Re: [ccp4bb] DNA in coot
Le 15/02/12 11:36, Tim Gruene a écrit : Hello Lisa, which version of coot do you use? Maybe it is outdated and that function not yet properly implemented. I can confirm Bill's comment, and we work with coot 0.6.2. Cheers, Tim On 02/15/2012 09:01 AM, LISA wrote: Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa Sorry for cross-posting, I thought some people might be interested and only in the coot list. Just to make clear my previous message: we have had exactly the same problem than Lisa reports using the latest version (0.7-pre-3971) available from Bill's repository of standalone Coot for Mac OSX 10.6. By default, this version uses Coot libraries (/Library/Coot/...) I managed to make it behave (in terms of DNA-related work) by forcing it to use CCP4 6.2.0 libraries and then adding (set-convert-to-v2-atom-names 0) to my ~/.coot file. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia signature.asc Description: OpenPGP digital signature
[ccp4bb] DNA in coot
Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa
Re: [ccp4bb] DNA in coot
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Lisa, which version of coot do you use? Maybe it is outdated and that function not yet properly implemented. I can confirm Bill's comment, and we work with coot 0.6.2. Cheers, Tim On 02/15/2012 09:01 AM, LISA wrote: Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPO4qsUxlJ7aRr7hoRAnEhAJwOJyQQxLO9N/7Hjusb2d4ATTwz/QCeNbNP XzRMHtlwg/Fka/9ks/7HtBo= =vqOw -END PGP SIGNATURE-
Re: [ccp4bb] DNA in coot
Hi Lisa, Please go check your PDB file. Are those bases written out like DT or THY or Td. Coot recognizes certain format for DNA bases but I forgot which one coot likes. I don't have my laptop with me right now. My guess would be Td. :) Best, Xun On Wednesday, February 15, 2012, LISA science...@gmail.com wrote: Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa -- Department of Molecular and Structural Biochemistry North Carolina State University
Re: [ccp4bb] DNA in coot
El 16/02/12 05:06, Xun Lu escribió: Hi Lisa, Please go check your PDB file. Are those bases written out like DT or THY or Td. Coot recognizes certain format for DNA bases but I forgot which one coot likes. I don't have my laptop with me right now. My guess would be Td. :) Best, Xun Hi, And that is compounded with the fact that depending on your installation, Coot may be using its own libraries or the CCP4 ones. And they may differ, especially if you're using the new dictionnaries for refmac5. Plus the fact that depending on your preferences Coot converts atoms to PDB v.2.x so they may not come back as you gave them to it. A mess... Paul, at the very least, it would be helpful if like in Lisa's case, an ideal DNA/RNA is created consistent with whatever libraries Coot is going to use for real space refining it. Best regards, -- Miguel On Wednesday, February 15, 2012, LISA science...@gmail.com mailto:science...@gmail.com wrote: Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa -- Department of Molecular and Structural Biochemistry North Carolina State University -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
