[ccp4bb] Fwd: Re: [ccp4bb] sugar and coot
Stuck email... try again... Original Message Subject:Re: [ccp4bb] sugar and coot Date: Wed, 30 Nov 2011 19:42:54 + From: Paul Emsley paul.ems...@bioch.ox.ac.uk To: d...@iwonka.med.virginia.edu d...@iwonka.med.virginia.edu CC: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK On 30/11/11 17:07, Heping Zheng wrote: The issue I have is to polysacchride chains refinement in general, but here more specific about branch chain of polysacchride chains. For example, if you think about the case of N-glycosylation Asn-NAG-beta1,4-NAG-beta1,4-Man-(alpha1,3-Man)-alpha1,6-Man ... Now you have a branch chain, Now if I assume the following resseq ASN A135 NAG A500 NAG A501 MAN A502 MAN A503 MAN A504 In my coot, version 0.6 revision 2540, You will be able to refine A500-A503 as a whole since they are consecutive in resseq. indeed. But when I need to refine NAG A500 together with ASN A135 locally, simply specify the range is not enough, I need to specify a small radius to get it work, even though the covalent link is defined in LINKR record. Quite so. As I said (or more accurately, implied) LINKR recognition is an on-going issue (i.e. it doesn't work yet). The same applies when I want to refine just A502-A504 alpha1,6 glycosidic bond without refine A503. Yes. I am just wondering what is the state of the art for branch chain handling in coot or another interactive refinement program. Well, I don't know much about about other programs, but in coot you can use refine-residues or Sphere Refinement. Even in 0.6. Paul.
Re: [ccp4bb] sugar and coot
The issue I would raise here is not just for coot, but also for PDB format itself. Last time I asked on ACA2011, Dr. Berman said polysacchride residues in PDB is still not yet uniformly represented. The issue I have is to polysacchride chains refinement in general, but here more specific about branch chain of polysacchride chains. For example, if you think about the case of N-glycosylation Asn-NAG-beta1,4-NAG-beta1,4-Man-(alpha1,3-Man)-alpha1,6-Man ... Now you have a branch chain, Now if I assume the following resseq ASN A135 NAG A500 NAG A501 MAN A502 MAN A503 MAN A504 In my coot, version 0.6 revision 2540, You will be able to refine A500-A503 as a whole since they are consecutive in resseq. But when I need to refine NAG A500 together with ASN A135 locally, simply specify the range is not enough, I need to specify a small radius to get it work, even though the covalent link is defined in LINKR record. The same applies when I want to refine just A502-A504 alpha1,6 glycosidic bond without refine A503. I am just wondering what is the state of the art for branch chain handling in coot or another interactive refinement program. best regards, Heping Zheng On 22/11/11 00:16, Jan van Agthoven wrote: Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Such a tool (if I understand correctly what you want) does not yet exist. However, I believe that things are not in as poor a state as one might infer from other posts. Using the pre-release, you can 1) ideally position a NAG onto ASN 2) use multi-residue torsion to position a NAG by rotation of ASN chi angles 3) use the Ligand builder to build new carbohydrate monomers (it is my experience that PRODRG respects the wedge bonds - but I have heard that this is not always the case) Using latest stable or later you can 4) multi-residue refinement (or sphere refine), which does a link analysis based on the coordinates of the residue selection (note that bonding atoms have to be within 3A to be considered a real glycosidic linkage) 5) add addition pseudo plane restraints to encourage ideal chair (in my experience, at low resolution or with poor density, carbohydrates tend to wander off and twist up without these) The JLigand-Coot interface has stalled a bit, but I hope should be available for the Study Weekend. The Refmac-Coot link-up using LINKR is under discussion with Garib and Eugene. I would recommend against making a synthetic disaccharide carbohydrate with PRODRG. Regards, Paul.
Re: [ccp4bb] sugar and coot
You can also try Jligand to generate your cif file J From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan van Agthoven Sent: Tuesday, 22 November 2011 1:17 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] sugar and coot Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Jan
Re: [ccp4bb] sugar and coot
On 22/11/11 00:16, Jan van Agthoven wrote: Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Such a tool (if I understand correctly what you want) does not yet exist. However, I believe that things are not in as poor a state as one might infer from other posts. Using the pre-release, you can 1) ideally position a NAG onto ASN 2) use multi-residue torsion to position a NAG by rotation of ASN chi angles 3) use the Ligand builder to build new carbohydrate monomers (it is my experience that PRODRG respects the wedge bonds - but I have heard that this is not always the case) Using latest stable or later you can 4) multi-residue refinement (or sphere refine), which does a link analysis based on the coordinates of the residue selection (note that bonding atoms have to be within 3A to be considered a real glycosidic linkage) 5) add addition pseudo plane restraints to encourage ideal chair (in my experience, at low resolution or with poor density, carbohydrates tend to wander off and twist up without these) The JLigand-Coot interface has stalled a bit, but I hope should be available for the Study Weekend. The Refmac-Coot link-up using LINKR is under discussion with Garib and Eugene. I would recommend against making a synthetic disaccharide carbohydrate with PRODRG. Regards, Paul.
[ccp4bb] sugar and coot
Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Jan
Re: [ccp4bb] sugar and coot
Hi, I'm not sure if that is what you are looking for, but if you want to use the real space refine zone function in coot with sugars that is possible. For a monosaccharide you will need a cif dictionary with the restraint definitions - in some cases present in the refmac monomer database, but be careful not all cif files there are correct. If none is present or if your monomer is disrupted during refinement you can look at the small molecule databases (Hic-Up etc) or calculate one with PRODRG (http://davapc1.bioch.dundee.ac.uk/prodrg/). Load it with File Import CIF dictionary and real space refinement should work. If you try to refine a polysaccharide it's a bit more difficult since coot will ignore any glycosidic bond restraints - if two sugars are close by and one has well defined density and the other one not it might even place them on top of each other. I like to use the anchor tool on the bonding atoms in those cases. The other option for a polysaccharide is to use PRODRG to generate a single monomer out of your polysaccharide. In any case at the end you have to inspect the geometry manually since the restraint definitions are often incomplete. Greetings Dirk Am 22.11.11 01:16, schrieb Jan van Agthoven: Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Jan
