Re: [ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins
Thanks to the mailing list I came across this: http://www.ncbi.nlm.nih.gov/pubmed/24167157 The C code to compute is available on the link mentioned in the paper. Best wishes, George On Wed, Aug 13, 2014 at 8:01 AM, Eugene Krissinel < eugene.krissi...@stfc.ac.uk> wrote: > It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather > than PISA -- Eugene > > On 13 Aug 2014, at 12:33, Eleanor Dodson wrote: > > I think PISA does this for you - it overlaps structural features and gives > an RMSD on those parts that fit and a useful list of matching residues. > You can run it from CCP4I or at PDBe. > > If you ant more than CA RMSD then you will need to select out the spans to > fit and use the LSQKAB overlap procedure > FIT MAIN RESi n n+m CHAIN A > MATCH RESI b b+m CHAIN C > > FIT …. > > etc > > for example - you can do that in the GUI > > Eleanor > > > On 13 August 2014 02:48, herman.schreu...@sanofi.com>> wrote: > Dear Sreetama, > > I use an ancient superposition program which rejects all atom pairs > deviating more than 3 sigma and repeats this procedure until convergence. > It then reports the RMSD for all atoms and for the atoms deviating less > than 3 sigma. I find this an excellent method to separate the core from > variable loop regions. It also ensures a robust superposition of the cores, > ignoring variable loops. > > Best, > Herman > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von sreetama das > Gesendet: Mittwoch, 13. August 2014 08:12 > An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > Betreff: [ccp4bb] RMSD between structures of homologous proteins > > Dear all, >When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > should be reported - an overall value which may be inflated due to the > deviations in the loops, or separate values for the core and loop regions? > What is the best way to calculate the RMSD for superposition of the cores > - should I prepare a separate PDB file by removing the coordinates of the > loop residues and then superpose? > > Thanks in advance, > Sreetama das, > PhD student, > Physics, IISc > > > > -- > Scanned by iCritical. > >
Re: [ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins
It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather than PISA -- Eugene On 13 Aug 2014, at 12:33, Eleanor Dodson wrote: I think PISA does this for you - it overlaps structural features and gives an RMSD on those parts that fit and a useful list of matching residues. You can run it from CCP4I or at PDBe. If you ant more than CA RMSD then you will need to select out the spans to fit and use the LSQKAB overlap procedure FIT MAIN RESi n n+m CHAIN A MATCH RESI b b+m CHAIN C FIT …. etc for example - you can do that in the GUI Eleanor On 13 August 2014 02:48, mailto:herman.schreu...@sanofi.com>> wrote: Dear Sreetama, I use an ancient superposition program which rejects all atom pairs deviating more than 3 sigma and repeats this procedure until convergence. It then reports the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find this an excellent method to separate the core from variable loop regions. It also ensures a robust superposition of the cores, ignoring variable loops. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von sreetama das Gesendet: Mittwoch, 13. August 2014 08:12 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [ccp4bb] RMSD between structures of homologous proteins Dear all, When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should be reported - an overall value which may be inflated due to the deviations in the loops, or separate values for the core and loop regions? What is the best way to calculate the RMSD for superposition of the cores - should I prepare a separate PDB file by removing the coordinates of the loop residues and then superpose? Thanks in advance, Sreetama das, PhD student, Physics, IISc -- Scanned by iCritical.
Re: [ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins
I think PISA does this for you - it overlaps structural features and gives an RMSD on those parts that fit and a useful list of matching residues. You can run it from CCP4I or at PDBe. If you ant more than CA RMSD then you will need to select out the spans to fit and use the LSQKAB overlap procedure FIT MAIN RESi n n+m CHAIN A MATCH RESI b b+m CHAIN C FIT …. etc for example - you can do that in the GUI Eleanor On 13 August 2014 02:48, wrote: > Dear Sreetama, > > > > I use an ancient superposition program which rejects all atom pairs > deviating more than 3 sigma and repeats this procedure until convergence. > It then reports the RMSD for all atoms and for the atoms deviating less > than 3 sigma. I find this an excellent method to separate the core from > variable loop regions. It also ensures a robust superposition of the cores, > ignoring variable loops. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *sreetama das > *Gesendet:* Mittwoch, 13. August 2014 08:12 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] RMSD between structures of homologous proteins > > > > Dear all, > >When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > should be reported - an overall value which may be inflated due to the > deviations in the loops, or separate values for the core and loop regions? > > What is the best way to calculate the RMSD for superposition of the cores > - should I prepare a separate PDB file by removing the coordinates of the > loop residues and then superpose? > > > > Thanks in advance, > > Sreetama das, > > PhD student, > > Physics, IISc >
[ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins
Dear Sreetama, I use an ancient superposition program which rejects all atom pairs deviating more than 3 sigma and repeats this procedure until convergence. It then reports the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find this an excellent method to separate the core from variable loop regions. It also ensures a robust superposition of the cores, ignoring variable loops. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von sreetama das Gesendet: Mittwoch, 13. August 2014 08:12 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] RMSD between structures of homologous proteins Dear all, When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should be reported - an overall value which may be inflated due to the deviations in the loops, or separate values for the core and loop regions? What is the best way to calculate the RMSD for superposition of the cores - should I prepare a separate PDB file by removing the coordinates of the loop residues and then superpose? Thanks in advance, Sreetama das, PhD student, Physics, IISc
Re: [ccp4bb] RMSD between structures of homologous proteins
Sreetama, See the following URL whether it is useful to solve your issue http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar > Dear all, > When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > should be reported - an overall value which may be inflated due to the > deviations in the loops, or separate values for the core and loop regions? > What is the best way to calculate the RMSD for superposition of the cores > - should I prepare a separate PDB file by removing the coordinates of the > loop residues and then superpose? > > Thanks in advance, > Sreetama das, > PhD student, > Physics, IISc > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > Could you kindly confirm the safe receipt of the mail please. All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Supercomputer Education and Research Centre Room No. 341, old Ecological Sciences Building (Second Floor) Indian Institute of Science Bangalore 560 012 INDIA E-mail:se...@physics.iisc.ernet.in se...@serc.iisc.ernet.in Tel: 91-(0)80-22933059/22933060/23600551 Fax: 91-(0)80-23600085 Home page: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html Google Scholar: http://scholar.google.co.in/citations?hl=en&user=CT0Z5kIJ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] RMSD between structures of homologous proteins
Dear all, When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should be reported - an overall value which may be inflated due to the deviations in the loops, or separate values for the core and loop regions? What is the best way to calculate the RMSD for superposition of the cores - should I prepare a separate PDB file by removing the coordinates of the loop residues and then superpose? Thanks in advance, Sreetama das, PhD student, Physics, IISc
