Dear Garib, I tried both methods as you advised, but they didn't work for me yet.
1. I ran refmac with the option "residues are close only" and included the keyword file which has the line "MAKE CHECK NONE" as recommended in the log file. However, the refinement was still aborted. It seems that the input keyword did not override the default option. 2. Jligand couldn't properly read my library file (find attached), though sketcher reads fine. Thanks, Young-Tae ________________________________________ From: Garib Murshudov [garib.murshu...@gmail.com] On Behalf Of Garib Murshudov [ga...@ysbl.york.ac.uk] Sent: Thursday, June 24, 2010 4:57 PM To: Young - Tae Lee Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] LINK option during refinement In your run with the option "residues are close only" refmac also should generate a pdb file with link records added. In very simple form you can edit this pdb file and remove all unnecessary links and leave link you want. Then you can rerun with normal options and generated library. Better option is to create links carefully with bond, anlges, chrialities etc. It can be done (I am repeating myself) using JLigand from: http://www.ysbl.york.ac.uk/mxstat/JLigand/1.html the second tutorial in this site is how can create and use covalent links (hopefully at some point it will be done via coot). If any question or problem please let me know and I will try to sort it out. regards Garib On 25 Jun 2010, at 00:42, Young-Tae Lee wrote: > Dear Dr. Murshudov, > > I am working on the heme protein with a surface Cys residue > covalenlty linked to another molecule through its SG atom. > > Here is a part of log file. > ------------------ > INFO: link is found (not be used) dist= 2.188 ideal_dist= > 2.300 > ch:AA res: 400 CYS at:SG .->ch:Aa res: 500 > HEM at:FE . > > INFO: link is found (not be used) dist= 2.316 ideal_dist= > 2.300 > ch:BB res: 400 CYS at:SG .->ch:Ba res: 500 > HEM at:FE . > > INFO: link is found (not be used) dist= 2.398 ideal_dist= > 1.610 > ch:BB res: 97 CYS at:SG .->ch:Bb res: 501 > R7A at:C49 . > ------------------- > How can I turn on only the third link? I am using the refmac5.5.0102 > on ccp4i. > > If I choose the link option "residues are close only" for non- > standard monomers (under "setup geometric restraints" menu), I see > the following messages but the refinement stops. > -------------------- > $TEXT:Warning: $$ Potential and actual links $$ > WARNING : link:CYS-HEM is found dist = 2.184 ideal_dist= > 2.300 > ch:AA res: 400 CYS at:SG .->Aa res: 500 > HEM at:FE . > $$ > $TEXT:Warning: $$ Potential and actual links $$ > WARNING : link:CYS-HEM is found dist = 2.315 ideal_dist= > 2.300 > ch:BB res: 400 CYS at:SG .->Ba res: 500 > HEM at:FE . > $$ > $TEXT:Warning: $$ Potential and actual links $$ > WARNING : description of link:CYS-R7A is not in the dictionary. > link will be created with bond_lenth = 1.610 > $$ > $TEXT:Warning: $$ Potential and actual links $$ > WARNING : link:CYS-R7A is found dist = 2.404 ideal_dist= > 1.610 > ch:BB res: 97 CYS at:SG .->Bb res: 501 > R7A at:C49 . > > If you are happy with the library description then use the keyword > (MAKE CHECK NONE) > I.e. do not check correctness of the coordinates > ===> Error: New ligand has been encountered. Stopping now > Refmac_5.5.0102: New ligand has been encountered. Stopping now > ------------------ > > I will appreciate solutions. > > Young-Tae
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