Dear all, Thanks for the suggestions. I'll give it a try and see how it goes.
Cheers, Catarina Silva On Wed, Aug 3, 2011 at 9:59 PM, Miller, Mitchell D. < [email protected]> wrote: > Hi Boas, > Yes, tlsanal would work but only if the structure was > refined with the keyword > TLSD waters exclude > either by explicitly including the keyword or > by using a version that of refmac that defaults to > TLSD waters exclude. I believe that recent > versions of refmac 5.6 default to tlsd waters exclude > but that all refmac 5.5 versions (or at least those > after 5.5.0036) default to TLSD water add. > > If the structure was refined with TLSD waters add, > then waters have residual B's but since refmac does > not update the TLS ranges to reflect which waters > are in which TLS group, tlsanal cannot add the TLS > component to the waters and you will end up with > a file with full-B on the residues in the TLS > range definition and residual B's on the waters. > > My reason for recommending running another refinement > round was that it was less complicated in my mind > then trying to explain the nuances of the effect of > TLSD waters exclude vs TLSD waters add on determining > whether or not tlsanal would be able to properly > convert the file. > > Regards, > Mitch > > -----Original Message----- > From: Boaz Shaanan [mailto:[email protected]] > Sent: Wednesday, August 03, 2011 1:40 PM > To: Miller, Mitchell D.; [email protected] > Subject: RE: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt > > Just wondering: wouldn't running tlsanal on the final refmac output as > Catarina has it now put the true aniso record straight? > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: [email protected] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Miller, > Mitchell D. [[email protected]] > Sent: Wednesday, August 03, 2011 11:14 PM > To: [email protected] > Subject: Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt > > Hi Catarina , > > For your final refmac refinement job, you need to include > the keyword > TLSO ADDU > to have the TLS contribution added to the residual B-factors. > This keyword can also be set from the recent version of the ccp4i > GUI by checking the checkbox for "Add TLS contribution to XYZOUT" > in the TLS section. > (This addu output file is needed for deposition but should not be > used for further TLS refinement with refmac). > > Also, depending on the version of refmac you are using, it may also > default to adding waters to TLS groups. If it does, then they > waters will have ANISOU records after TLS refinement. Note that > refmac does not update the TLS range records to reflect this change. > If you want to exclude water from TLS assignment, you can > also include the "TLSD waters exclude" keyword. > > Regards, > Mitch > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Catarina Silva > Sent: Wednesday, August 03, 2011 12:47 PM > To: [email protected] > Subject: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt > > Dear all, > > I am trying to deposit a pdb containing TLS groups. PDB instructions > states: > "As we have mentioned on the start page for autodep, entries refined using > REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM > records, with the TLS contribution coded into ANISOU records." > > I did run Refmac with TLS parameters and, as such, I would expect that all > the values necessary to pdb deposition would be on the pdb coming out from > refmac. However, when I deposit the pdb a 'serious error' comes up, not > allowing me to deposit the coordinates: > > "You will NOT be allowed to proceed for deposition unless these issues are > corrected. > TLS and ANISOU/RESIDUAL B-FACTORS. > As we have mentioned on the start page for autodep, entries refined using > REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM > records, with the TLS contribution coded into ANISOU records.Your entry > contains TLS records but no ANISOU records OR Residual B-factors. Please > correct this and reupload your structure for validation" > > I don't really understand why these supposed missing values are not already > contained in the pdb file, and I can't figure out how to get them. Does > anyone knows how to fix this situation? > > Thanks in advance! > > Catarina Silva >
