Afaik Refmac will apply the right restraints, iff there is only one type of LINK between those atoms. Particularly with carbohydrates, it's better to be explicit.
Cheers, Robbie Sent from my Windows 10 phone ________________________________ From: Edward A. Berry <ber...@upstate.edu> Sent: Tuesday, May 15, 2018 8:07:38 PM To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problems with HEC in CCP4 Does this mean- if the pdb file has standard PDB link records involving HEC, like LINK SG CYS A 32 CAB HEM A 93 1555 1555 1.82 LINK SG CYS A 35 CAC HEM A 93 1555 1555 1.81 then refmac will look up the necessary modifications in the ccp4 dictionary? Or do we need to tell refmac to apply those mods? eab On 05/15/2018 05:00 AM, Robbie Joosten wrote: > Addendum: > > 4qo5 actually lacks the right LINK records altogether. It will only work if > you add these by hand. Perhaps you should ask the depositors or the PDB to > add the appropriate LINK records. > > Cheers, > Robbie > >> -----Original Message----- >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robbie >> Joosten >> Sent: Tuesday, May 15, 2018 10:51 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Problems with HEC in CCP4 >> >> Hi Eugene, >> >> The problem is not in the HEC.cif file but with the LINKs which modify the >> chemistry. These were fixed a while ago and the LINKs were added to the >> CCP4 dictionary. I thought these were released already. If not, they will be >> soon. >> >> Cheers, >> Robbie >> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of >> Eugene >>> Osipov >>> Sent: Tuesday, May 15, 2018 10:36 >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Problems with HEC in CCP4 >>> >>> Dear CCP4 developers, >>> please fix errors with heme c dictionary file HEC.cif. >>> Edward Berry described this problem in detail 4 years ago: >>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36393.html >>> This error already affects deposited entries, e.g.: 4QO5 clearly >>> contains errors in vynil groups of heme c. >>> >>> >>> -- >>> >>> Eugene Osipov >>> Junior Research Scientist >>> Laboratory of Enzyme Engineering >>> A.N. Bach Institute of Biochemistry >>> Russian Academy of Sciences >>> Leninsky pr. 33, 119071 Moscow, Russia >>> e-mail: e.m.osi...@gmail.com <mailto:e.m.osi...@gmail.com>
