Hi again,
Thank you for your replies. I am jast running CNS translation function to learn
it. Phaser has successfully solved that but I also want to learn how CNS do the
MR.
My protein is a tetramer. I will be highly benifitted if kindly one help me
instructing how to fit the multimers while using CNS MR module.
Thank you all of you
Sincerely Yours
Debajyoti Dutta
On Fri, 11 Jul 2008 Ed Pozharski wrote :
>There is only one map format in CNS, and mapman should open it. Then
>you can convert it to all other formats. Does mapman report some error?
>
>You can rotate/translate molecules with CNS using
>realspace_transform.inp (when you have a question like that it always
>helps to read the list of available scripts). However, what you have in
>mind will not work (if I understand correctly what you have in mind).
>Let's say there is strong peak in self-rotation function and that
>indicates that you have more than one copy in asu and gives you the
>correct rotation to obtain mutual orientation of copies. But you can't
>create a useful model from this because you don't know the translation
>for the copies.
>
>There is, however, the so-called locked rotation function, which takes
>the self-rotation peaks into account. This is not, to my knowledge,
>available in CNS, but you can try AmoRe or glrf. Why do you want to do
>this anyway - is your MR not working? Then try phaser first.
>
>Good luck.
>
>On Fri, 2008-07-11 at 06:31 +0000, Debajyoti Dutta wrote:
> >
> > Hallow,
> >
> > Thank you for your kind attention. I am using CNS 1.2 to solve my
> > structure with molecular replacement. As a novice CNS user, I was
> > trying to follow the tutorial given at the CNS website. I have a
> > tetramer. I have two queries.
> >
> > 1. There are two maps prepared from the self_rotaion.inp. Those are
> > patterson maps, namely
> > self_rotation_ p1.map and
> > self_rotation_ p2.map
> >
> > I was trying to open those with mapman but probably mapman is more
> > inclined to electron density maps,(may be wrong as I am very new user
> > of these softwares). While trying to convert it into ps file with o2d,
> > pltdev etc I was not successful. I am just inquiring if there is any
> > tool to convert those map files to *.ps file, or can see those map
> > files.
> >
> > 2. Another thing I want to learn if there is any direct way in CNS
> > (such as feeding the self_rotation_list or self_rotation_ matrix to)
> > to automatically find out all the different chains present in an
> > asymmetric unit and prepare the model (with all chains). Because
> > from the CNS tutorial I follow the way to fit my search model into my
> > data.hkl as a dimer but It is a tertamer. Then after fitting the dimer
> > I follow the same way { translation. inp --> merge_structure. inp -->
> > shift_molecules. inp} to fit the next monomer into the dimer but
> > unfortunately it is failing at the stage of merge molecules as
> > trimer.The coordinates assigned, which seems totally rubbish
> >
> > ATOM 1 CB ALA 1 9999.0009999. 0009999.000 1.00 0.00 A
> > etc...
> > (omitted the total chain: all are same coordinates and occupancy and B
> > factor)
> > and for B chain
> >
> > ATOM 2555 CB ALA 1 9999.0009999. 0009999.000 1.00 0.00 B
> > etc...
> > (omitted the total chain: all are same coordinates and occupancy and B
> > factor)
> > and for C chain
> >
> > ATOM 5109 CB ALA 1 32.637 74.346 146.854 1.00 20.00
> > C etc..
> > (Omitted the total chain: all are taking a reasonable values)
> >
> > Will you please help me with these problems. Thank you very much for
> > your attention and suggestions in advance.
> >
> > Your Sincerely
> > Debajyoti Dutta
> >
> >
> >
> >
> >
> > Rediff Shopping
>--
>Edwin Pozharski, PhD, Assistant Professor
>University of Maryland, Baltimore
>----------------------------------------------
>When the Way is forgotten duty and justice appear;
>Then knowledge and wisdom are born along with hypocrisy.
>When harmonious relationships dissolve then respect and devotion arise;
>When a nation falls to chaos then loyalty and patriotism are born.
>------------------------------ / Lao Tse /
>
>
>
