Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps
Hi Jan, I would advise against playing with occupancies because it adds a complication that has side effects on the density and is easily overlooked by the users of your model. There are many Jeffamines on the market, so figuring out which is the one you have is the first step. Depending on how much effort you want to put in you can do the following: - Figure out the register of the oxygens if the density allows you to place atoms (i.e. it is not a tube without peaks). I would use a PEG molecule for this. If you have no meaningful contacts you can refine alternative models and see which refines best. There are just three options. - The next step depends on the type of jeffamine you have. If it is just blocks of propylene glycol. You have two options for the methyl group register. You can try both. If it is a mixture of ethylene and propylene glycol blocks, this is where I would give up and not place any methyls unless they are really obvious. - Depending on the size of your blob and the type of Jeffamine you may, or may not see the termini of you molecule and you can try to model those. If this all is a bit much for your project you can do the 'UNL' trick and just refine a string of carbons and explain what you did in the paper and model annotation. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Jan > Stransky > Sent: Friday, August 19, 2022 15:39 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution > maps > > Hi Matthew, > > thanks for the thought. > > Yes, I agree, that it is average whole lot of conformations. I am aware of > FEMs, it is great tool, but I got similar results as with Polder maps. > > Modelling just the "main chain" and calling it Jeffamin, is also an option I > was > considering. It is part of the question, how to do properly for the PDB > deposition. If I do just the Jeffamin "mainchain", it would be effectively PEG > library, but not named as PEG. I think that would be confusing. > > However, really treating it as aa residue with invisible sidechain is > interesting > option. Our lab consensus is to keep the atoms, but reduce occupancy to > almost 0. I think, I could do that for the methyl groups in Jeffamin. > > Best regards, > > Jan > > > > > > On 8/19/22 11:42, Matthew Snee wrote: > > > Hi > > It is likely that your density is a consensus of multiple different > jeffamines binding at different rotational orientations, so that at 2.6A the > methyl groups are essentially averaged out, and therefore the density may > not exist to be found. > > Phenix has a tool called "feature enhanced maps" which is designed > to reverse the flattening of weak features, but I find its important to have > the best possible phases (I.E most accurate model) before using it. > > I suppose you could model jeffamine, and delete the methyl groups > (I.E treat is like a residue with an unresolved sidechain). > > Cheers > > Matthew. > > > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Jan Stransky > <mailto:jan.stransky.c...@gmail.com> > Sent: 18 August 2022 10:37 > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Polymer ligand (Jefffamin) modeling in low > resolution maps > > > Dear all, > > we have a structure at not the greatest resolution (~2.6A) of which > crystal was grown in crystallization condition with Jeffamin. In the > maps, we see typical PEG-like sausages. Jeffamin is basically a PEG > decorated with some methyl groups and it is terminated with amine > groups. > > Now, the question is how to interpret such blobs? To my > understanding > the methyl decoration is not regular, and it is not obviously visible in > the maps. Nor is clear, if there is a contact to the amine group. When > we tried to put in PEG models as placeholders, it explains the density > fine, but the contacts are nothing great, e.g. position of the oxygens > in the polymer is not clear. > > Calculating Polder maps does not clear things up. > > How would you deal with interpretation such maps? > > Thank you for your ideas :-) > > Jan > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA- > JISC
Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps
Hi Matthew, thanks for the thought. Yes, I agree, that it is average whole lot of conformations. I am aware of FEMs, it is great tool, but I got similar results as with Polder maps. Modelling just the "main chain" and calling it Jeffamin, is also an option I was considering. It is part of the question, how to do properly for the PDB deposition. If I do just the Jeffamin "mainchain", it would be effectively PEG library, but not named as PEG. I think that would be confusing. However, really treating it as aa residue with invisible sidechain is interesting option. Our lab consensus is to keep the atoms, but reduce occupancy to almost 0. I think, I could do that for the methyl groups in Jeffamin. Best regards, Jan On 8/19/22 11:42, Matthew Snee wrote: Hi It is likely that your density is a consensus of multiple different jeffamines binding at different rotational orientations, so that at 2.6A the methyl groups are essentially averaged out, and therefore the density may not exist to be found. Phenix has a tool called "feature enhanced maps" which is designed to reverse the flattening of weak features, but I find its important to have the best possible phases (I.E most accurate model) before using it. I suppose you could model jeffamine, and delete the methyl groups (I.E treat is like a residue with an unresolved sidechain). Cheers Matthew. *From:* CCP4 bulletin board on behalf of Jan Stransky *Sent:* 18 August 2022 10:37 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps Dear all, we have a structure at not the greatest resolution (~2.6A) of which crystal was grown in crystallization condition with Jeffamin. In the maps, we see typical PEG-like sausages. Jeffamin is basically a PEG decorated with some methyl groups and it is terminated with amine groups. Now, the question is how to interpret such blobs? To my understanding the methyl decoration is not regular, and it is not obviously visible in the maps. Nor is clear, if there is a contact to the amine group. When we tried to put in PEG models as placeholders, it explains the density fine, but the contacts are nothing great, e.g. position of the oxygens in the polymer is not clear. Calculating Polder maps does not clear things up. How would you deal with interpretation such maps? Thank you for your ideas :-) Jan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps
Hello Jan Not a very helpful suggestion, but using rcsb's ligand-expo site I did find some structures of similar resolution in the PDB with jeffamine present. I don't know if looking at them would be helpful and you have probably done that already. Sent from ProtonMail mobile Original Message On 18 Aug 2022, 10:37, Jan Stransky wrote: > Dear all, we have a structure at not the greatest resolution (~2.6A) of which > crystal was grown in crystallization condition with Jeffamin. In the maps, we > see typical PEG-like sausages. Jeffamin is basically a PEG decorated with > some methyl groups and it is terminated with amine groups. Now, the question > is how to interpret such blobs? To my understanding the methyl decoration is > not regular, and it is not obviously visible in the maps. Nor is clear, if > there is a contact to the amine group. When we tried to put in PEG models as > placeholders, it explains the density fine, but the contacts are nothing > great, e.g. position of the oxygens in the polymer is not clear. Calculating > Polder maps does not clear things up. How would you deal with interpretation > such maps? Thank you for your ideas :-) Jan > To > unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps
Dear all, we have a structure at not the greatest resolution (~2.6A) of which crystal was grown in crystallization condition with Jeffamin. In the maps, we see typical PEG-like sausages. Jeffamin is basically a PEG decorated with some methyl groups and it is terminated with amine groups. Now, the question is how to interpret such blobs? To my understanding the methyl decoration is not regular, and it is not obviously visible in the maps. Nor is clear, if there is a contact to the amine group. When we tried to put in PEG models as placeholders, it explains the density fine, but the contacts are nothing great, e.g. position of the oxygens in the polymer is not clear. Calculating Polder maps does not clear things up. How would you deal with interpretation such maps? Thank you for your ideas :-) Jan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
