Re: [ccp4bb] Command line tool for RMSD calculation
Dear all, Thanks a lot for your input. Later I found a R package called bio3d that is very suitable for my purpose. Best, Chen On Wed, Oct 15, 2014 at 5:53 PM, Steven Chou stevezc...@gmail.com wrote: Hi Chen, I used SUPPOSE previously. It worked very well. The compositions of the structures have to be the same! It works on Linux. http://structbio.vanderbilt.edu/~jsmith/suppose/ If the compositions of your structures are different, you may first load them to PyMOL, then align them use its commandline. http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ If the compositions/sequences of your structures are very very different, but their overall structure are similar, you can do the alignment using a PyMOL plugin called 'cealign'. It works on both Mac and Linux. http://pymolwiki.org/index.php/Cealign Here is my note on how to run SUPPOSE. remove the outputs from the previous runs rm -rf *.rot.pdb mean.pdb all.pdb # if the input file names are XXX.pdb, those of the output files are XXX.rot.pdb and a mean.pdb fit the structrue models based on the CA atoms, and then calculate the RMSD of the backbone atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C,CA,N restrt_*.pdb # 0.639 fit the structrue models based on the CA atoms, and then calculte the RMSD of the heavy atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C*,N*,O*,S* restrt_*.pdb # 1.23 # Do not visulize the rotated pdb files with molmol at this step, because molmol will shift the individual files. # That is, the output files have already been perfectly supperimposed, # but molmol gives an illusion that they have not been rotated correctly. join the pdb with the AWK script ./joinpdb -o all.pdb *.rot.pdb # input files: *.rot.pdb # output file: all.pdb display the rotated pdb with molmol now. molmol all.pdb # molmol can only display the combined pdb (i.e., 20 models in one file) correctly!!! HTH, Steven On Wed, Oct 15, 2014 at 4:05 PM, Chen Zhao c.z...@yale.edu wrote: Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen -- Steven Chou
Re: [ccp4bb] Command line tool for RMSD calculation
Mentioned recently but worth mentioning again? I have used Chimera rmsd from its own command line (find the command line under the 'favorites' tab) - it is scriptable. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html Must have equal number of atoms matched - use selection to make that true - for example restricting to Calpha atoms. Cheers - Martyn Cambridge Original message From : c.z...@yale.edu Date : 15/10/2014 - 21:05 (GMTDT) To : CCP4BB@JISCMAIL.AC.UK Subject : [ccp4bb] Command line tool for RMSD calculation Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen
[ccp4bb] Command line tool for RMSD calculation
Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen
Re: [ccp4bb] Command line tool for RMSD calculation
Hi Chen, I used SUPPOSE previously. It worked very well. The compositions of the structures have to be the same! It works on Linux. http://structbio.vanderbilt.edu/~jsmith/suppose/ If the compositions of your structures are different, you may first load them to PyMOL, then align them use its commandline. http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ If the compositions/sequences of your structures are very very different, but their overall structure are similar, you can do the alignment using a PyMOL plugin called 'cealign'. It works on both Mac and Linux. http://pymolwiki.org/index.php/Cealign Here is my note on how to run SUPPOSE. remove the outputs from the previous runs rm -rf *.rot.pdb mean.pdb all.pdb # if the input file names are XXX.pdb, those of the output files are XXX.rot.pdb and a mean.pdb fit the structrue models based on the CA atoms, and then calculate the RMSD of the backbone atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C,CA,N restrt_*.pdb # 0.639 fit the structrue models based on the CA atoms, and then calculte the RMSD of the heavy atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C*,N*,O*,S* restrt_*.pdb # 1.23 # Do not visulize the rotated pdb files with molmol at this step, because molmol will shift the individual files. # That is, the output files have already been perfectly supperimposed, # but molmol gives an illusion that they have not been rotated correctly. join the pdb with the AWK script ./joinpdb -o all.pdb *.rot.pdb # input files: *.rot.pdb # output file: all.pdb display the rotated pdb with molmol now. molmol all.pdb # molmol can only display the combined pdb (i.e., 20 models in one file) correctly!!! HTH, Steven On Wed, Oct 15, 2014 at 4:05 PM, Chen Zhao c.z...@yale.edu wrote: Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen -- Steven Chou
