On Mon, Sep 06, 2004 at 01:45:02PM +0300, vivek sharma wrote:
> Problems are:
>
> 1. What each column in *.D* file, which contains details about the
> optimization, represents? Also, does this file contains details of
> optimization of molecular pdf as well as Molecular Dynamics? and how to
> differentiate between them?
See http://salilab.org/modeller/manual6v2/node116.html
> 2. Running Modeler gives the following warnings:
>
> Number of templates for coordinate transfer: 3
> After transfering coordinates of the equivalent template atoms,
> there are defined, undefined atoms in MODEL: 3290 1048
> TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF
>
> build___466W> Some coordinates in MODEL not assigned.
> build___468W> Some coordinates in MODEL are still undefined.
> build___464W> Inventing the MODEL coordinates.
>
>
> I understand that these atoms are undefined because it doesn't found
> equivalent atoms (same atom name and equivalent residue) in templates but
> then those atoms are given coordinates by BUILD_MODEL command, but can you
> tell me how one can find out which are those 'still' undefined atoms , even
> which are not covered by 'BUILD_MODEL' command and why this is so? Please
> explain this a bit.
BUILD_MODEL determines the coordinates of any atoms undefined in the
template by using the topology information. If insufficient information
is available in the topology files to do this, then some atoms will
'still' be undefined after this step. In this case, the coordinates are
'invented' - i.e. they are guessed as being close to neighboring atoms.
This is all explained at
http://salilab.org/modeller/manual6v2/node56.html
> 3. Also, another problem is:
> New residue types defined in restyp as well as top_heav.lib.
> I am using this type of restyp.lib (residue defined for use in template)
>
> 141 | AAA | ? | A123 | residue XXX
> 142 | BBB | " | A234 | patch for residue XXX
> 143 | BBB | ? | A345 | patch for residue XXX
>
> and alignment like
>
> template : ----/"/?-----
> target : ----/?/?----- (for this patches are defined explicitly by PATCH
>
> command in top file)
Patches shouldn't be placed in your alignment files - they are used to
alter (patch) existing residues.
Ben Webb, Modeller Caretaker
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