Re: Full analysis issue

Hi, I've been thinking about this one for a while, but I don't know exactly what the problem is. I have a few ideas that may help though. This could either be some type of interesting dynamics, or be caused by something a bit more sobering. Firstly though, it is worth comparing the local tm

Re: Error message with the script palmer.py

Hi, This problem is a hard one to handle. There is already a bit of code in relax's parser of Modelfree's mfout STAR formatted file which handles corrupted mfout files (the problem was with fused columns with many *). But catching this one is much harder. The easy fix here it to put an

Re: Hybrid model and writing of results

. However, I would like to know if it is possible to calculate the AIC for a given hybrid... and possibly compare different hybrids together within relax... Thanks ! Have a nice day ! Séb :) Edward d'Auvergne wrote: Hi, This problem has quite a simple answer. There is no results

Re: Constraints in full_analysis.py

Hi Seb, That's an interesting one. That message is a debugging statement that should only be triggered if someone goes into the relax source code and tries to reprogram the constraints algorithm or tries to implement a completely new algorithm. It shouldn't appear in the 1.2 stable releases and

Re: Model selection and local_tm

On Wed, Apr 2, 2008 at 4:23 PM, Carl Diehl [EMAIL PROTECTED] wrote: On Mon, 2008-03-31 at 11:28, Edward d'Auvergne wrote: On Fri, Mar 28, 2008 at 2:59 PM, Carl Diehl [EMAIL PROTECTED] wrote: Hi. I used the full_analysis.py script for testing and evaluating relax in comparison

Re: AIC from ModeFree data

On Wed, Apr 2, 2008 at 7:11 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I tried to use the palmer.extract() function, with no real success... I have to admit that my Modelfree star format parser is not of very high quality. It woks if you use the palmer.py sample script, but obviously

Re: AIC from ModeFree data

loads a saved state from stage 1 where all those information were input... For the run 'None' being selected, yes, it is for all spins... Running with the '--debug' flag doesn't change anything... Cheers, Séb Edward d'Auvergne wrote: On Wed, Apr 2, 2008 at 7:11 PM, Sébastien

Re: AIC from ModeFree data

Hi, This is simple enough to do. The user function palmer.extract() will extract all the data (well that used by relax) out of Modelfree's mfout files. Regards, Edward On Tue, Apr 1, 2008 at 11:41 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I have different model-free analysis that

Re: Model selection and local_tm

Hi, Please see below for my replies. On Fri, Mar 28, 2008 at 2:59 PM, Carl Diehl [EMAIL PROTECTED] wrote: Hi. I used the full_analysis.py script for testing and evaluating relax in comparison with published data. The system was calcium-loaded Calbindin D9k, with R1 NOE at 600 MHz and

Re: problems with relax_data.back_calc?

Hi, This error looks like a bug in relax. I haven't tested the back calculation code for a little while, and I haven't noticed this problem before. I do have a few ideas as to what the problem is but, to help fix this issue, would you be able to create a bug report at

Re: Spectral Density Mapping Problem

Hi, I've also cut and pasted the numbers into files, and run the script using various versions of relax (1.2.10, 1.2.11, 1.2 repository line, 1.3.0), and all works fine for me too. I get Grace plots with all points shown. I'm not sure what is happening, but we should be able to get to the

Re: Constraints

of the protein (up to the huge correlation time of 200 ns !) does not influence the results... As usual, relax is extremely professional... Thanks Ed ! Cheers ! Séb Edward d'Auvergne wrote: Hi, Unless turned off, the constraints are used all of the time. In the minimisation

Re: Constraints

Hi, Unless turned off, the constraints are used all of the time. In the minimisation this turns on the Method of Multipliers (also known as the Augmented Lagrangian) algorithm. In the grid search, any points outside of the limits are dropped. Unfortunately these constraints are hard coded as I

Re: Lagrange multiplier warning

On Fri, Feb 22, 2008 at 6:03 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I am trying to use the full_analysis.py script for optimizing model m11 to m15 (m1 to m5 with CSA) for a system for which I have datasets at three magnetic fields (500, 600, 800 MHz). The optimization is quite

Re: relax: data at one field, 2H relaxation

Dear Keith, I'm sorry for the late response, I've only just come back from the ENC conference. The software relax can operate without problem using single field strength data and should be able to replicate all published model-free results (after significantly decreasing its precision and

Re: 15N data at 1 field, 2H data

Hi, If you are following this thread from the relax-users mail archive (https://mail.gna.org/public/relax-users/), then you will find the response at https://mail.gna.org/public/relax-users/2008-03/msg4.html. Regards, Edward On Tue, Mar 18, 2008 at 1:01 PM, Keith L Constantine [EMAIL

Re: R1 and R2 for MF analysis

On Feb 8, 2008 4:54 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I have a theoretical question about Model-Free analysis concerning the minimum amount of data required... In ModelFree, it is possible to obtain fitted parameters for residues for which only one R1 and one R2 datasets are

Re: Rex vs magnetic field

Hi, In relax, the Rex reported will be that of the first input field strength. The frequency of the Rex value is documented in the header line of the results file. This is a deliberate design to increase the flexibility of relax - Rex is automatically handled for you. If you would like to

Re: Model elimination

Sorry for the delayed response. Work has been quite hectic at the moment. This is a clear bug, so if you could submit a bug report, that would be much appreciated. A catch for n == 0 could be added to fix this problem, but I am very interested in why this situation occured in the first place.

Re: influence of pdb orientation on model-free optimization?

? Doug On Jan 10, 2008, at 2:36 PM, Edward d'Auvergne wrote: Yes, with 4 data sets you could remove tm6 to tm8. You would also need to remove m8. But in this situation, you will be significantly biasing the initial position (the starting universe will be further away from

Re: relax 1.3: run.create error

. relax repository checkout Protein dynamics by NMR relaxation data analysis Copyright (C) 2001-2006 Edward d'Auvergne Copyright (C) 2006-2008 the relax development team

Re: relax 1.3: run.create error

Copyright (C) 2001-2006 Edward d'Auvergne Copyright (C) 2006-2008 the relax development team This is free software which you are welcome to modify and redistribute under the conditions of the GNU General Public License (GPL). This program, including all

Re: relax 1.3: run.create error

? The 'diff_tensor_pdb.py' script seems to output only a subset of atoms to a residue called 'TNS'. Thanks again, Doug On Jan 24, 2008, at 11:16 AM, Edward d'Auvergne wrote: Hi, The 'diff_tensor_pdb.py' script has no chance of currently running on the 1.3 repository line code! The reason

Re: influence of pdb orientation on model-free optimization?

Hi, If you have 5 relaxation data sets, you can use the full_analysis.py script but you will need to remove model tm8. This is the only model with 6 parameters and doing the analysis without it might just work (the other tm0 to tm9 models may compensate adequately). I've looked at the script

Re: influence of pdb orientation on model-free optimization?

} be removed to use the full_analysis.py protocol? Thanks, Doug On Jan 10, 2008, at 1:31 PM, Edward d'Auvergne wrote: Hi, If you have 5 relaxation data sets, you can use the full_analysis.py script but you will need to remove model tm8. This is the only model with 6 parameters

Re: The use of a pdb with the sphere diffusion tensor

Done! See https://mail.gna.org/public/relax-commits/2008-01/msg00376.html. The current version of the script in the 1.2 line will now properly handle not having a PDB file if you set the value of PDB_FILE to None. Nevertheless, I would be very careful with the conclusions. If there are regions

Re: The use of a pdb with the sphere diffusion tensor

On Jan 10, 2008 10:06 PM, Douglas Kojetin [EMAIL PROTECTED] wrote: A question re: unresolved residues. Is it necessary to list unresolved residues in this file if no data was supplied for these residues? Example r1 file (made up): 1 2 3 2.7114 0.05 4. 2.6151 0.04 Do residues 1 and 2

Re: The use of a pdb with the sphere diffusion tensor

unselect.read(run='tm0', file=None, dir=None, change_all=0, column=0) RelaxError: The file name argument None must be a string. However, UNRES = 'None' does not yield this error and the script proceeds... Am I right ? Séb :) Edward d'Auvergne wrote: On Jan 10, 2008 9:59

Re: tensor angles

Hi, From the diffusion_tensor.init() documentation for the spheroid: The spherical angles {theta, phi} orienting the unique axis of the diffusion tensor within the PDB frame are defined between Similarly for the ellipsoid: The angles alpha, beta, and gamma are the Euler angles describing the

My XH bond distribution scripts, Re: NH bond vector orientation figure in pymol/molmol

Hi, I didn't include the XH bond distribution scripts with relax. There were a couple of these to generate the figure. These 2 file have been attached to this message. 'dist.py' generates parts c and d whereas 'dist_core.py' generates parts a and b. For those who are interested, this figure

Diffusion tensor figure.

: The Brownian rotational diffusion tensor of OMP as determined by the new model-free optimisation protocol ? Thanks, Doug On Dec 9, 2007, at 9:49 AM, Edward d'Auvergne wrote: Hi, I didn't include the XH bond distribution scripts with relax. There were a couple of these to generate

Re: PDB orientation

Hi, On Nov 9, 2007 4:20 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi Ed, Your comments are interesting... but nevertheless trouble me... My comments being troubling is a common occurance ;) I talked with the guy who makes the MD simulation with my protein. He noticed that some NH

Re: Reduced spectral density mapping at three fields

). === Let me know if something misses... Regards Séb :) Edward d'Auvergne wrote: Hi, Prior to me committing these patches, would you be able to write the full commit message for these so I can just cut and paste them? For example links to posts

Re: Reduced spectral density mapping at three fields

different magnetic fields (at least two) can be input at once and correlation plots made automatically as long as correlation, skewness and kurtosis coefficients calculated also automatically... Cheers Sébastien :) Edward d'Auvergne wrote: On 10/16/07, Sebastien Morin [EMAIL

Re: PDB orientation

? Would you suggest another approach ? Cheers Sébastien :) Edward d'Auvergne wrote: Hi, The only differences in the analysis should be due to different bond orientations. The PDB reference frame doesn't matter - this will only change the values Euler angles of the diffusion

Re: relax-users Digest, Vol 16, Issue 9

Gary, Thanks for the response. I have applied Doug's patch 'patch2' attached to the bug #10022 report at https://gna.org/bugs/?10022. This simple patch solves the issue by catching the problematic situations and just ignoring them. The solution is similar to your last example. Regards, Edward

Re: Extremely long optimization times

) # Write the results. ... That should be enough to solve the problem (hopefully). Cheers, Edward I think that's almost everything I can find now... Let me know if you know how to catch those problems before they appear... Cheers Séb :) Edward d'Auvergne wrote: Hi, I've

Re: Error propagation for duplicates, triplicates, quadriplicates...

Hi, You have to be careful with error analysis as the errors are as important as the data itself! By 4 sets of R1 values, I would assume that you have these all at the same field strength. With this data there are a number of ways the data can be used in relax and a number of ways its error can

Re: looping the optimization in full_analysis.py

, in __init__ converged = self.convergence(run=name) File full_analysis.py, line 368, in convergence curr_models = curr_models + self.relax.data.res[run][i].model AttributeError: Element instance has no attribute 'model' Thanks, Doug On Jun 27, 2007, at 11:22 AM, Edward d'Auvergne wrote

Re: NOE errors

Hi, This is exactly correct. The formula you report Seb should be sd(NOE) = NOE * sqrt({sd(sat)/I(sat)}^2 + {sd(unsat)/(unsat)}^2). Note the division rather than the multiplication. This formula is directly from Farrow et al. (Biochem. (1994), 33, 5984-6003). If you replace the

Re: relax and modelfree

Hi, Sorry, I'm not exactly sure what the graphs correspond to. Is 't-rex-sim.agr' Modelfree4 using the prolate (or oblate) spheroid (this is axially symmetric anisotropic Brownian rotational diffusion)? And is 't-rex-relax.agr' the results from relax using the spheroid tensor? Have you used

Re: CSA bond length

A for bond length and -172 ppm for CSA (for 15N-1H vectors). Should the default values in the relax code be modified, changing the CSA from -170 (at least in the jw_mapping code) to -172 ppm ? Cheers Séb :) Edward d'Auvergne wrote: There has been much work describing

Re: two questions: hybrid analysis and convergence problems

now without any luck]. Doug On Jun 25, 2007, at 9:01 AM, Edward d'Auvergne wrote: Hi, Would you be able to print the AIC and k values as well? k is the number of parameters in the model. The places where the chi-squared value increases rather than decreases is because of a collapse

Re: two questions: hybrid analysis and convergence problems

Hi, The first part of your post is simple to respond to as I have used exactly this approach in my PhD thesis. This is described in Chapter 7 of the thesis which can be downloaded from http://eprints.infodiv.unimelb.edu.au/archive/2799/ . The hybridisation function docstring

Re: Error in Monte Carlo Simulations

On 1/8/07, Hongyan Li [EMAIL PROTECTED] wrote: Dear Relax-users, I am trying to use RELAX to fit my dynamic data and now I have tried the simplest model (isotropic) to simulate the data and get a proper model for each residue and I would like to do Mone Carlo Simulations like that:

Re: scripts

On 1/8/07, Chris MacRaild [EMAIL PROTECTED] wrote: I certainly expect Chi-squared and the dynamic parameters to be highly dependent on the value of tm. This is why I recomend the extensive iteration of steps 2-4 below, in an attempt to find the optimal fit. I would expect if you start the

Re: Relax installation question

Hi Barbara, Welcome to the relax users mailing list. The problem you're experiencing is an interesting one, I've not seen it before. Under MS Windows, I run relax under GNU/Linux though, the program versions I have which allow relax to run flawlessly are: Windows: XP Python: 2.4.3 relax:

Re: errors in mf-multimodel.py with Monte Carlo simulations

Actually this is a real bug which has now been fixed. This issue is related to bug #7755 (https://gna.org/bugs/index.php?7755). For an identical error message, see the post by Stephen Headey (https://gna.org/users/sjheadey) located at

Re: full_analysis.py

Hi Sebastien, This is just a follow up query from an old post. Did your calculations using the new model-free optimisation protocol implemented in the 'full_analysis.py' script eventually finish? If so, did it take much longer than a week? Cheers, Edward On 10/17/06, Sebastien Morin

Re: problems reading Xeasy format

I've now fixed the issue. Steve reported the problem as bug #7676 (https://gna.org/bugs/index.php?7676), and the fine details of the fix are available at that link. The problem was that relax was assuming that the w1 dimension in the XEasy text file was the proton dimension. There was also a

Re: problems reading Xeasy format

Hi, Welcome to the relax-users mailing list. Using your attached data I've been able to replicate the issue. I think I know what is occurring, but relax's print out doesn't really tell you what the issue is. This can easily be fixed though. Would you like to create a bug report at

Brownian rotational diffusion mini-tutorial.

In a post to the relax-devel mailing list (https://mail.gna.org/public/relax-devel/2006-10/msg00136.html, Message-id: [EMAIL PROTECTED]) I discussed an idea about representing the Brownian rotational diffusion tensor superimposed onto the 3D molecular structure. For a better understanding of the

Re: Plotting the Reduced spectral density mapping

On 10/23/06, Daniel Perez [EMAIL PROTECTED] wrote: Hi Edward, the function grace.write for the spectral density results is working fine for the most. I just got an error when I tried to plot the simulations ('sims'). To help solve the problem, would you be able post the details of the issue?

Re: Plotting the Reduced spectral density mapping

On 10/23/06, Edward d'Auvergne [EMAIL PROTECTED] wrote: On 10/23/06, Daniel Perez [EMAIL PROTECTED] wrote: Hi Edward, the function grace.write for the spectral density results is working fine for the most. I just got an error when I tried to plot the simulations ('sims'). To help solve

Re: Plotting the Reduced spectral density mapping

The 'grace.write()' user function is now implemented for reduced spectral density mapping. Daniel, would you be able to test this code to see if everything works well for you? I've tested the changes on some basic data and the user function appears to be operating OK. Edward

Re: full_analysis.py

Diffusion modelRoundMachine Time Time_for_opt/ ======== = local_tm --- Pelican 15h00 sphere MII initPelican

Re: analysis of limited data sets

the largest CS, but that's just me. dzz is more often than not the direction perpindicular to the base plane, although it varies with your choice of CSA tensor source (DFT, SS NMR, Solution NMR, etc.). Alex On 10/5/06, Edward d'Auvergne [EMAIL PROTECTED] wrote: That's a good idea, the eigenvector

Re: analysis of limited data sets

Hi, In relaxation data analysis, you can only view the components of the Brownian rotational diffusion tensor that the XH bond vectors sample. So if your macromolecule diffuses as a prolate spheroid but the XH bond vectors are close to perpendicular to the unique axis of the tensor, the only

Re: frustrated in michigan

On 9/28/06, Alexandar Hansen [EMAIL PROTECTED] wrote: Hello, I would first like to apologize that this post is going to be painfully remedial and likely nothing more than spam to most, but I am really having trouble getting relax to work and I don't know if it's because of me, or if I don't

Re: Using relax with RNA

relax is only requires residue numbers. The residue name can be absolutely anything! Therefore as long as there is one data set per residue then it should be fine. If there are two or more data sets per residue, then relax will have problems. That should be fixable if required though. Edward

Re: Tabs and spaces in inputs

For the input of data into relax, the difference between spaces, tabs, and other whitespace characters doesn't matter. relax will treat all whitespace the same. And the number of whitespace characters in a row is inconsequential as well. As long as the columns are clearly separated by

Re: Accounting for N1 and N3 CSA differences in RNA

Unfortunately this approach won't work. You would need to create an additional loop where you loop through the residues (in the future maybe data sets) and set the value on a per residue basis. You would need something like: value.set(name, 1.01 * 1e-10, 'bond_length')

Re: relax in Windows

I've created a bug report for this problem - bug #6980 located at https://gna.org/bugs/?6980. Edward On 9/13/06, Edward d'Auvergne [EMAIL PROTECTED] wrote: That one is a real bug. The problem is a typo, the double = sign should be a single = sign. The line should read self.SYS = 'Win'. I

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