Hi Xiao,

Could you look in your original PDB file and see if there is in fact duplication of atom names? If there is then it would be good to backtrack to the place where this occurred and change it, as it isn't allowable to have atoms with duplicate names.

If on the other hand autobuild is doing this, then I will be happy to fix the problem if you could send me (off-list) the input files and your full log file.

All the best,

Tom T

From: [email protected] [[email protected]] on behalf of Xiao Lei [[email protected]]
Sent: Friday, July 24, 2015 3:31 PM
To: PHENIX user mailing list
Subject: [phenixbb] Phenix Autobuild error

Hi All,

I am using Phenix autobuild (version 1.10pre on CentOS) and I failed with an error message (I put it below). My input experimental data (in MTZ format) is 2.5A, with space group C2, and 1 molecule per ASU (No NCS copies), the molecule contains two protein chains and one double-strand DNA (heterodimer protein bound to dsDNA). It seems to me the error is because in my model PDB there are different atoms in DNA with the same name.

How can I fix this problem?

Error message from phenix.refine: number of groups of duplicate atom labels: 4

total number of affected atoms: 8

group "HETATM 4930 O3' DT C 716 .*. O "

"HETATM 5471 O3' DT C 716 .*. O "

group "HETATM 4937 C7 DT C 716 .*. C "

"HETATM 5472 C7 DT C 716 .*. C "

group "HETATM 4950 O3' DG C 717 .*. O "

"HETATM 5473 O3' DG C 717 .*. O "

group "HETATM 4964 O6 DG C 717 .*. O "

"HETATM 5474 O6 DG C 717 .*. O "

Refinement failed...

Thanks ahead.

Xiao