Re: [ccp4bb] Question on calculation of RMSD
My favorite tools for doing this are: http://webapps.embl-hamburg.de/rapido/ and/or http://www.theseus3d.org/ Reading some of the associated papers will not hurt inchoosing when to apply which one! A On Nov 14, 2010, at 22:52, E rajakumar wrote: Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan- Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] Question on calculation of RMSD
The lowest rmsd might not be the biological relevant one True, however the least square fit using the right residues (thus producing the lowest rmsd possible) can really tell you the most significant differences (or not signifcant ones) that cause biological changes. Human eyes are often not good in doing this. Using automated lsq fit programs can give you precise (initial) information using the lowest human effort and low chance of human error. Clement As confucius would say, don't trust the output of a program if you have not programmed it yourself or know what it's doing. Last words of wisdom for tonight. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote: DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the pairwise alignment function. It is all automatic and will give you the lowest rmsd. Note, however, that it will omit parts that are very different for calculation. Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the residues you want to use for calculation for the lsq fit function. Regards, Clement Angkawidjaja, PhD Specially Appointed CMP Assistant Professor Graduate School of Engineering Osaka University 2-1 Yamadaoka GSE Commoon East 8F Suita-shi, Osaka 565-0871, Japan Tel/Fax +81-6-6879-4580 http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html /// G30 Chemistry/Biology Combined Major Program http://cmp.sci.osaka-u.ac.jp/CMP/ -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
Take any protein where a helix moves as a rigid body and look at your results. Then fix the alpha helix and superimpose the rest of the structure on that moving helix and compare both results. If you want to give it a shot try 2pc4 and the unliganded structure. You see the difference in both methods ? From a structural/functional perspective one method will highlight the real differences in terms of movements. For an initial understanding I recommend SSM and a morphing movie, that helps dissecting what might be going on. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Nov 16, 2010, at 19:58, Clement Angkawidjaja clem...@bio.mls.eng.osaka-u.ac.jp wrote: The lowest rmsd might not be the biological relevant one True, however the least square fit using the right residues (thus producing the lowest rmsd possible) can really tell you the most significant differences (or not signifcant ones) that cause biological changes. Human eyes are often not good in doing this. Using automated lsq fit programs can give you precise (initial) information using the lowest human effort and low chance of human error. Clement As confucius would say, don't trust the output of a program if you have not programmed it yourself or know what it's doing. Last words of wisdom for tonight. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote: DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the pairwise alignment function. It is all automatic and will give you the lowest rmsd. Note, however, that it will omit parts that are very different for calculation. Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the residues you want to use for calculation for the lsq fit function. Regards, Clement Angkawidjaja, PhD Specially Appointed CMP Assistant Professor Graduate School of Engineering Osaka University 2-1 Yamadaoka GSE Commoon East 8F Suita-shi, Osaka 565-0871, Japan Tel/Fax +81-6-6879-4580 http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html /// G30 Chemistry/Biology Combined Major Program http://cmp.sci.osaka-u.ac.jp/CMP/ -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed firstmonomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
I think it is still hard to beat lsq_imp as implemented in 'O'. http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_e-l.html#anchor1342614 Cheers, Martin On Nov 15, 2010, at 2:32 AM, Clement Angkawidjaja wrote: DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the pairwise alignment function. It is all automatic and will give you the lowest rmsd. Note, however, that it will omit parts that are very different for calculation. Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the residues you want to use for calculation for the lsq fit function. Regards, Clement Angkawidjaja, PhD Specially Appointed CMP Assistant Professor Graduate School of Engineering Osaka University 2-1 Yamadaoka GSE Commoon East 8F Suita-shi, Osaka 565-0871, Japan Tel/Fax +81-6-6879-4580 http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html /// G30 Chemistry/Biology Combined Major Program http://cmp.sci.osaka-u.ac.jp/CMP/ -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
I would first calculate least square superposition of the first monomer between 2 structures (one to be fixed and one to be moved) using a program such as lsqkap or any other programs suggested by others. You may need to define a relevant region for the superimposition. Then take the output of the moved structure and calculate another least square superposition of the second monomer in the dimer to the second monemer of the fixed structure. Look at the rotation and translation matrix from the output (or log file). That will give you information of how the second monomer is different in the 2 structures. You can calculate the orientation difference (in degrees) from trace of the rotation matrix. Alternatively, after the first monomers are superimposed, you can use program lsqman (or other programs that calculate rmsd of the second monomers without doing least square superposition) if you prefer an rmsd value instead of a rotational angle. George Wisedchasri On Sun, 14 Nov 2010, E rajakumar wrote: Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
Raj, There are many programs that will give you an RMSD per residue difference between your bound and un-bound protein. Some will even write the RMSDs to the B-factor column of your PDB. You can then visualize regions in your protein that have structural changes/movement in the bound vs. unbound by using B-factor putty in Pymol or coloring by B-factor. I refer you to a previous post on the subject in the CCP4BB archives: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14496.html On Mon, Nov 15, 2010 at 1:07 PM, Goragot Wisedchaisri gora...@u.washington.edu wrote: I would first calculate least square superposition of the first monomer between 2 structures (one to be fixed and one to be moved) using a program such as lsqkap or any other programs suggested by others. You may need to define a relevant region for the superimposition. Then take the output of the moved structure and calculate another least square superposition of the second monomer in the dimer to the second monemer of the fixed structure. Look at the rotation and translation matrix from the output (or log file). That will give you information of how the second monomer is different in the 2 structures. You can calculate the orientation difference (in degrees) from trace of the rotation matrix. Alternatively, after the first monomers are superimposed, you can use program lsqman (or other programs that calculate rmsd of the second monomers without doing least square superposition) if you prefer an rmsd value instead of a rotational angle. George Wisedchasri On Sun, 14 Nov 2010, E rajakumar wrote: Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] Question on calculation of RMSD
Coot And I would use LSQKAB instead of the SSM method. First look at what stays rigid in one subunit and define those residues for the superposition, then look at the text window where it will report you the rmsd for each position and chain. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Nov 14, 2010, at 4:52 PM, E rajakumar wrote: Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the pairwise alignment function. It is all automatic and will give you the lowest rmsd. Note, however, that it will omit parts that are very different for calculation. Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the residues you want to use for calculation for the lsq fit function. Regards, Clement Angkawidjaja, PhD Specially Appointed CMP Assistant Professor Graduate School of Engineering Osaka University 2-1 Yamadaoka GSE Commoon East 8F Suita-shi, Osaka 565-0871, Japan Tel/Fax +81-6-6879-4580 http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html /// G30 Chemistry/Biology Combined Major Program http://cmp.sci.osaka-u.ac.jp/CMP/ -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
The lowest rmsd might not be the biological relevant one As confucius would say, don't trust the output of a program if you have not programmed it yourself or know what it's doing. Last words of wisdom for tonight. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote: DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the pairwise alignment function. It is all automatic and will give you the lowest rmsd. Note, however, that it will omit parts that are very different for calculation. Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the residues you want to use for calculation for the lsq fit function. Regards, Clement Angkawidjaja, PhD Specially Appointed CMP Assistant Professor Graduate School of Engineering Osaka University 2-1 Yamadaoka GSE Commoon East 8F Suita-shi, Osaka 565-0871, Japan Tel/Fax +81-6-6879-4580 http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html /// G30 Chemistry/Biology Combined Major Program http://cmp.sci.osaka-u.ac.jp/CMP/ -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] Question on calculation of RMSD
Andrew Martin's ProFit program is another option: http://www.bioinf.org.uk/software/profit/doc/node11.html Having fitted the structures using the ZONE and ATOMS commands to specify which residues and atoms should be included in the fitting, the RMS deviation may then be calculated over a different region of the structure and/or a different atom set. This is achieved using the RZONE and RATOMS commands. The syntax of these commands is identical to that of the ZONE and ATOMS commands described in Sections 8 and 9. -Eric -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) -- -- Eric Bennett, er...@pobox.com Drawing on my fine command of the language, I said nothing. -Robert Benchley
