Hmm - yes. For refmac the default scaling is: 2) Mask based bulk solvent correction. It is activated using the following keywords to build a mask based bulk solvent correction:
scale type simple solvent yes The solvent mask is generated with default parameters to mask the whole model : vdwprobe 1.2 ionprobe 0.8 rashrink 0.8 I am not sure whether the mask is built taking into account atoms with occ = 0.00 or not.. Will ask the experts. But what happens to scaling when you do an OMIT map? Scaling is often a problem, especially at limited resolution. I like to look at a plot of <Fobs> v <Fcalc> which you can find in REFMAC outputs if you know where to look, but often the scaling procedure is shrouded in mystery.. Eleanor On Wed, 7 Apr 2021 at 11:59, Dirk Kostrewa < dirk.kostr...@lrz.uni-muenchen.de> wrote: > Dear Eleanor, > > setting occupancies of omitted atoms to zero has the danger of leaving a > hole with the shape of these atoms in the bulk solvent mask, leading to > positive difference density just because of the missing bulk solvent > density. Since the days of X-PLOR, I always removed the omitted atoms. I > never tried this with REFMAC5, though. > > Cheers, > > Dirk. > On 07.04.21 11:46, Eleanor Dodson wrote: > > Well - I use COOT for this sort of task, and dont trust the automated > tools. > my procedure is > load COOT - probably after a refinement cycle > set occupancy of ligand(s) to 0.00 ( Measures - residue information - > change occupancy) > Look at the environment critically . eg if an ARG or other bulky side > chain nearby , or waters etc selectively set occupancies to 0.00 > > Doo some more cycles of refinement with this coordinate set to remove any > memory of the ligand. > > Look at the map - if the ligand and other zero occ atoms is still in the > right place reinstate them, or try to reinterpret density.. > Eleanor > > > > On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund <bjarte.l...@uit.no> wrote: > >> Dear Hari, >> >> >> >> With regards to 1) Is 15 the number of atoms in your molecule? Or is it >> the number of hydrogens? The CIF file may have the wrong residue name or >> lack the hydrogens depending on how you built the ligand-protein complex. >> >> There is also a phenixbb for phenix questions, >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> >> Kind regards, >> >> >> >> Bjarte Aarmo Lund >> >> Postdoc >> >> UiT The Arctic University of Norway >> >> >> >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> * On Behalf Of *Hari >> shankar >> *Sent:* Wednesday, April 7, 2021 08:47 >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [ccp4bb] Omit maps in phenix and ccp4 >> >> >> >> >> Dear All, >> >> >> >> I have a ligand-protein complex and I wish to calculate different kinds >> of omit maps (say, composite omit maps, simulated annealing maps, other >> unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space >> around it. I have tried phenix for this purpose but get this error message >> consistently. >> >> >> >> "Fatal problems interpreting model file: no of atoms with unknown >> nonbonded energy type symbols: 15 Please edit the model file to resolve the >> problems and/of supply a CIF file with matching restraint definitions, >> along with apply_cif_modification and apply_cif_link parameter definitions >> if necessary." >> >> >> >> This error occurs despite supplying the CIF file for the ligand. I have >> tried to remake the CIF/PDB files from SMILES strings, by drawing the >> molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). >> Nothing seems to work. >> >> >> >> 1. Is there something I have missed out that can solve this issue? >> >> 2. Is there a program in CCP4i that can be used to generate the required >> omit maps? >> >> 3. In general, how do I omit 3.5 ang of the space around the ligand >> during this map calculations? >> >> >> Thank you so much for your time. >> Hari >> >> >> >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > > ******************************************************* > Dirk Kostrewa > Gene Center Munich > Department of Biochemistry, AG Hopfner > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76998 > E-mail: dirk.kostr...@lmu.de > kostr...@genzentrum.lmu.de > WWW: www.genzentrum.lmu.de > ******************************************************* > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
