[ccp4bb] correct atom name

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: mapmask flip the cutted map if input map is huge
From: Jinghua Tang jinghua {- at -} UCSD {- dot -} EDU
Date: 2008-11-01

Next message:
Subject: Re: correct atom name
From: Kevin Jude kjude {- at -} BERKELEY {- dot -} EDU
Date: 2008-11-01

Subject: correct atom name
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-11-01

Dear Friends,
I am tired of renaming an atom name every time I want to switch among the programs cns, phenix and ccp4 particularly for a carbon atom C5A of Thymine given below. What name I should give to this atom specially for cns? Is it C7 or C5A or C5M?

ATOM 1541 P THY K 5 -33.604 -2.379 -7.017 1.00293.90 K P
ATOM 1542 O1P THY K 5 -33.190 -3.005 -5.747 1.00305.95 K O
ATOM 1543 O2P THY K 5 -33.393 -3.107 -8.289 1.00298.26 K O
ATOM 1544 O5' THY K 5 -32.867 -0.964 -7.135 1.00278.14 K O
ATOM 1545 N1 THY K 5 -32.261 0.951 -3.645 1.00297.58 K N
ATOM 1546 C6 THY K 5 -32.334 -0.383 -3.282 1.00295.41 K C
ATOM 1547 C2 THY K 5 -33.001 1.906 -2.968 1.00292.90 K C
ATOM 1548 O2 THY K 5 -32.983 3.098 -3.232 1.00291.97 K O
ATOM 1549 N3 THY K 5 -33.786 1.406 -1.958 1.00289.04 K N
ATOM 1550 C4 THY K 5 -33.903 0.087 -1.558 1.00286.25 K C
ATOM 1551 O4 THY K 5 -34.635 -0.264 -0.640 1.00287.39 K O
ATOM 1552 C5 THY K 5 -33.104 -0.855 -2.294 1.00284.89 K C
ATOM 1553 C5A THY K 5 -33.151 -2.313 -1.950 1.00269.91 K C
ATOM 1554 C2' THY K 5 -30.072 0.525 -4.886 1.00288.00 K C
ATOM 1555 C5' THY K 5 -31.443 -0.886 -7.113 1.00269.59 K C
ATOM 1556 C4' THY K 5 -31.054 0.568 -6.965 1.00273.61 K C
ATOM 1557 O4' THY K 5 -31.989 1.179 -6.040 1.00282.58 K O
ATOM 1558 C1' THY K 5 -31.349 1.354 -4.783 1.00292.39 K C
ATOM 1559 C3' THY K 5 -29.708 0.843 -6.325 1.00277.20 K C
ATOM 1560 O3' THY K 5 -29.453 2.227 -6.477 1.00283.69 K O

Is there any common name of this atom which can be used for all the programs?
Thanks for any suggestion.

Raja

Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

CCP4bb navigation

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

Previous message:
Subject: Re: mapmask flip the cutted map if input map is huge
From: Jinghua Tang jinghua {- at -} UCSD {- dot -} EDU
Date: 2008-11-01

Next message:
Subject: Re: correct atom name
From: Kevin Jude kjude {- at -} BERKELEY {- dot -} EDU
Date: 2008-11-01