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[ccp4bb]: selenomet (MSE) and Refmac5
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Dear All,
I am using Refmac5 through the CCP4I-4.1.1 interface and am wondering
whether selenomethionine (MSE) is being recognized properly on
coordinate file input.
To start, I mutated MET to MSE in "O" and here is representative output
of the relevant part of the coordinate file from "O":
ATOM 320 N MSE X 41 29.824 31.488 35.626 1.00 11.19 7
ATOM 321 CA MSE X 41 29.652 32.610 36.538 1.00 11.64 6
ATOM 322 CB MSE X 41 28.225 33.094 36.510 1.00 12.01 6
ATOM 323 CG MSE X 41 27.852 33.686 35.170 1.00 14.13 6
ATOM 324 SE MSE X 41 28.681 35.384 34.700 1.00 20.00 34
ATOM 325 CE MSE X 41 27.259 36.407 35.447 1.00 17.00 6
ATOM 326 C MSE X 41 30.038 32.246 37.955 1.00 11.06 6
ATOM 327 O MSE X 41 30.707 33.006 38.648 1.00 10.75 8
Note "34" for SE in the last column of the fifth row.
Using the above coordinate file from "O" as input, here is the resulting
relevant part of the output file after refinement with Refmac5:
ATOM 629 N MSE X 41 29.826 31.486 35.628 1.00
11.15 N
ATOM 631 CA MSE X 41 29.653 32.611 36.538 1.00
11.57 C
ATOM 633 CB MSE X 41 28.227 33.091 36.512 1.00
11.90 C
ATOM 636 CG MSE X 41 27.851 33.685 35.175 1.00
14.00 C
ATOM 639 SE MSE X 41 28.681 35.387 34.704 1.00
5.03 S
ATOM 640 CE MSE X 41 27.244 36.414 35.435 1.00
16.74 C
ATOM 644 C MSE X 41 30.036 32.247 37.952 1.00
10.98 C
ATOM 645 O MSE X 41 30.706 33.002 38.641 1.00
10.84 O
>From the above, Refmac5 appears to be interpreting the SE atom (34
electrons) as sulfur (16 electrons) (I guess also giving the
unexpectedly low B value for Se).
I'd appreciate any advice or help.
Thanks -- David
--
David R. Buckler
CABM/UMDNJ
679 Hoes Lane
Piscataway, NJ 08854
phone: (732) 235-5164
fax: (732) 235-5289
e-mail: buckler@cabm.rutgers.edu
http://lion.cabm.rutgers.edu/~stock/mem/