Thank You very much !
I have zipped all my files to Fei Tan's file(AMBER) and it includes a cnoe.upl file that lists all peaks from cnoesy pearliest, a cnoe.map file that list all ambiguous assignments,a cnoe0613 file that is the output from a automatic assignment program SANE that explains in detail what the precise assignment for each peak cnoesy peak really is My protein is a dimeric protein, so the residue number doubles, and it makes almost all the peaks double ambiguous. rst file is the makeDIST_RST output of the cnoe.upl and cnoe.map files.
Sincerely Fei Tan----- ÔʼÓʼþ -----
·¢¼þÈË£º"Duggan, Brendan" <bmduggan.ucsd.edu>
ÊÕ¼þÈË£º"amber.ambermd.org" <amber.ambermd.org>
³ËÍÈË£º"tanfei777.sina.cn" <tanfei777.sina.cn>
Ö÷Ì⣺Re: Help me with double ambiguous noe.map files!!! PLEASE
ÈÕÆÚ£º2016Äê06ÔÂ14ÈÕ 01µã26·Ö
Dear members: I am currently working on an NMR structure calculation using amber . I am also using SANE to select the most probable NOE assignments based on structure filters. However, I encountered some problems when preparing for distance restraint rst files, more specifically, in understanding double ambiguous noe.map files. For example, for CNOESY peak #74 , SANE outputs includes
0 AMB 20-2:74 0 AMB 20-1:74 4.50 # 74:20 Double Ambig
map file for this peak :
AMBIG 20-2:74 = HG1- 155 HG1+ 155 HG1- 55 HG1+ 55 HG1+ 155 HG1+ 55 HB+ 61
AMBIG 20-1:74 = HA 153 HA 53 HA 154 HA 54
The dyana format upl corresponding to this peak is :
Contribution filtering eliminated 5 possibilities
MET_153:HA ILE_155:HG1- MET_153:CA 0.016 -0.002 -0.096 4.64 6.07 0.16094
MET_153:HA ILE_155:HG1+ MET_153:CA 0.016 -0.020 -0.096 4.64 6.07 0.16094
MET_53:HA ILE_55:HG1- MET_53:CA 0.016 -0.002 -0.096 4.92 6.03 0.11371
MET_53:HA ILE_55:HG1+ MET_53:CA 0.016 -0.020 -0.096 4.92 6.03 0.11371
MET_154:HA ILE_155:HG1- MET_154:CA 0.005 -0.002 -0.092 5.17 6.10 0.08477
MET_154:HA ILE_155:HG1+ MET_154:CA 0.005 -0.020 -0.092 5.17 6.10 0.08477
MET_54:HA ILE_55:HG1- MET_54:CA 0.005 -0.002 -0.092 5.21 6.11 0.08026
MET_54:HA ILE_55:HG1+ MET_54:CA 0.005 -0.020 -0.092 5.21 6.11 0.08026
MET_54:HA LEU_61:HB+ MET_54:CA 0.005 -0.022 -0.092 6.03 6.83 0.03365
Restraint written as :0 AMB 20-2:74 ( HG1- 155 HG1+ 155 HG1- 55 HG1+ 55 HG1+ 155 HG1+ 55 HB+ 61 ) --- 0 AMB 20-1:74 ( HA 153 HA 53 HA 154 HA 54 )
what I am confused about is the translation rule between the map file and the upper distance restraint
For some peak, it seems that the correspondence of the ambiguous possibilities is one to one, but in this case HG1+ 155 and HG1+ 55 in the indirect dimension in the map file is written twice
Can you please help me with this , Thank you very much!!Yours sincerely
Hi Fei Tan
It does look a little odd that HG1+ 155 and HG1+ 55 appear twice in the restraint. If you could zip up all your input files and send them to me I will look at them to see what is going on.
Brendan
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Received on Mon Jun 13 2016 - 20:30:03 PDT
