Modelling Dimers in Ranch

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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greatscott
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Modelling Dimers in Ranch

#1 Post by greatscott » 2007.09.28 17:59

Hello
I would like to model a dimeric model in RANCH, and then use the models for selection using GAJOE. Is this there a cunning way to do this in the software?
regards
Dave Scott

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Saxologos
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#2 Post by Saxologos » 2007.10.01 14:18

We plan to release a version that supports multimers/symmetries but the current version does not.
What you CAN try to do however is to fool the program that you have just one polypetide chain, i.e. create a "double" sequence potentially by adding a small linker between the different chains.

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OneFile

#3 Post by greatscott » 2008.02.25 20:22

I have constructed dimers of my model protein and have generated Crysol26 files and now want to put them altogether in ONEFILE2 so as to input into GAJOE. However, I cannot get ONEFILE2 to recognise my file extention, it keeps returning "No file with this extension" despite the fact that I am using the correct procedure of naming in the EOM manual.
Any hints? :)

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#4 Post by Saxologos » 2008.02.25 20:29

First of all make sure all the files are consecutive (either in the form 1,2,3... or 00001, 00002,... with NO missing numbers).
If your original pdb files are named something like 00001sth.pdb then the int files will be named 00001sth00.int. When onefile2 asks for an extension you should answer sth00.int (you might as well omit .int since it is the default extension).

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Onefile2

#5 Post by greatscott » 2008.02.25 23:02

Nope! Hasn't worked. Is there a particular directory I need to have ONEFILE2 working from? Can send my .int files for inspection if need be.
cheers :D

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#6 Post by Saxologos » 2008.02.26 13:23

Can you send me the first 10 of them? (I do not need all of them, just to see if it works for me). Also send me exactly the filenames of the corresponding pdbs (I do not need the pdbs themselves just the names).
Thanks.

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Re: Modelling Dimers in Ranch

#7 Post by Yann » 2012.06.11 16:11

Hi lads,

has any solution been found in the end? I am struggling with a similar problem.

I have generated a pool of conformers using flexible meccano and get the following output files after running crysol: 0a_71_sccomp00.int until 999a_71_sccomp00.int.

When I try to run 'one file' (I am running on a Mac), one file will only read around 50 files sometimes and in other cases it also reports that there are no such extensions.

Can anybody give me a pointer?

Much appreciated,

Yann

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Re: Modelling Dimers in Ranch

#8 Post by greatscott » 2012.06.11 16:35

Hia Yann,
In the end I got someone to script me some code using LSQKAB in CCP4. Basically we had a dimerisation domain, so we made 20000 halves (i.e. monomers) and then lined them up using LSQKAB to make dimers. The results were published a couple of years ago:

Rajeskar, K.V., Muntaha, S.T., Tame, J.R.H., Wharton, C.M., Thomas, C.M., White, S.A., Hyde, E.I. and Scott, D.J. (2010). Order and disorder in the domain organisation of the plasmid partition protein KorB
J. Biol. Chem. 285, 15440-15449

As long as you rename all the files and check for clashes (which you can by calling a second CCP4 module), you can get good dimers constructed. Funnily enough I am now looking at the Flexible Meccano program as a better way of doing this. Let me know how you get on!

Best

Dave Scott

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Re: Modelling Dimers in Ranch

#9 Post by Yann » 2012.06.11 16:48

Hi Dave,

Thanks for the quick reply. This will come in handy for sure.

Other than a construction of a pool of dimers I was mainly referring to the issue of ONEFILE keeping returning "No file with this extension" despite the fact that I am using the correct procedure of naming in the EOM manual.

Any pointers?

Thanks a bunch,

Yann

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Re: Modelling Dimers in Ranch

#10 Post by Giancarlo » 2012.06.18 14:45

Hi all,

In the current release of ATSAS there is now an experimental version of "Advanced EOM 2.0" where is possible to model oligomers as well as complex protein-dna. The oligomers can be modelled by either a contact condition file or passing directly the high resolution pdb (dimer/trimer/whatever) as input in case of any. Ranch will add the missing sections in symmetric as well as asymmetric way. The full manual is still missing but how to set up the environment should be quite straightforward.

Please keep in mind that this is an experimental version and the definitive one will be released later on in the summer.
I am now collecting bugs therefore in case of any do not hesitate to address them to me: g_i_a_n_c_a_r_l_o_._t_r_i_a_@_e_m_b_l-h_a_m_b_u_r_g_._d_e ( of course, removing the underscore :-) )

Ciao,
Giancarlo

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Re: Modelling Dimers in Ranch

#11 Post by franke » 2012.06.18 17:27

Giancarlo wrote:In the current release of ATSAS there is now an experimental version of "Advanced EOM 2.0"
Please note: Windows only!

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Re: Modelling Dimers in Ranch

#12 Post by Yann » 2012.06.19 13:58

Hi guys,

great news about the progress in EOM!

I don't mean to nag, but could anybody help me out with my previous question?

Thanks,

Yann

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