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Re: [ccp4bb]: cannot calculate structure factors



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On Fri, 14 Feb 2003, Richard Baxter wrote:

> because I thought I had already adjusted the position of my atom name to
> the left. However, on closer inspection I realise that my atom names are
> all justified to column 14 rather than column 13. Correcting this for the
> Magnesium ion allows the script to run successfully.

right


> For the record, I am using Charlie Bond's PDB mode for Xemacs to
> manipulate my PDB files:
> 
> http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html
> 
> I think it is very good - I see that the majority of the atom names (that
> are three letters long) are right justified to column 16 and two or
> one-letter atom names left justified wrt to those, hence my C-alpha
> carbons have the 'C' in column 14 of the PDB file, I presume this avoids
> incorrect assignment to calcium?

right


> So my final question is about the other atom names in my PDB file that
> might give me trouble, the iron ions FE, and the four porphyrin nitrogens
> NA, NB, NC and ND. Currently these are all left justified to column 14 of
> the PDB record. Will this be correct to identify them as iron rather than
> flourine, and nitrogens rather than sodium, niobium and neodynium?

no, the iron is wrong.

The PDB format is to put the names of the elements into columns
13-14 _RIGHT_ justified, and the additional marking of the atom
into columns 15-17. Thus " CA" = C-alpha is distinguished from
"CA " = calcium and " FE" = fluorine-epsilon from "FE " = iron.

Therefore, your iron atom must have been considered fluorine in
the calculation. You better correct its position the same way as
your magnesium.


Manfred
----------------------------------------------------------
 Dr. Manfred Buehner             Phone:  +49-931-888-4100
 Physiologische Chemie           FAX:    +49-931-888-4150
 Theodor-Boveri-Institut fuer Biowissenschaften
 Biozentrum der Universitaet Wuerzburg
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 Email:  buehner@biozentrum.uni-wuerzburg.de
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