Well - I only understand REFMAC but call the the Cl something different to the ligand - set both to have occupancy 0.5 , then the program will not check for clashes. You will need a dictionary to describe the ligand, and LINK records to define any contacts from protein to the CL.
Is that clear enough? Eleanor On Wed, 5 Mar 2025 at 15:43, stephen.c...@rc-harwell.ac.uk < 00008f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear CCP4 bb, > > I am trying to refine a ligand in the active site of my protein where the > ligand occupancy is ~50%. The empty active site contains two chloride ions > and the residual density from these ions is very prominent when the model > is refined with the ligand alone. To satisfy a reviewer I would like to > refine the model with both the ligand and chloride ions present and have > been trying with the ligand and chloride as alternate conformations of the > same residue but with no luck. I'm assuming that since the Cl ions > more-or-less directly overlay atoms from the ligand positional refinement > keeps pushing them out of the density even though the relative occupancies > are sensible. I'm sure there is a simple way to get around this and I > would be grateful for any suggestions. > > Best wishes, > Steve > > > > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email stephen.c...@rc-harwell.ac.uk > tel 01235 567717 > This email and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorized recipient of the > addressee, please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > this email. Any views or opinions presented are solely those of the author > and do not necessarily represent those of the Research Complex at Harwell. > There is no guarantee that this email or any attachments are free from > viruses and we cannot accept liability for any damage which you may sustain > as a result of software viruses which may be transmitted in or with the > message. We use an electronic filing system. Please send electronic > versions of documents, unless paper is specifically requested. This email > may have a protective marking, for an explanation, please see: > http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. > > > ------------------------------ > > 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/
