Re: [ccp4bb] Normal mode refinement
Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
Re: [ccp4bb] Normal mode refinement
Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 21 October 2014 07:39, Appu kumar appu.kum...@gmail.com wrote: Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
Re: [ccp4bb] Normal mode refinement
On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote: Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. Please keep in mind that if the density is poor because the protein really is disordered, a perfect description of those disordered cell contents will perfectly reproduce that poor density. So improved description does not necessarily imply improved map quality. This is quite different from the case of a poor model for a well-ordered structure. Here also you will see a low quality map, but in this case it will improve as your description of the cell contents improves. Ethan I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in -- mail: Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] Normal mode refinement
Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu
Re: [ccp4bb] Normal mode refinement
On Monday, 20 October, 2014 18:10:03 Appu kumar wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions The previously published examples of normal-mode refinement that I know about used private external programs to generate thermal ellipsoids for each atom, and then used those as fixed ADPs while refining coordinates in refmac or similar standard program. Again speaking only of the examples I have looked at in detail, the result was better (had lower R factors) than a conventional isotropic refinement but was not nearly as good as a multi-group TLS refinement of the same structure (TLSMD + refmac). On the other hand, there is a quite different way normal modes can be used in refinement. As I understand it (perhaps Garib will add addtional details) the jellybody refinement mode of recent refmac versions can be viewed as restraining the model shifts to be consistent with the principle normal mode. In this way the normal mode contributes to the path of the refinement, but is not explicitly part of the final model. So it may be that using TLSMD + refmac jellybody TLS refinement would get you the best of both approaches, though I have not gone back to look again at the published example structures since the advent of jellybody refinement. But note that jellybody is primarily useful when you already have a high-qualityl, good geometry, starting model. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] Normal mode refinement
I agree with Ethan. In philosophy, NMA is a useful analysis to study low frequency collective motions. That is true by taking a stand-alone structure and explore such motions of biological interest. Domain motions in the crystallographic environment need not necessarily correspond to those of the isolated molecule. Also, please remember, many a times the most significant modes (say mode 7 or mode 8) in NMA do not represent the motions of biological interest. One is usually recommended to analyze many significant modes to extract the useful information, and in the extremes of argument, making at times this as a subjective exercise. In any case, I would strongly argue for TLSMD, as Ethan has pointed out, as that represents modeling disorder in crystallographic environment. In one of the examples where we were studying the relationship between NMA (for a stand-alone molecule) and TLS, we could correlate the two for the 11th and the 12th mode, suggesting clearly that 7th- 10th modes did not show a good correlation. By incorporating the 7-10th modes in crystallographic refinement, we would have clearly not made the model better! Shekhar On Tue, Oct 21, 2014 at 6:22 AM, Ethan A Merritt merr...@u.washington.edu wrote: On Monday, 20 October, 2014 18:10:03 Appu kumar wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions The previously published examples of normal-mode refinement that I know about used private external programs to generate thermal ellipsoids for each atom, and then used those as fixed ADPs while refining coordinates in refmac or similar standard program. Again speaking only of the examples I have looked at in detail, the result was better (had lower R factors) than a conventional isotropic refinement but was not nearly as good as a multi-group TLS refinement of the same structure (TLSMD + refmac). On the other hand, there is a quite different way normal modes can be used in refinement. As I understand it (perhaps Garib will add addtional details) the jellybody refinement mode of recent refmac versions can be viewed as restraining the model shifts to be consistent with the principle normal mode. In this way the normal mode contributes to the path of the refinement, but is not explicitly part of the final model. So it may be that using TLSMD + refmac jellybody TLS refinement would get you the best of both approaches, though I have not gone back to look again at the published example structures since the advent of jellybody refinement. But note that jellybody is primarily useful when you already have a high-qualityl, good geometry, starting model. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 -- Shekhar C. Mande (शेखर चिं मांडे) Director, National Centre for Cell Science Ganeshkhind, Pune 411 007 Email: shek...@nccs.res.in, direc...@nccs.res.in Phone: +91-20-25708121 Fax:+91-20-25692259
Re: [ccp4bb] Normal mode refinement
Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
