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I'd like to add the more current CCP4 solution: AceDRG. It works really well and you only need to feed it the SMILES string of your compound. Also keep in mind that many compounds are actually already in the CCP4 dictionary. Finding out whether a compound is, is a two-step procedure: 1) Go to http://ligand-expo.rcsb.org/ and use the search option to find out whether the compound is already in the PDB 2) If it is, you now have a residue name. To check whether the compound is also in the CCP4 dictionary, just use the 'Get monomer' option in Coot. HTH, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > zaigham mahmood khan > Sent: Friday, July 06, 2018 15:30 > To: [log in to unmask] > Subject: Re: [ccp4bb] Unidentified electron density blob > > Hey Uma > > Yes, you are right that PFPE is too big for this density. Also, more experienced > scientist in this field has already commented on it. > > For the second part of your query, this is how one can generate the > "crystallographic information file" - .cif for the ligand of choice (in case it is not > available): > > 1. Using Prodrg server (http://prodrg1.dyndns.org/submit.html) > 2. Phenix Ligands (i usually use eLBOW), but this will require smile > strings for the molecules not listed in PDB (and hence 3-letter code is not > available). I use Chemdraw to obtain the Smile Strings.. > > > Best wishes > > > -Z > > > Zaigham Mahmood Khan, PhD > > Icahn School of Medicine at Mount Sinai > Department of Oncological Sciences > 1470 Madison Avenue > New York > > On Fri, Jul 6, 2018 at 5:42 AM, Wim Burmeister <[log in to unmask]> > wrote: > > > Hello, > a really molecule should show up also in the 2Fo-Fc type map. This > appears not to be the case. > So indeed it is likely that your density corresponds to some alternate > conformation of the surrounding residues present with low occupancy. The > glutamic acid sidechain could be modelled, but I have some doubts about the > rest. > If the refinement is almost finished, it could simply be noise. > Best > Wim > > > On 03/07/2018 04:23, Uma Gabale wrote: > > > > Dear all, > > > We came across a blob of unidentified electron density in a > shallow cavity of a bacterial protein structure (pictures attached). It is > surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp. > > > The protein was expressed in E. coli BL21(DE3) and purified > on Ni-NTA followed by gel filtration. The purification buffers included Tris, > crystallization condition had HEPES and PEG3350; perfluoropolyether was > used as a cryoprotectant. > > We would appreciate any help in identifying it. > > > Thanks and regards, > > > Uma. > > -- > Uma Gabale, PhD > Research Associate > Molecular and Cellular Biochemistry > Indiana University Bloomington > > > > ________________________________ > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi- > bin/webadmin?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi- > bin/webadmin?SUBED1=CCP4BB&A=1> > > > -- > > > Wim Burmeister > Professeur > Institut de Biologie Structurale (IBS) CIBB > 71 avenue des Martyrs > <https://maps.google.com/?q=71+avenue+des+Martyrs&entry=gmail&sour > ce=g> > > CS 20192 > 38044 Grenoble Cedex 9, FRANCE > E-mail: [log in to unmask] > Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00 > website <http://www.ibs.fr/research/research-groups/viral- > replication-machines-group-m-jamin/team-03/article/poxvirus-replication- > machinery-presentation/> > map > <https://www.openstreetmap.org/?mlat=45.20762&mlon=5.69255#map=17 > /45.20762/5.69255> > > > > > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi- > bin/webadmin?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi- > bin/webadmin?SUBED1=CCP4BB&A=1> > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1