From: Bradley H. <bra...@ag...> - 2010-12-09 17:09:59
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Hi, I'm using pymol 1.3 and I have a pml script. when I do a show as command the right-hand column disappears. I appears again if i puch escape to access the command line. Anyone have any idea what is going on here? Bradley -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
From: Julio C. da S. <jul...@ln...> - 2010-12-09 19:13:09
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Good afternoon, 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? A fictitious example: Protein sequence: ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK... Peptide: GKTQKV I know that I can search manually this peptide in the sequence using the PyMOL. However, for huge protein, it takes a lot of time. Is there any automated routine to do this? Thank you in advance. Júlio César da Silva Brazilian Bioscience Laboratory Campinas, SP - Brazil + 55 (19) 3512-1116 jul...@ln...<mailto:jul...@ln...> (novo e-mail: favor atualizar o seu cadastro) www.lnbio.org.br<http://www.lnls.br/> -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
From: Jason V. <jas...@sc...> - 2010-12-09 19:19:05
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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) Jas...@sc... (o) +1 (603) 374-7120 |
From: Keitaro Y. <yam...@ca...> - 2010-12-10 06:48:50
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It's very useful. How about RNA/DNA sequence? Thanks in advance, Keitaro 2010/12/10 Jason Vertrees <jas...@sc...>: > 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) Jas...@sc... > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Jason V. <jas...@sc...> - 2010-12-10 17:10:20
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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 <yam...@ca...> wrote: > It's very useful. > How about RNA/DNA sequence? > > Thanks in advance, > > Keitaro > > 2010/12/10 Jason Vertrees <jas...@sc...>: >> 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) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > ------------------------------------------------------------------------------ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Keitaro Y. <yam...@ca...> - 2010-12-11 02:26:10
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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 <jas...@sc...>: > 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 > <yam...@ca...> wrote: >> It's very useful. >> How about RNA/DNA sequence? >> >> Thanks in advance, >> >> Keitaro >> >> 2010/12/10 Jason Vertrees <jas...@sc...>: >>> 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) Jas...@sc... >>> (o) +1 (603) 374-7120 >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Jason V. <jas...@sc...> - 2010-12-10 17:12:04
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Hi Bradley, This sounds like a mobile video card problem. Are you on a laptop? Perhaps one with an Intel GM45 card? What OS? Cheers, -- Jason On Thu, Dec 9, 2010 at 11:13 AM, Bradley Hintze <bra...@ag...> wrote: > Hi, > > I'm using pymol 1.3 and I have a pml script. when I do a show as command the > right-hand column disappears. I appears again if i puch escape to access the > command line. Anyone have any idea what is going on here? > > Bradley > > -- > Bradley J. Hintze > Graduate Student > Duke University > School of Medicine > 801-712-8799 > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Bradley H. <bra...@ag...> - 2010-12-10 17:58:06
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Hi Jason, I'm using Snow Leopard. It only happens when i run my .pml script. If I put 'load xxxx.pdb' at the end of the script the panel stays but if I turn on and off the objects created in my script the panel disappears. It appears my system is up to date. I'm not sure what the deal is. Bradley On Fri, Dec 10, 2010 at 12:11 PM, Jason Vertrees < jas...@sc...> wrote: > Hi Bradley, > > This sounds like a mobile video card problem. Are you on a laptop? > Perhaps one with an Intel GM45 card? What OS? > > Cheers, > > -- Jason > > On Thu, Dec 9, 2010 at 11:13 AM, Bradley Hintze > <bra...@ag...> wrote: > > Hi, > > > > I'm using pymol 1.3 and I have a pml script. when I do a show as command > the > > right-hand column disappears. I appears again if i puch escape to access > the > > command line. Anyone have any idea what is going on here? > > > > Bradley > > > > -- > > Bradley J. Hintze > > Graduate Student > > Duke University > > School of Medicine > > 801-712-8799 > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
From: Thomas H. <sp...@us...> - 2010-12-10 18:03:13
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What does this .pml script do? I once had artefacts on the interface after loading an incomplete CGO object. Cheers, Thomas Bradley Hintze wrote, On 12/10/10 18:26: > Hi Jason, > > I'm using Snow Leopard. It only happens when i run my .pml script. If I > put 'load xxxx.pdb' at the end of the script the panel stays but if I > turn on and off the objects created in my script the panel disappears. > It appears my system is up to date. I'm not sure what the deal is. > > > Bradley > > On Fri, Dec 10, 2010 at 12:11 PM, Jason Vertrees > <jas...@sc... <mailto:jas...@sc...>> > wrote: > > Hi Bradley, > > This sounds like a mobile video card problem. Are you on a laptop? > Perhaps one with an Intel GM45 card? What OS? > > Cheers, > > -- Jason > > On Thu, Dec 9, 2010 at 11:13 AM, Bradley Hintze > <bra...@ag... <mailto:bra...@ag...>> > wrote: > > Hi, > > > > I'm using pymol 1.3 and I have a pml script. when I do a show as > command the > > right-hand column disappears. I appears again if i puch escape to > access the > > command line. Anyone have any idea what is going on here? > > > > Bradley |
From: Bradley H. <bra...@ag...> - 2010-12-11 22:28:13
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Thanks, putting the missing END element seemed to rectify the problem. On Sat, Dec 11, 2010 at 4:26 AM, Thomas Holder < sp...@us...> wrote: > do you have END as last element of obj? This is required for LINES. > > Bradley Hintze wrote, On 12/10/10 19:25: > >> It crates vectors as shown below: >> >> obj = [ BEGIN, LINES, COLOR, 1.000, 0.365, 0.000, VERTEX, >> -122.605,-63.053,26.985, VERTEX,... >> cmd.load_cgo(obj,'hotpink_spikes') >> >> On Fri, Dec 10, 2010 at 1:03 PM, Thomas Holder < >> sp...@us... <mailto:sp...@us...>> >> wrote: >> >> What does this .pml script do? I once had artefacts on the interface >> after loading an incomplete CGO object. >> >> Cheers, >> Thomas >> > -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |