[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ccp4bb]: Dual conformations

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

On Tue, 17 Oct 2000, Bart Hazes wrote:

> The answer is simple; use REFMAC. I used CNS until I ran into multiple
> sidechain conformations. Inserting them is really trivial, I would almost say
> fun, in Xfit and the remodelled coordinates can go straight into REFMAC. No
> fuss with topology files etc.

i have had troubles with Xfit, some of which pertain directly to alternate
conformations.  if you split a residue into 2 conformations, no
problem. if you try to add a third conformation you will find that it does
not function properly.  there is no function for 'un-splitting' a
residue.  selecting an atom from the model window for centering, etc. does
not function properly for an atom with more than one conformation. there
is no feature for adjusting the occupancy of all atoms in an alternate as
a group.  it appears to me that support for alternate conformations is a
recent addition to Xfit that has not been adequately debugged or worked
into the rest of the program.  and when i report these problems to the
program author i get absolutely no response.

unfortunately not many other graphic model building programs of the
free/cheap academic nature handle alternate conformations and anisotropic
thermal  factors well (or even at all).  if anyone has info on one that
does, i'd like to hear about it.  otherwise i shall continue to look
forward to the eventual release of a CCP4 3D program.


"The Wrong Hat is like wearing an enormous sign, duct-taped to a plumber's
helper stuck to your head, that says, "I'm a moron."  - Mimi Pond
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine