Re: [phenixbb] NAG-NAG description
Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote:
Dear Chris, this did it for me.
Create a file which you can call whatever you want even the extension doesn't matter. E.g.: cif_link.params
Put in this file your links: (Which Atom of residue1 will be connected to which Atom in residue2 is already defined in mon_lib_list.cif)
refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname ASN and resid 297 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname NAG and resid 501 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 501 residue_selection_2 = chain A and resname BMA and resid 502 } refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-3.
residue_selection_1 = chain A and resname BMA and resid 502 residue_selection_2 = chain A and resname MAN and resid 503 }
4) add this file in the GUI
Or run % phenix.refine model.pdb data.hkl cif_link.params
5)Trouble shooting
a)run iotbx.phil cif_link.params (this checks if the syntax is right)
b) check .eff file the links should be added there. You can also check the . geo file if you see anything strange.
c)Having unknown to phenix.refine item in PDB file (novel ligand, etc... (BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as the source of stereochemical information for building geometry restraints and reporting statistics. If phenix.refine is unable to match an item in input PDB file against the Monomer Library it will stop with "Sorry" message explaining what to do and listing the problem atoms. If this happened, it is necessary to obtain a cif file (parameter file, describing unknown molecule) by either making it manually or having eLBOW program to generate it:
phenix.elbow model.pdb --do-all --output=all_ligands
this will ask eLBOW to inspect the model_new.pdb file, find all unknown items in it and create one cif file for them all_ligands.cif. Alternatively, one can specify a three-letters name for the unknown residue:
phenix.elbow model.pdb --residue=MAN --output=man
!Check the file if everything is ok!
Please correct if this is not ok, or there is an easier way now.
Kind regards George.
-----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Chris Ulens Gesendet: Monday, May 31, 2010 9:14 PM An: PHENIX user mailing list Betreff: Re: [phenixbb] NAG-NAG description
Dear glycobiologists and phenixfriends.
I am trying to refine a NAG-NAG chain attached to an Asn122 in my (pentameric) structure. What is the proper description in the cif_link.params that is the equivalent of the pdb description pasted below that phenix so kindly ignores? Also, what is the proper way to define the cif_link.params file in the GUI?
Thank you. -Chris
LINK ND2 ASN A 122 C1 NAG A 834 1555 1555 1.37 LINK O4 NAG A 834 C1 NAG A 835 1555 1555 1.43 LINK ND2 ASN B 122 C1 NAG B 834 1555 1555 1.37 LINK O4 NAG B 834 C1 NAG B 835 1555 1555 1.43 LINK ND2 ASN C 122 C1 NAG C 834 1555 1555 1.37 LINK O4 NAG C 834 C1 NAG C 835 1555 1555 1.43 LINK ND2 ASN D 122 C1 NAG D 834 1555 1555 1.37 LINK O4 NAG D 834 C1 NAG D 835 1555 1555 1.43 LINK ND2 ASN E 122 C1 NAG E 834 1555 1555 1.37 LINK O4 NAG E 834 C1 NAG E 835 1555 1555 1.43
--------------------------------------------------- Chris Ulens, Ph.D. Lab of Structural Neurobiology Department of Molecular Cell Biology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium e [email protected] t +32 16 345812 f +32 16 345699 w http://www.xtal.be
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Hi Chris, Your selection is 'empty' because your NAG is not resid 122 but 834. Your ASN has resid 122. You'll have to come to something like this; this correctly makes the connections you want; apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 834" residue_selection_2 = "chain A and resname ASN and resid 122" } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = "chain A and resname NAG and resid 835" residue_selection_2 = "chain A and resname NAG and resid 834" } HTH Jonathan Elegheert Ghent University Op 01/06/10 13:44, Chris Ulens schreef:
Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement.pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122"
Thanks. -Chris
On 31 May 2010, at 21:34, Georg Mlynek wrote:
Dear Chris, this did it for me.
Create a file which you can call whatever you want even the extension doesn't matter. E.g.: cif_link.params
Put in this file your links: (Which Atom of residue1 will be connected to which Atom in residue2 is already defined in mon_lib_list.cif)
refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname ASN and resid 297 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname NAG and resid 501 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 501 residue_selection_2 = chain A and resname BMA and resid 502 } refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-3.
residue_selection_1 = chain A and resname BMA and resid 502 residue_selection_2 = chain A and resname MAN and resid 503 }
4) add this file in the GUI
Or run % phenix.refine model.pdb data.hkl cif_link.params
5)Trouble shooting
a)run iotbx.phil cif_link.params (this checks if the syntax is right)
b) check .eff file the links should be added there. You can also check the . geo file if you see anything strange.
c)Having unknown to phenix.refine item in PDB file (novel ligand, etc... (BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as the source of stereochemical information for building geometry restraints and reporting statistics. If phenix.refine is unable to match an item in input PDB file against the Monomer Library it will stop with "Sorry" message explaining what to do and listing the problem atoms. If this happened, it is necessary to obtain a cif file (parameter file, describing unknown molecule) by either making it manually or having eLBOW program to generate it:
phenix.elbow model.pdb --do-all --output=all_ligands
this will ask eLBOW to inspect the model_new.pdb file, find all unknown items in it and create one cif file for them all_ligands.cif. Alternatively, one can specify a three-letters name for the unknown residue:
phenix.elbow model.pdb --residue=MAN --output=man
!Check the file if everything is ok!
Please correct if this is not ok, or there is an easier way now.
Kind regards George.
-----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Chris Ulens Gesendet: Monday, May 31, 2010 9:14 PM An: PHENIX user mailing list Betreff: Re: [phenixbb] NAG-NAG description
Dear glycobiologists and phenixfriends.
I am trying to refine a NAG-NAG chain attached to an Asn122 in my (pentameric) structure. What is the proper description in the cif_link.params that is the equivalent of the pdb description pasted below that phenix so kindly ignores? Also, what is the proper way to define the cif_link.params file in the GUI?
Thank you. -Chris
LINK ND2 ASN A 122 C1 NAG A 834 1555 1555 1.37 LINK O4 NAG A 834 C1 NAG A 835 1555 1555 1.43 LINK ND2 ASN B 122 C1 NAG B 834 1555 1555 1.37 LINK O4 NAG B 834 C1 NAG B 835 1555 1555 1.43 LINK ND2 ASN C 122 C1 NAG C 834 1555 1555 1.37 LINK O4 NAG C 834 C1 NAG C 835 1555 1555 1.43 LINK ND2 ASN D 122 C1 NAG D 834 1555 1555 1.37 LINK O4 NAG D 834 C1 NAG D 835 1555 1555 1.43 LINK ND2 ASN E 122 C1 NAG E 834 1555 1555 1.37 LINK O4 NAG E 834 C1 NAG E 835 1555 1555 1.43
--------------------------------------------------- Chris Ulens, Ph.D. Lab of Structural Neurobiology Department of Molecular Cell Biology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium e [email protected] t +32 16 345812 f +32 16 345699 w http://www.xtal.be
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
As a follow-up on the NAG-NAG question I was wondering if other insect
cell users could point me to the proper sources in the literature that
describe the most common glycosylation forms in Sf9/Sf21 insect cells.
It seems we have chains composed of up to 4 sugar molecules attached
to an Asn residue and it would be helpful to know which sugars are
most likely to follow after NAG-NAG.
Thanks.
-Chris
On Jun 1, 2010, at 1:44 PM, Chris Ulens wrote:
Thanks for the feedback.
I would like to refine a NAG-NAG chain attached to residue Asn122 in
my structure. There are 5 identical subunits.
Could you verify my .params file?
I get the following error:
Empty atom selection
refinement
.pdb_interpretation.apply_cif_link.residue_selection_1="chain A and
resname NAG and resid 122"
Thanks.
-Chris
If you look up glycobiology textbooks, you can find a general scheme for insects. Check out the free book Essentials in Glycobiology on NCBI's Books collection. I am sure you can also find more on lepidopteran cell lines (such as Sf9, High five). http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2&part=ch19&rendertype=figure&id=ch19.f2 shows you how it is in insects and other main taxa. To summarize, for insects in general, I would expect this: ASN-(beta1)NAG-(beta1,4)NAG-(beta1,4)BMA-(alpha1,3)MAN | | | (alpha1,3)FUC (alpha1,6)FUC (alpha1,6)MAN Hope this helps a little. Most people are surprised to find the fucose on the C3 of the first NAG, because that does not appear in mammals, but can in insects. I am sure experts can chime in more. Engin On 6/2/10 12:27 PM, Chris Ulens wrote:
As a follow-up on the NAG-NAG question I was wondering if other insect cell users could point me to the proper sources in the literature that describe the most common glycosylation forms in Sf9/Sf21 insect cells. It seems we have chains composed of up to 4 sugar molecules attached to an Asn residue and it would be helpful to know which sugars are most likely to follow after NAG-NAG.
Thanks. -Chris
On Jun 1, 2010, at 1:44 PM, Chris Ulens wrote:
Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122"
Thanks. -Chris
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-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
participants (3)
-
Chris Ulens -
Engin Ozkan -
Jonathan Elegheert