Hi Pradeep,
You CCP4 installation is ancient. Both REFMAC and the dictionary have improved a lot since version 6.3. AF2 and CFZ are in the current dictionary as DNA type. This means that you need not add any LINK records if the residues are numbered sensibly. You also do not need to add any restraint files for these compounds or LINKs to your REFMAC job. So I guess the first thing to do is update your CCP4 to something recent. The rest should work then.
Cheers,
Robbie
PS if you want to test with the latest REFMAC and CCP4 before you update ,you can send your model through the PDB_REDO server and send me an e-mail off-list to check if everything works as expected.
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Pradeep Pallan
> Sent: Tuesday, July 19, 2016 18:29
> To: [log in to unmask]
> Subject: [ccp4bb] Refmac link and constraints
>
> Hi All,
>
> I am refining a protein nucleic acid complex in Refmac5 and came across a
> couple of issues. Some of the nucleic acid residues are modified [eg: 2'-
> Fluoro cytidine monophosphate (CFZ) and 2'Fluoro adenosine
> monophosphate (AF2); both the monomer dictionaries are defined in CCP4
> database (ccp4-6.3.0, linux version). While refining, the program gives the
> message "link is found (not be used)". Why this happens and how to fix this?
>
> -------------(from log file)
> I am reading library. Please wait.
> mon_lib.cif
> INFO: link is found (not be used) dist= 1.411 ideal_dist= 1.510
> ch:CC res: 5 CFZ at:P .->ch:CC res: 104 AF2 at:OP2 .
> INFO: link is found (not be used) dist= 1.539 ideal_dist= 1.510
> ch:CC res: 5 CFZ at:P .->ch:CC res: 104 AF2 at:OP1 .
> INFO: link is found (not be used) dist= 1.698 ideal_dist= 1.610
> ch:CC res: 5 CFZ at:P .->ch:CC res: 104 AF2 at:O5' .
> INFO: link is found (not be used) dist= 1.412 ideal_dist= 1.510
> ch:CC res: 5 CFZ at:O1P .->ch:CC res: 104 AF2 at:P .
> INFO: link is found (not be used) dist= 0.112 ideal_dist= 1.150
> ch:CC res: 5 CFZ at:O1P .->ch:CC res: 104 AF2
> at:OP1 .
> INFO: link is found (not be used) dist= 1.650 ideal_dist= 1.510
> ch:CC res: 5 CFZ at:O2P .->ch:CC res: 104 AF2 at:P .
> INFO: link is found (not be used) dist= 0.715 ideal_dist= 1.150
> ch:CC res: 5 CFZ at:O2P .->ch:CC res: 104 AF2
> at:OP2 .
> INFO: link is found (not be used) dist= 1.725 ideal_dist= 1.610
> ch:CC res: 5 CFZ at:O5' .->ch:CC res: 104 AF2 at:P .
>
> ..........................and so on
>
> -------------(also for CFZ)
> INFO: link is found (not be used) dist= 0.140 ideal_dist= 2.214
> ch:CC res: 6 CFZ at:P .->ch:CC res: 105 CFZ at:P .
> INFO: link is found (not be used) dist= 1.490 ideal_dist= 1.510
> ch:CC res: 6 CFZ at:P .->ch:CC res: 105 CFZ at:O1P .
> INFO: link is found (not be used) dist= 1.397 ideal_dist= 1.510
> ch:CC res: 6 CFZ at:P .->ch:CC res: 105 CFZ at:O2P .
> INFO: link is found (not be used) dist= 1.596 ideal_dist= 1.610
> ch:CC res: 6 CFZ at:P .->ch:CC res: 105 CFZ at:O5' .
> INFO: link is found (not be used) dist= 1.427 ideal_dist= 1.510
> ch:CC res: 6 CFZ at:O1P .->ch:CC res: 105 CFZ at:P .
> INFO: link is found (not be used) dist= 0.146 ideal_dist= 1.150
> ch:CC res: 6 CFZ at:O1P .->ch:CC res: 105 CFZ
>
>
> ............................ and so on
>
>
> In addition, in the output PDB, I find a few angles that are not ideal 97
> degrees (ideal 109 deg) and 129 degrees (ideal 109 deg). For the links, is it
> necessary to put the link records in the pdb and then define it in the
> dictionary as well? Is there a column format that one should follow in order
> to get the dictionary to be read?
> In this particular case, the dictionary contains only description of links as the
> monomers are available in the ccp4 database.
>
>
> # --- DESCRIPTION OF LINKS ---
> .
> .
> .
>
> data_link_AF2-CFZ
> #
> loop_
> _chem_link_bond.link_id
> .
> .
> .
> AF2-CFZ 1 "O3'" 2 P single 1.580 0.020
> loop_
> _chem_link_angle.link_id
> .
> .
> .
> AF2-CFZ 1 "C3'" 1 "O3'" 2 P 118.7 3.00
> AF2-CFZ 1 "O3'" 2 P 2 O1P 108.7 3.00
> AF2-CFZ 1 "O3'" 2 P 2 O2P 108.7 3.00
> AF2-CFZ 1 "O3'" 2 P 2 "O5'" 108.7 3.00
>
>
> What's the best way to correct the above errors, any suggestions?
>
> Thank you,
> Pradeep Pallan
>
>
> pradeeppallan[at] gmail [dot] com
>
> --
>
>
> -------------------------------------------------------------------
> Pradeep Pallan
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