Dear all, could I use eLBOW to create a .cif file for a B-DNA to restrain sugar puckers? Maia
Maia The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library. Nigel On 10/23/08 10:28 PM, chern wrote:
Dear all, could I use eLBOW to create a .cif file for a B-DNA to restrain sugar puckers?
Maia ------------------------------------------------------------------------
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library.
This is more a chemistry question than a formatting question. Since I'm not deeply familiar with the DNA chemistry, I was pointing Maia to phenixbb in hopes that someone may already have figured out the list of torsion angle restraints to fix sugar puckers. What Maia really wants is:
could you please send me a specific example of how to modify a cif file to specify the sugar puckers in DNA (I want them C2'-endo).
Has anyone on this list done this already? Ralf
Maia If you have an example geometry of the C2'-endo eLBOW can generate the restraints. I'm happy to generate them for you if you have one. I'm provide a detailed procedure to list after. Nigel On 10/24/08 9:03 AM, Ralf W. Grosse-Kunstleve wrote:
The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library.
This is more a chemistry question than a formatting question. Since I'm not deeply familiar with the DNA chemistry, I was pointing Maia to phenixbb in hopes that someone may already have figured out the list of torsion angle restraints to fix sugar puckers.
What Maia really wants is:
could you please send me a specific example of how to modify a cif file to specify the sugar puckers in DNA (I want them C2'-endo).
Has anyone on this list done this already?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Dear Nigel, I am sending you an ideal double-stranded B-DNA that I made in coot, but I was puzzled that it had C3*-exo puckers instead of C2*-endo. Probably they are equivalent. Anyway, if you can generate cif for me, I would appreciate it. Maia Nigel W Moriarty wrote:
Maia
If you have an example geometry of the C2'-endo eLBOW can generate the restraints. I'm happy to generate them for you if you have one. I'm provide a detailed procedure to list after.
Nigel
On 10/24/08 9:03 AM, Ralf W. Grosse-Kunstleve wrote:
The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library.
This is more a chemistry question than a formatting question. Since I'm not deeply familiar with the DNA chemistry, I was pointing Maia to phenixbb in hopes that someone may already have figured out the list of torsion angle restraints to fix sugar puckers.
What Maia really wants is:
could you please send me a specific example of how to modify a cif file to specify the sugar puckers in DNA (I want them C2'-endo).
Has anyone on this list done this already?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Ralf,
thank you for your help. I think that I need 3 atoms of the sugars (C1*, O4*
and C4*) to be in a plane. I don't know what the proper esd for the plane
is. This will be enough for me. I want to see what C2* and C3* would do.
Maia
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library.
This is more a chemistry question than a formatting question. Since I'm not deeply familiar with the DNA chemistry, I was pointing Maia to phenixbb in hopes that someone may already have figured out the list of torsion angle restraints to fix sugar puckers.
What Maia really wants is:
could you please send me a specific example of how to modify a cif file to specify the sugar puckers in DNA (I want them C2'-endo).
Has anyone on this list done this already?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Sorry, I gave a wrong subject name in my previous e-mails. Should've been
sugar puckering in DNA.
I am wondering why the default .cif file for DNA does not include all
information about sugar puckers.
I do not have some fancy nucleotides. They are regular.
Maia
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
The answer is yes but there may be better options. Ralf is the best person to answer this question but one option is to start with the .cif file in the monomer library.
This is more a chemistry question than a formatting question. Since I'm not deeply familiar with the DNA chemistry, I was pointing Maia to phenixbb in hopes that someone may already have figured out the list of torsion angle restraints to fix sugar puckers.
What Maia really wants is:
could you please send me a specific example of how to modify a cif file to specify the sugar puckers in DNA (I want them C2'-endo).
Has anyone on this list done this already?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (4)
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chern -
Maia Cherney
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Nigel W Moriarty -
Ralf W. Grosse-Kunstleve