Dear Hari, Thanks so much for your kind words! We try very hard to make useful tools and to answer everyone's questions. (1) FindHBond. I can't say exactly what happened without seeing your input and knowing each step you tried. However, here are some guesses. "inter-model" means between two different input files. Did you open the two proteins from two different files? If they are in the same file you should use "intra-model" (or "both") instead. Then, if you only want to look for H-bonds *between* the proteins, you could select one of the proteins and then set the option "Only find H-bonds with [exactly one end] selected." FindHBond also has variable "Relax H-bond constraint" parameters, but the defaults ("Relax..." turned on, 0.4 angstroms, 20 degrees) are generally reasonable. Manual page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... (2) Find Clashes/Contacts. The meaning of your results depends on what values you use. The manual page gives suggested ranges of values for finding "clashes" (unfavorable interactions where the atoms are too close together) and "contacts" (atoms within favorable interaction distances - thus all kinds of interactions, polar and nonpolar, plus the clashes): "For detecting clashes, cutoff values of 0.4-1.0 Å and allowance values of 0.2-0.6 Å are generally reasonable (default criteria 0.6 and 0.4 Å, respectively). For detecting contacts, negative cutoff values of 0.0-(–1.0) Å with an allowance of 0.0 Å are generally reasonable (default contact criteria – 0.4 and 0.0 Å, respectively)." If you are using the graphical interface, you can just click the buttons "Default [clash]/[contact] criteria" to insert the default values, which are within the suggested ranges. There is no single best number because it depends on the quality of your structure and for what purpose you are planning to use the results. You have to use your judgement. The quality of the results also depends on the quality of your input structure, not just on what numbers you use. However, in most cases, values in the suggested ranges are appropriate. We use published VDW radii and have tried the values on many structures. Just make sure you use the clash range if you want clashes, the contact range if you want contacts! For publication purposes, you could just say you used this tool with recommended values to find contacts (or clashes). It is not necessary to add hydrogens. Manual page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash... VDW radii: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html For example, if I open 2gbp (glucose binding protein and glucose; does not have hydrogens), select ligand (glucose), click Designate, check against "all other atoms" and then use the default clash criteria, nothing is found. There are no clashes with the glucose. If I use the default contact criteria, there are 52 atom-atom contacts between the glucose and the binding protein. I chose the option to "Select" the atoms. Then Selection Inspector (Actions... Inspect) tells me that 14 residues and 39 atoms are selected. If I deselect the glucose (command: ~sel ligand) then 13 residues and 27 atoms are selected. These are the protein residues and water residues interacting with the glucose. If you are using values in the recommended range for clashes and get very many clashes, it may be that the docking program tends to put atoms close together. That doesn't mean the program is bad, just that it generates approximate positions. (3) There IS a minimization tool, see Tools... Structure Editing... Minimize Structure! However, it may not meet your definition of user- friendly, and it is fairly slow. Calculations like minimization that involve force fields tend to be complicated because they involve many parameters, such as the size and charge of each atom. You have to add hydrogens, but the tool will guide you through the process. You might want to select as many atoms as possible to be "frozen" (held fixed) in place during the minimization. Fewer movable atoms makes the calculation faster. Man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h... As an alternative to minimization, you might want to take a look at the Rotamers tool (under Tools... Structure Editing). With this tool you can see if different non-clashing conformations of the sidechains may be possible. Using this would only be reasonable if there are only a few clashing side chains here and there, not a big cluster, and if backbone motion is not required. Maybe you are already using the Rotamers tool to make your mutations! Man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h... I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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 On Apr 25, 2008, at 3:49 PM, Harinathachari Bahudhanapati wrote:
Dear chimera support, I am a huge fan of chimera and I have so say I spend a lot of time on chimera these days, as a part of writing for my dissertation. I have a few questions and I sincerely you to request to help me out.
1. About findHbond: I never seem to get this one right. I model Enzyme-inhibitor complexes on patchdock. The inhibitor templates are either pdbs from rcsb or modelled on swissmodel. I am not able to locate or find any hbonds newly formed in the docked models, when I search for intermodel hbonds (I am looking for protein-protein interactions). Are there any special criteria or am I missing some thing? I want something similar to that of the output of HBPLUS (I never seem to get this working either - very frustrating)
2. About find clashes: What are the ideal parameters for clashes and contacts. I tried several things, they give me several no of overlaps for several different parameters. Are these vanderwaals interactions? because some times I see more than 40 interactions between two residues -i.e., between the atoms of Enzyme and inhibitor? How reliable are these interactions (I need to publish my data) This tool does not seem to work unless I add hydrogens to both the chains.
3. It would be great, if there was a energy minimization tool in chimera because I introduce mutations. Please kindly suggest me if there are any easy to use tools for this. I tried COOT and swisspdbviewer, but not really that user-friendly.
I read all the newsletter e-mails from CHIMERA users-list everyday. Thanks to Elaine, tom, eric and conrad. You guys rock.. sincerely Hari hbahudha@fau.edu