Re: [PyMOL] Selecting subsequence in PyMol
Hi Keitaro, Code has been started for nucseq and the shorthand ns.. I think it was not completed because at first glance it appears less than straightforward: ps. searches for the one-letter residue names, but ns. would have to map one-letter codes to those commonly used in the data, DA DT, etc. Cheers, -- Jason On Fri, Dec 10, 2010 at 1:48 AM, Keitaro Yamashita yamash...@castor.sci.hokudai.ac.jp wrote: It's very useful. How about RNA/DNA sequence? Thanks in advance, Keitaro 2010/12/10 Jason Vertrees jason.vertr...@schrodinger.com: Hi Julio, I'm using PyMOL 1.3 and I would like to select one specific part of the molecule based on a peptide sequence that it is presented in protein. Is there any way to select subsequences in PyMOL? Protein sequence: ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK... Peptide: GKTQKV Use the 'ps.' (peptide sequence) modifier: select targetSeq, ps. GKTQKV Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting subsequence in PyMol
Dear Jason, I know there are many residue naming of RNA/DNA depending on what software is used. (for example, Adenine: ADE, A, Ar, Ad,... ) I hope PyMOL would support any naming! Thanks, Keitaro 2010/12/11 Jason Vertrees jason.vertr...@schrodinger.com: Hi Keitaro, Code has been started for nucseq and the shorthand ns.. I think it was not completed because at first glance it appears less than straightforward: ps. searches for the one-letter residue names, but ns. would have to map one-letter codes to those commonly used in the data, DA DT, etc. Cheers, -- Jason On Fri, Dec 10, 2010 at 1:48 AM, Keitaro Yamashita yamash...@castor.sci.hokudai.ac.jp wrote: It's very useful. How about RNA/DNA sequence? Thanks in advance, Keitaro 2010/12/10 Jason Vertrees jason.vertr...@schrodinger.com: Hi Julio, I'm using PyMOL 1.3 and I would like to select one specific part of the molecule based on a peptide sequence that it is presented in protein. Is there any way to select subsequences in PyMOL? Protein sequence: ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK... Peptide: GKTQKV Use the 'ps.' (peptide sequence) modifier: select targetSeq, ps. GKTQKV Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting subsequence in PyMol
Hi Julio, I'm using PyMOL 1.3 and I would like to select one specific part of the molecule based on a peptide sequence that it is presented in protein. Is there any way to select subsequences in PyMOL? Protein sequence: ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK... Peptide: GKTQKV Use the 'ps.' (peptide sequence) modifier: select targetSeq, ps. GKTQKV Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting subsequence in PyMol
It's very useful. How about RNA/DNA sequence? Thanks in advance, Keitaro 2010/12/10 Jason Vertrees jason.vertr...@schrodinger.com: Hi Julio, I'm using PyMOL 1.3 and I would like to select one specific part of the molecule based on a peptide sequence that it is presented in protein. Is there any way to select subsequences in PyMOL? Protein sequence: ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK... Peptide: GKTQKV Use the 'ps.' (peptide sequence) modifier: select targetSeq, ps. GKTQKV Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
