Re: [ccp4bb] another quick question...

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: experiences on fluidigm topaz system
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2007-05-24

Next message:
Subject: Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2007-05-24

Subject: Re: another quick question...
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-24

James,

The "stars" are atoms in a residue that are no longer within
recognizable bonding distances of other atoms. Somewhere along the way
these residues were mangled to the point that some atoms are no longer
within bonding distance of each other. (In Refmac, for example, this can
happen if the X-ray weighting term is too high for the resolution of the
data,and atoms start "wandering off" during refinement.)

I'm not terribly familiar with Molrep, but most MR programs do rigid
body searches, and do not normally alter the geometry of the search
model. Is the original search model geometrically correct? Whatever the
cause, you can at least snap residues back into line by doing a
"regularize zone" in Coot. That should round up all the wayward atoms.

Cheers,

___________________________________________
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
James Pauff
Sent: Thursday, May 24, 2007 9:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] another quick question...

Good day all,

In COOT, when I view my coordinate pdb file with my
ccp4 map file (using "Auto-open mtz"), I have a couple
residues for which only a part of the peptide chain is
visible. E.g. for a Lys, only the terminal nitrogens
at the end of the R-group chain are visible as bonds.
The other parts of the residue (and even parts of
adjacent residues) are visible only as stars/stellate
points that may or may not be within my blue electron
density. If I click on the stars, the atom names that
appear are consistent with the missing peptide chain,
and correspond to the "missing" amino acid that has
the occassional visible R group.

Just wondering what this means, that I am seeing
stellate points that seem to be acting as place
holders for my residues in a couple locations in my
structure. The structure was obtained using molrep.

Thank you,
James Pauff

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: experiences on fluidigm topaz system
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2007-05-24

Next message:
Subject: Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2007-05-24