles <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
- rotate torsions, with automatic update of any distance measurements <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
- draw lines between any pair of atoms, with control over color and optional label of each line. You would do that by creating a simple text file describing the lines and reading it in with Pseudobond Reader. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
However, you would still have to calculate the violations yourself and assign colors accordingly -- not nearly as automatic and convenient as using NOESHOW. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 24, 2009, at 8:52 AM, Randazzo Antonio wrote:
Hi all,
I am new of chimera and I am trying to display the NOEs that I have used in my calculations along with the structured I have obtained. With my big surprise I have discovered that in a previous version of the program (MIDAS) this was possible (by the command NOESHOW), but it seems that this features is not supported in this version of the program. Do you have any clue in how to resolve this? Is there a workaround or I have to use another program? If this is the case, which program (sometimes I need to display an Amber restraint file or a Discover restraint file).
Thanks in advance for your help
On Apr 27, 2009, at 9:39 AM, Elaine Meng wrote:
- draw lines between any pair of atoms, with control over color and optional label of each line. You would do that by creating a simple text file describing the lines and reading it in with Pseudobond Reader. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
However, you would still have to calculate the violations yourself and assign colors accordingly -- not nearly as automatic and convenient as using NOESHOW.
Also, if the violation criteria were uniform, or only depended on heavy-atom element types or atom types, then it wouldn't be too hard to write a Python script to color the pseudobonds after they were read in. More sophisticated analysis that noeshow was capable of, such as exponential averaging across an ensemble of structures, would be some work though. --Eric
participants (3)
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Elaine Meng -
Eric Pettersen -
Randazzo Antonio