Re: Model-free analysis error
Hi Ivan, If you could create a bug report using the link https://gna.org/bugs/?func=additemgroup=relax, that would be appreciated. Please try to include as much information as possible. The best would be if you could attach a truncated data set, the minimum required to trigger the bug (slightly randomised if you would like to keep it private). If I can reproduce the bug myself, I can normally have a fix for it within 5-10 minutes. Oh, it would be good to check that you are using the latest version of relax - currently 3.1.6 (http://www.nmr-relax.com/download.html) - just in case the bug has already been fixed. Cheers, Edward On 25 March 2014 15:33, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote: Dear Edward, I have now conducted measurements (T1, T2 and NOE) in two seperate fields (600 and 700 MHz) as suggested in your previous email. I have upload six different files onto the Relaxation Data List. The data is in the following format 2 ALA 5.49631746729691 N 3 ASP 3.74279511939516 N 4 ASP 6.12594952217594 N 6 SER 6.75812664729337 N However, after I click the Dipolar relaxation button, the programme freezes up when I press Apply or Next. I encountered no problem with the other three buttons (CSA relaxation / X isotope / H isotope) I wonder if it is because I am not supplying the right type of data to the software, or if this is a python problem? Thanks and I hope to hear back from you soon! Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 10 February 2014 16:09 To: Ivanhoe Leung Cc: relax-users@gna.org Subject: Re: Model-free analysis error Hi Ivan, To continue: On another note, I wonder if it is possible to modify the nmr-relax programme so that I can do model-free analysis with data from only one field strength? Alternatively, do you know of any programme (that can be installed on Windows) that can do such analysis? My work focused mainly on small molecule and ligand-based NMR and I have only just very recently started looking in to protein dynamics so I am still experimentinng different software and data treatment etc. Firstly, the subject of single field strength data has been discussed numerous times on this mailing list. I would recommend you read my previous responses to questions relating to single field strength data, and look the other messages in those threads. You will find these discussions quite informative and highly detailed: - Martin Ballaschk: http://thread.gmane.org/gmane.science.nmr.relax.user/1409/focus=1438 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1367/focus=1369 - Mengjun Xue: http://thread.gmane.org/gmane.science.nmr.relax.user/1276/focus=1277 - Fernando Amador: http://article.gmane.org/gmane.science.nmr.relax.user/84 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1086/focus=1087 - Dhanasekaran Muthu: http://thread.gmane.org/gmane.science.nmr.relax.user/1152/focus=1153 - Vitaly Vostrikov: http://thread.gmane.org/gmane.science.nmr.relax.user/1147/focus=1150 - Aldino Viegas: http://thread.gmane.org/gmane.science.nmr.relax.user/1127/focus=1128 - Pierre-Yves Savard: http://thread.gmane.org/gmane.science.nmr.relax.user/724/focus=725 - Keith Constantine: http://thread.gmane.org/gmane.science.nmr.relax.user/513/focus=517 - Clare-Louise Evans: http://thread.gmane.org/gmane.science.nmr.relax.user/326/focus=332 - Hongyan Li: http://thread.gmane.org/gmane.science.nmr.relax.devel/694/focus=701 These will have lots of additional information. This is just a selection of possibly the most useful messages. You will soon see that this is a complicated topic. Note that relax is capable of performing 100% of the functionality of Modelfree4 (with or without the Fast-Modelfree GUI interface), Dasha, Tensor2, and DYNAMICS. If you play with the optimisation settings you can even find identical results to within machine precision - relax can mimic these other softwares. The key is that the full analysis protocol is rather complicated - many people don't understand this - and that these softwares do not implement the full iterative protocol. Therefore you either have to perform it manually or write a script to perform all of the steps. The protocol is described in the relax manual in figure 7.2 (http://www.nmr-relax.com/manual/diffusion_seeded_paradigm.html). In summary: a) Find an initial diffusion tensor estimate (you can do this in relax by only using model m0). This requires all non-mobile residues and side chain spins to be excluded, and this can be problematic. See the d'Auvergne and Gooley, 2008b paper at http://dx.doi.org/10.1007/s10858-007-9213-3 for an example of the catastrophic failure that this initial estimate can result in. Or the bacteriorhodopsin fragment of Korzhnev
RE: Model-free analysis error
Dear Edward, I have now conducted measurements (T1, T2 and NOE) in two seperate fields (600 and 700 MHz) as suggested in your previous email. I have upload six different files onto the Relaxation Data List. The data is in the following format 2 ALA 5.49631746729691 N 3 ASP 3.74279511939516 N 4 ASP 6.12594952217594 N 6 SER 6.75812664729337 N However, after I click the Dipolar relaxation button, the programme freezes up when I press Apply or Next. I encountered no problem with the other three buttons (CSA relaxation / X isotope / H isotope) I wonder if it is because I am not supplying the right type of data to the software, or if this is a python problem? Thanks and I hope to hear back from you soon! Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 10 February 2014 16:09 To: Ivanhoe Leung Cc: relax-users@gna.org Subject: Re: Model-free analysis error Hi Ivan, To continue: On another note, I wonder if it is possible to modify the nmr-relax programme so that I can do model-free analysis with data from only one field strength? Alternatively, do you know of any programme (that can be installed on Windows) that can do such analysis? My work focused mainly on small molecule and ligand-based NMR and I have only just very recently started looking in to protein dynamics so I am still experimentinng different software and data treatment etc. Firstly, the subject of single field strength data has been discussed numerous times on this mailing list. I would recommend you read my previous responses to questions relating to single field strength data, and look the other messages in those threads. You will find these discussions quite informative and highly detailed: - Martin Ballaschk: http://thread.gmane.org/gmane.science.nmr.relax.user/1409/focus=1438 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1367/focus=1369 - Mengjun Xue: http://thread.gmane.org/gmane.science.nmr.relax.user/1276/focus=1277 - Fernando Amador: http://article.gmane.org/gmane.science.nmr.relax.user/84 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1086/focus=1087 - Dhanasekaran Muthu: http://thread.gmane.org/gmane.science.nmr.relax.user/1152/focus=1153 - Vitaly Vostrikov: http://thread.gmane.org/gmane.science.nmr.relax.user/1147/focus=1150 - Aldino Viegas: http://thread.gmane.org/gmane.science.nmr.relax.user/1127/focus=1128 - Pierre-Yves Savard: http://thread.gmane.org/gmane.science.nmr.relax.user/724/focus=725 - Keith Constantine: http://thread.gmane.org/gmane.science.nmr.relax.user/513/focus=517 - Clare-Louise Evans: http://thread.gmane.org/gmane.science.nmr.relax.user/326/focus=332 - Hongyan Li: http://thread.gmane.org/gmane.science.nmr.relax.devel/694/focus=701 These will have lots of additional information. This is just a selection of possibly the most useful messages. You will soon see that this is a complicated topic. Note that relax is capable of performing 100% of the functionality of Modelfree4 (with or without the Fast-Modelfree GUI interface), Dasha, Tensor2, and DYNAMICS. If you play with the optimisation settings you can even find identical results to within machine precision - relax can mimic these other softwares. The key is that the full analysis protocol is rather complicated - many people don't understand this - and that these softwares do not implement the full iterative protocol. Therefore you either have to perform it manually or write a script to perform all of the steps. The protocol is described in the relax manual in figure 7.2 (http://www.nmr-relax.com/manual/diffusion_seeded_paradigm.html). In summary: a) Find an initial diffusion tensor estimate (you can do this in relax by only using model m0). This requires all non-mobile residues and side chain spins to be excluded, and this can be problematic. See the d'Auvergne and Gooley, 2008b paper at http://dx.doi.org/10.1007/s10858-007-9213-3 for an example of the catastrophic failure that this initial estimate can result in. Or the bacteriorhodopsin fragment of Korzhnev et al., 1999 (http://dx.doi.org/10.1023/a:1008356809071) where this complete failure was earlier demonstrated. b) Optimise all of the model-free models from m0 to m9. This requires high precision optimisation, for a comparison of all the softwares see the d'Auvergne and Gooley, 2008a model-free optimisation paper at http://dx.doi.org/10.1007/s10858-007-9214-2. Only relax and Dasha implement the full range of model-free models, though the models m6, m7, and m8 cannot be used if only single field strength data is used (m6 is the original 2-time scale motion model of Clore et al., 1990). c) Eliminate failed models (this is only available in relax, see the d'Auvergne and Gooley, 2006 model elimination paper at http://dx.doi.org/10.1007/s10858-006-9007-z). d) Select the best
RE: Model-free analysis error
Dear Edward, I have submitted a bug report as requested https://gna.org/bugs/index.php?21862 Thanks Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 25 March 2014 14:43 To: Ivanhoe Leung Cc: relax-users@gna.org Subject: Re: Model-free analysis error Hi Ivan, If you could create a bug report using the link https://gna.org/bugs/?func=additemgroup=relax, that would be appreciated. Please try to include as much information as possible. The best would be if you could attach a truncated data set, the minimum required to trigger the bug (slightly randomised if you would like to keep it private). If I can reproduce the bug myself, I can normally have a fix for it within 5-10 minutes. Oh, it would be good to check that you are using the latest version of relax - currently 3.1.6 (http://www.nmr-relax.com/download.html) - just in case the bug has already been fixed. Cheers, Edward On 25 March 2014 15:33, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote: Dear Edward, I have now conducted measurements (T1, T2 and NOE) in two seperate fields (600 and 700 MHz) as suggested in your previous email. I have upload six different files onto the Relaxation Data List. The data is in the following format 2 ALA 5.49631746729691 N 3 ASP 3.74279511939516 N 4 ASP 6.12594952217594 N 6 SER 6.75812664729337 N However, after I click the Dipolar relaxation button, the programme freezes up when I press Apply or Next. I encountered no problem with the other three buttons (CSA relaxation / X isotope / H isotope) I wonder if it is because I am not supplying the right type of data to the software, or if this is a python problem? Thanks and I hope to hear back from you soon! Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 10 February 2014 16:09 To: Ivanhoe Leung Cc: relax-users@gna.org Subject: Re: Model-free analysis error Hi Ivan, To continue: On another note, I wonder if it is possible to modify the nmr-relax programme so that I can do model-free analysis with data from only one field strength? Alternatively, do you know of any programme (that can be installed on Windows) that can do such analysis? My work focused mainly on small molecule and ligand-based NMR and I have only just very recently started looking in to protein dynamics so I am still experimentinng different software and data treatment etc. Firstly, the subject of single field strength data has been discussed numerous times on this mailing list. I would recommend you read my previous responses to questions relating to single field strength data, and look the other messages in those threads. You will find these discussions quite informative and highly detailed: - Martin Ballaschk: http://thread.gmane.org/gmane.science.nmr.relax.user/1409/focus=1438 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1367/focus=1369 - Mengjun Xue: http://thread.gmane.org/gmane.science.nmr.relax.user/1276/focus=1277 - Fernando Amador: http://article.gmane.org/gmane.science.nmr.relax.user/84 - Shantanu Bhattacharyya: http://thread.gmane.org/gmane.science.nmr.relax.user/1086/focus=1087 - Dhanasekaran Muthu: http://thread.gmane.org/gmane.science.nmr.relax.user/1152/focus=1153 - Vitaly Vostrikov: http://thread.gmane.org/gmane.science.nmr.relax.user/1147/focus=1150 - Aldino Viegas: http://thread.gmane.org/gmane.science.nmr.relax.user/1127/focus=1128 - Pierre-Yves Savard: http://thread.gmane.org/gmane.science.nmr.relax.user/724/focus=725 - Keith Constantine: http://thread.gmane.org/gmane.science.nmr.relax.user/513/focus=517 - Clare-Louise Evans: http://thread.gmane.org/gmane.science.nmr.relax.user/326/focus=332 - Hongyan Li: http://thread.gmane.org/gmane.science.nmr.relax.devel/694/focus=701 These will have lots of additional information. This is just a selection of possibly the most useful messages. You will soon see that this is a complicated topic. Note that relax is capable of performing 100% of the functionality of Modelfree4 (with or without the Fast-Modelfree GUI interface), Dasha, Tensor2, and DYNAMICS. If you play with the optimisation settings you can even find identical results to within machine precision - relax can mimic these other softwares. The key is that the full analysis protocol is rather complicated - many people don't understand this - and that these softwares do not implement the full iterative protocol. Therefore you either have to perform it manually or write a script to perform all of the steps. The protocol is described in the relax manual in figure 7.2 (http://www.nmr-relax.com/manual/diffusion_seeded_paradigm.html). In summary: a) Find an initial diffusion tensor estimate (you can
Re: ref/set intensity plots don't get written
Hi Justin. I guess that you trying to plot a parameter as function of residue number. I guess that something is wrong with: y_data_type='ref' or y_data_type='sat' If you go into the spin viewer, and select a spin, you should be able to find the parameter which you can plot? Best Troels 2014-03-25 15:51 GMT+01:00 Justin Lecher j.lec...@fz-juelich.de: Hi, I am using the sample script for noe analysis, which runs fine aka calculates the NOE values. But following two commands don't work, relax grace.write(x_data_type='res_num', y_data_type='ref', spin_id=None, plot_data='value', file='600NOEcAMP_ref.agr', dir='grace', force=True, norm=False) Opening the file 'grace/600NOEcAMP_ref.agr' for writing. RelaxWarning: No data could be found, creating an empty file. relax grace.write(x_data_type='res_num', y_data_type='sat', spin_id=None, plot_data='value', file='600NOEcAMP_sat.agr', dir='grace', force=True, norm=False) Opening the file 'grace/600NOEcAMP_sat.agr' for writing. RelaxWarning: No data could be found, creating an empty file. The NOE plot is fine. Any suggestion? Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: ref/set intensity plots don't get written
On 25/03/14 17:12, Troels Emtekær Linnet wrote: Hi Justin. I guess that you trying to plot a parameter as function of residue number. I guess that something is wrong with: y_data_type='ref' or y_data_type='sat' If you go into the spin viewer, and select a spin, you should be able to find the parameter which you can plot? Best Troels Hi Troels, I have the corresponding intensities under intensities. But in contrast to the noe which can be plotted, the intensities are a dictionary. How do I plot those? I have taken the sample script and just filled in my values. So the pipe should be equal. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: Model-free analysis error
Cheers! I can confirm the problem - the identification of the @N and @H atom pairs takes a long, long time. However it does successfully complete after a few minutes. There are two problems I can identify. Solving the first will be the easiest. From the saved state file that you uploaded, I can see that you have loaded all atoms of the PDB file into relax as nuclear spins. For your analysis this is not necessary, just load the @N and @H atoms. Then the interatom.define user function will operate much faster as then it will not need to loop over all these 1231 atoms (1231^2 times) but only the 296 @H and @N atoms. See http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_setting_up_spin.html and http://www.nmr-relax.com/manual/GUI_mode_spins_from_structural_data.html for more details (the PDF version of the manual at http://download.gna.org/relax/manual/relax.pdf is of higher quality). The second problem is in relax. There must be an inefficiency somewhere in the relax code which causes this to take so long. I'll look and see if this function can be sped up, but it might require modifying the internal PDB reader in relax to automatically determine connected atoms for the standard protein/DNA/RNA residues. Fixing this is a lot of work, so the first option might be fastest for you. As connected atoms in the protein were not automatically detected by the relax PDB reader, relax must first loop over each atoms to check for connections and for each it must then loop over all other atoms and determine if those atoms are within a certain short distance. If so, it will consider the atoms to be bonded. Because of these two nested loops, for 1231 atoms there would be 1231^2 = 1515361 interatomic distance checks. This is why it is slow. For just the @N and @H spins the number of checks would be ~20 times less. Regards, Edward P. S. For any relax developers out there, the fix is to support the standard PDB atom naming in the Chemical Component Dictionary, as described in http://www.wwpdb.org/documentation/format33/sect9.html#ATOM and found at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/. The ATOM records in a PDB file must conform to this nomenclature and the given CONECT records. All the definitions are in the single file ftp://ftp.wwpdb.org/pub/pdb/data/monomers/het_dictionary.txt. For example to see glycine, search for HETGLY. The number of spaces is essential here. We could add the standard amino acid HET dictionaries to relax and use the CONECT records in these to bond all atoms together. Some problems are that in X-ray structures certain random atoms will be missing and that encountering non-standard or modified amino acids is not uncommon. Therefore the distance-based algorithm would be always needed as a fallback if the relax PDB reader does not find connected atoms for a given atom. On 25 March 2014 16:34, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote: Dear Edward, I have submitted a bug report as requested https://gna.org/bugs/index.php?21862 Thanks Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 25 March 2014 14:43 To: Ivanhoe Leung Cc: relax-users@gna.org Subject: Re: Model-free analysis error Hi Ivan, If you could create a bug report using the link https://gna.org/bugs/?func=additemgroup=relax, that would be appreciated. Please try to include as much information as possible. The best would be if you could attach a truncated data set, the minimum required to trigger the bug (slightly randomised if you would like to keep it private). If I can reproduce the bug myself, I can normally have a fix for it within 5-10 minutes. Oh, it would be good to check that you are using the latest version of relax - currently 3.1.6 (http://www.nmr-relax.com/download.html) - just in case the bug has already been fixed. Cheers, Edward On 25 March 2014 15:33, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote: Dear Edward, I have now conducted measurements (T1, T2 and NOE) in two seperate fields (600 and 700 MHz) as suggested in your previous email. I have upload six different files onto the Relaxation Data List. The data is in the following format 2 ALA 5.49631746729691 N 3 ASP 3.74279511939516 N 4 ASP 6.12594952217594 N 6 SER 6.75812664729337 N However, after I click the Dipolar relaxation button, the programme freezes up when I press Apply or Next. I encountered no problem with the other three buttons (CSA relaxation / X isotope / H isotope) I wonder if it is because I am not supplying the right type of data to the software, or if this is a python problem? Thanks and I hope to hear back from you soon! Ivan From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 10 February 2014 16:09
