Search found 100 matches

by Hayds
2018.08.16 11:15
Forum: Mixtures and Flexible Systems
Topic: Reg : EOM structures and RDC refinement
Replies: 2
Views: 844

Re: Reg : EOM structures and RDC refinement

Dear vas2201, can you explain a little more what you mean by the "global orientation of the domains from the EOM structures" ? I assume you don't mean the orientation of the domains relative to each other in each model as that is pretty straight forward. I'm not sure what you're after exactly. Cheer...
by Hayds
2018.04.20 12:44
Forum: Working with Models
Topic: Trouble in data collection or analysis
Replies: 2
Views: 1029

Re: Trouble in data collection or analysis

Dear Kermani, the issue could be the system itself. The data looks like it comes from a membrane protein in detergent, is this the case? If so, one thing you can do is extract only the "shape" scattering by using the data up to the first minimum in the curve as input for DAMMIN/DAMMIF. You need to c...
by Hayds
2018.04.04 11:35
Forum: Mixtures and Flexible Systems
Topic: NMR models to define domain
Replies: 2
Views: 947

Re: NMR models to define domain

Hi James, the most straight forward thing to do is extract the representative model (usually MODEL 1) from the PDB file. Check the PDB entry to make sure the first model is considered to be the representative one of the ensemble. Then just use this as your input rigid body. Although I have not teste...
by Hayds
2017.09.21 09:17
Forum: Mixtures and Flexible Systems
Topic: PROBLEM: The sequence presents a residue (0) not recognized
Replies: 5
Views: 1617

Re: PROBLEM: The sequence presents a residue (0) not recogni

Hi Julie, I just removed all the extra characters and EOM runs fine with the modified sequence file (EOM run without using any rigid bodies, just random coil from sequence). In your case I assume you have corresponding rigid bodies. Do you have anything in the PDB files that is unusual? Cheers, Haydyn
by Hayds
2017.09.19 16:04
Forum: Mixtures and Flexible Systems
Topic: PROBLEM: The sequence presents a residue (0) not recognized
Replies: 5
Views: 1617

Re: PROBLEM: The sequence presents a residue (0) not recogni

Hi Julie, try removing all the non-alphabetical characters from the sequence files, you should only have something like this: MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQG ELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLI YTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYL...
by Hayds
2017.09.19 15:02
Forum: Mixtures and Flexible Systems
Topic: PROBLEM: The sequence presents a residue (0) not recognized
Replies: 5
Views: 1617

Re: PROBLEM: The sequence presents a residue (0) not recogni

Hi Julie,

can you please pm me your sequence file? Is the EOM run using any PDB files or just random structure?
by Hayds
2017.03.24 11:23
Forum: Announcements
Topic: EMBO Global Lecture Course Singapore 2017
Replies: 0
Views: 2922

EMBO Global Lecture Course Singapore 2017

Structural and biophysical methods for biological macromolecules in solution Singapore • 06 – 14 December 2017 poster.png [/url] About the course: Structural methods applicable to solutions facilitate structural and functional studies on biological macromolecules under close to native conditions. F...
by Hayds
2016.11.17 12:26
Forum: Mixtures and Flexible Systems
Topic: Alignment Problems: check the sequence and the domains
Replies: 1
Views: 1885

Re: Alignment Problems: check the sequence and the domains

Hi, one typically sees this problem if you have no "flexible" sequence for EOM to generate. There must be some sequence missing between the n-terminal and c-terminal domain PDB files. So for example, if the sequence is: AAAAAAAAAABBBBBBBBBBCCCCCCCCCC and PDB file 1 contains the residues: AAAAAAAAAA ...
by Hayds
2016.01.22 11:46
Forum: Mixtures and Flexible Systems
Topic: best-curve001.txt file in EOM and frequency of structures
Replies: 4
Views: 3587

Re: best-curve001.txt file in EOM and frequency of structure

Dear vb, it will take a bit of time to reimplement a best_curve001.txt output file from EOM 2.1. In the meantime you can use the -w flag to write out all the work files used by the genetic algorithm. The GA_CYCLE files list the selected curves for each ensemble, from these files you could estimate t...
by Hayds
2016.01.12 10:39
Forum: Mixtures and Flexible Systems
Topic: best-curve001.txt file in EOM and frequency of structures
Replies: 4
Views: 3587

Re: best-curve001.txt file in EOM and frequency of structure

Dear vb,

We did indeed remove this file at some point and as you noted it is no longer part of the output in EOM 2.0. I was not sure people actually used it. I will see what can be done to recreate it (or reintroduce it into EOM again).

Cheers,

Haydyn
by Hayds
2015.08.05 05:17
Forum: Mixtures and Flexible Systems
Topic: R Sigma Value
Replies: 4
Views: 3250

Re: R Sigma Value

Hi thd1,

I'm a bit interested in why the Rflex is higher for the selected ensemble than the pool. Does it make sense in this particular case? I assume you are using rigid bodies and a flexible region between?

Haydyn
by Hayds
2015.08.05 04:14
Forum: Mixtures and Flexible Systems
Topic: GAJOE 2.1 Output Files
Replies: 1
Views: 2226

Re: GAJOE 2.1 Output Files

Hi Abhi, the output files include for example: CaCa_distr_001_1.dat --> distribution of end to end distances Size_distr_001_1.dat --> ensemble size (Dmax) distribution pdbs --> conformations in the selected ensemble statistics_flexibility.svg --> a vector graphic summarising the flexibility metrics ...
by Hayds
2015.08.05 03:56
Forum: Mixtures and Flexible Systems
Topic: GAJOE 2.1 vs 1.3
Replies: 1
Views: 1974

Re: GAJOE 2.1 vs 1.3

Dear Abhijit,

I just want to make sure I understand your question. Are you asking if the number of ensembles can be fixed or the number of conformations in each ensemble?

Cheers,

Haydyn
by Hayds
2015.03.24 09:37
Forum: Mixtures and Flexible Systems
Topic: number of ensembles option in gajoe
Replies: 2
Views: 1682

Re: number of ensembles option in gajoe

Hi Erik,

The number of ensembles used for the crossing procedure in the genetic algorithm is not hard limited to 200. 200 is just a suggested max for the sake of computation time. Have you tried using more than 200?

Cheers,

Haydyn
by Hayds
2015.01.20 16:59
Forum: Mixtures and Flexible Systems
Topic: Gajoe on external pool error
Replies: 9
Views: 3500

Re: Gajoe on external pool error

Ah I see,

so you can run it successfully on a subset of this pool? Does GAJOE crash on a particular PDB file?

Haydyn