From: Maurício M. R. <mau...@gm...> - 2012-09-14 17:44:53
|
Dear Pymol users, > > I'm a begginer with command lines in Pymol. I'm trying to complete the > following task through a pymol script: > > 1) Write a file named "file1.txt" with an aminoacid sequence (e.g. CVGLTUW) > > 2) Open a .pdb molecule (file2.pdb) with the same number of residues, but > with a different sequence (e.g. ALTWSIK) > > 3) Write a code where the pymol will pick each residue of the file2.pdb (I > believe that this could be made by the mutagenesis wizard command) and > mutate for the respective aminoacid written in my file1.txt > > 4) Save the new filein .pdb format (file3.pdb) > > I'll be very greatful for any help! > > Thanks in advance, > -- > M.Sc. Maurício Menegatti Rigo > Núcleo de Bioinformática do Laboratório de Imunogenética > Departamento de Genética > Instituto de Biociências > Universidade Federal do Rio Grande do Sul - Campus do Vale > Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M > CEP:91501-970 Caixa Postal 15053 > Porto Alegre, RS, Brasil > Tel: +55 51 3308 9938 > |
From: Thomas H. <sp...@us...> - 2012-09-14 18:16:05
|
Hi Maurício, what you describe here is called homology modeling. Although PyMOL has some modeling capabilities, I'd strongly recommend to use a real homology modeling tool such as MODELLER to do this. http://salilab.org/modeller/ Hope that helps. Cheers, Thomas Maurício Menegatti Rigo wrote, On 09/14/12 19:44: > Dear Pymol users, > > I'm a begginer with command lines in Pymol. I'm trying to > complete the following task through a pymol script: > > 1) Write a file named "file1.txt" with an aminoacid sequence (e.g. > CVGLTUW) > > 2) Open a .pdb molecule (file2.pdb) with the same number of > residues, but with a different sequence (e.g. ALTWSIK) > > 3) Write a code where the pymol will pick each residue of the > file2.pdb (I believe that this could be made by the mutagenesis > wizard command) and mutate for the respective aminoacid written in > my file1.txt > > 4) Save the new filein .pdb format (file3.pdb) > > I'll be very greatful for any help! > > Thanks in advance, > -- > M.Sc. Maurício Menegatti Rigo > Núcleo de Bioinformática do Laboratório de Imunogenética > Departamento de Genética > Instituto de Biociências > Universidade Federal do Rio Grande do Sul - Campus do Vale > Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M > CEP:91501-970 Caixa Postal 15053 > Porto Alegre, RS, Brasil > Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938> -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Maurício M. R. <mau...@gm...> - 2012-09-14 18:26:57
|
Hi Thomas, thank you for your response. Actually, the modeling part comes later in the process. First, I need to perform this step in pymol. In fact, it would facilitate the modeling process. Sincerely, -- Maurício M Rigo 2012/9/14 Thomas Holder <sp...@us...> > Hi Maurício, > > what you describe here is called homology modeling. Although PyMOL has > some modeling capabilities, I'd strongly recommend to use a real homology > modeling tool such as MODELLER to do this. > > http://salilab.org/modeller/ > > Hope that helps. > > Cheers, > Thomas > > Maurício Menegatti Rigo wrote, On 09/14/12 19:44: > >> Dear Pymol users, >> >> I'm a begginer with command lines in Pymol. I'm trying to >> complete the following task through a pymol script: >> >> 1) Write a file named "file1.txt" with an aminoacid sequence (e.g. >> CVGLTUW) >> >> 2) Open a .pdb molecule (file2.pdb) with the same number of >> residues, but with a different sequence (e.g. ALTWSIK) >> >> 3) Write a code where the pymol will pick each residue of the >> file2.pdb (I believe that this could be made by the mutagenesis >> wizard command) and mutate for the respective aminoacid written in >> my file1.txt >> >> 4) Save the new filein .pdb format (file3.pdb) >> >> I'll be very greatful for any help! >> >> Thanks in advance, >> -- M.Sc. Maurício Menegatti Rigo >> Núcleo de Bioinformática do Laboratório de Imunogenética >> Departamento de Genética >> Instituto de Biociências >> Universidade Federal do Rio Grande do Sul - Campus do Vale >> Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M >> CEP:91501-970 Caixa Postal 15053 >> Porto Alegre, RS, Brasil >> Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938> >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- M.Sc. Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul - Campus do Vale Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M CEP:91501-970 Caixa Postal 15053 Porto Alegre, RS, Brasil Tel: +55 51 3308 9938 |
From: Troels E. L. <tl...@gm...> - 2012-09-19 19:32:56
|
Hi. I tried a little: *test1.pml* # See http://www.pymolwiki.org/index.php/Peptide_Sequence # See http://www.pymolwiki.org/index.php/propka reinitialize cd C:\Users\tlinnet\Desktop python for aa in "CVGLTSW": cmd._alt(string.lower(aa)) python end create pdb1, cys remove cys delete cys save pdb1.fasta, pdb1 #######First time #python #for aa in "ALTWSIK": # cmd._alt(string.lower(aa)) #python end #create pdb2, ala #remove ala #delete ala #translate [-6,-15,0], pdb2 #save pdb2.pdb, pdb2 ####### Second time load pdb2.pdb alter pdb1, chain='A' alter pdb2, chain='A' rebuild create pdb3, pdb1 chainresnresi3 = [] chainresnresi2 = [] iterate pdb3 and name CA, chainresnresi3.append(["pdb3",chain,resn,resi]) iterate pdb2 and name CA, chainresnresi2.append(["pdb2",chain,resn,resi]) #print chainresnresi3 #print chainresnresi2 python cmd.wizard("mutagenesis") for i in range(len(chainresnresi2)): cmd.do("refresh_wizard") cmd.get_wizard().set_mode("%s"%chainresnresi2[i][2]) #print "%s"%chainresnresi2[i][2] selection="/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) #print "/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) cmd.get_wizard().do_select(selection) cmd.frame(1) cmd.get_wizard().apply() python end cmd.set_wizard("done") translate [10,-25,0], pdb3 *test2.pml* reinitialize cd C:\Users\tlinnet\Desktop fab CVGLTSW, pdb1, resi=1, chain=A save pdb1.fasta, pdb1 fab ALTWSIK, pdb2, resi=1, chain=A translate [0,-15,0], pdb2 create pdb3, pdb1 translate [0,-30,0], pdb3 chainresnresi3 = [] chainresnresi2 = [] iterate pdb3 and name CA, chainresnresi3.append(["pdb3",chain,resn,resi]) iterate pdb2 and name CA, chainresnresi2.append(["pdb2",chain,resn,resi]) print chainresnresi3 print chainresnresi2 python cmd.wizard("mutagenesis") for i in range(len(chainresnresi2)): cmd.do("refresh_wizard") cmd.get_wizard().set_mode("%s"%chainresnresi2[i][2]) #print "%s"%chainresnresi2[i][2] selection="/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) #print "/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) cmd.get_wizard().do_select(selection) cmd.frame(1) cmd.get_wizard().apply() python end cmd.set_wizard("done") *test3.pml* reinitialize cd C:\Users\tlinnet\Desktop load pdb1.fasta load pdb2.fasta translate [0,-15,0], pdb2 create pdb3, pdb1 translate [0,-30,0], pdb3 chainresnresi3 = [] chainresnresi2 = [] iterate pdb3 and name CA, chainresnresi3.append(["pdb3",chain,resn,resi]) iterate pdb2 and name CA, chainresnresi2.append(["pdb2",chain,resn,resi]) print chainresnresi3 print chainresnresi2 python cmd.wizard("mutagenesis") for i in range(len(chainresnresi2)): cmd.do("refresh_wizard") cmd.get_wizard().set_mode("%s"%chainresnresi2[i][2]) #print "%s"%chainresnresi2[i][2] selection="/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) #print "/%s//%s/%s"%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3]) cmd.get_wizard().do_select(selection) cmd.frame(1) cmd.get_wizard().apply() python end cmd.set_wizard("done") *pdb1.fasta* >pdb1 CVGLTSW *pdb2.fasta* >pdb2 ALTWSIK Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2012/9/14 Maurício Menegatti Rigo <mau...@gm...> > Hi Thomas, > > thank you for your response. Actually, the modeling part comes later in > the process. First, I need to perform this step in pymol. In fact, it > would facilitate the modeling process. > > Sincerely, > -- > Maurício M Rigo > > > 2012/9/14 Thomas Holder <sp...@us...> > >> Hi Maurício, >> >> what you describe here is called homology modeling. Although PyMOL has >> some modeling capabilities, I'd strongly recommend to use a real homology >> modeling tool such as MODELLER to do this. >> >> http://salilab.org/modeller/ >> >> Hope that helps. >> >> Cheers, >> Thomas >> >> Maurício Menegatti Rigo wrote, On 09/14/12 19:44: >> >>> Dear Pymol users, >>> >>> I'm a begginer with command lines in Pymol. I'm trying to >>> complete the following task through a pymol script: >>> >>> 1) Write a file named "file1.txt" with an aminoacid sequence (e.g. >>> CVGLTUW) >>> >>> 2) Open a .pdb molecule (file2.pdb) with the same number of >>> residues, but with a different sequence (e.g. ALTWSIK) >>> >>> 3) Write a code where the pymol will pick each residue of the >>> file2.pdb (I believe that this could be made by the mutagenesis >>> wizard command) and mutate for the respective aminoacid written in >>> my file1.txt >>> >>> 4) Save the new filein .pdb format (file3.pdb) >>> >>> I'll be very greatful for any help! >>> >>> Thanks in advance, >>> -- M.Sc. Maurício Menegatti Rigo >>> Núcleo de Bioinformática do Laboratório de Imunogenética >>> Departamento de Genética >>> Instituto de Biociências >>> Universidade Federal do Rio Grande do Sul - Campus do Vale >>> Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M >>> CEP:91501-970 Caixa Postal 15053 >>> Porto Alegre, RS, Brasil >>> Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938> >>> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > > > -- > M.Sc. Maurício Menegatti Rigo > Núcleo de Bioinformática do Laboratório de Imunogenética > Departamento de Genética > Instituto de Biociências > Universidade Federal do Rio Grande do Sul - Campus do Vale > Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M > CEP:91501-970 Caixa Postal 15053 > Porto Alegre, RS, Brasil > Tel: +55 51 3308 9938 > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > 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: Martin H. <ma...@bl...> - 2012-09-20 09:46:41
|
Dear PyMOL users Is it possible to somehow assign "page up" or "page down" keys to switch from one loaded model to the next one in the PyMOL models list? This would be useful because I often have several similar models listed and in doing so it would be easier and convenient to identify changes within them. Thanks for any hints Martin |
From: Jason V. <jas...@sc...> - 2012-09-20 16:33:05
|
Hi Martin, > Is it possible to somehow assign "page up" or "page down" keys to switch > from one loaded model to the next one in the PyMOL models list? > This would be useful because I often have several similar models listed > and in doing so it would be easier and convenient to identify changes > within them. How about something like http://pymolwiki.org/index.php/ObjectFocus. It's cool what you can do with PyMOL and 8 minutes of coding. Two changes to the script you might want: * replace 'orient' with 'zoom' * don't animate the change, remote ',animate=1' from the orient command. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Tsjerk W. <ts...@gm...> - 2012-09-20 17:38:09
|
Hi :) You can also add cmd.disable('all') cmd.enable(cur_obj) To have all other objects turned off. This is one I'm definitely going to use :) Cheers, Tsjerk On Thu, Sep 20, 2012 at 6:32 PM, Jason Vertrees <jas...@sc...> wrote: > Hi Martin, > >> Is it possible to somehow assign "page up" or "page down" keys to switch >> from one loaded model to the next one in the PyMOL models list? >> This would be useful because I often have several similar models listed >> and in doing so it would be easier and convenient to identify changes >> within them. > > How about something like http://pymolwiki.org/index.php/ObjectFocus. > It's cool what you can do with PyMOL and 8 minutes of coding. > > Two changes to the script you might want: > * replace 'orient' with 'zoom' > * don't animate the change, remote ',animate=1' from the orient command. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://ad.doubleclick.net/clk;258768047;13503038;j? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands |
From: Martin H. <ma...@bl...> - 2012-09-21 09:14:19
|
Sweet:) I disabled the animate but I can see its applicability in some situations though (makes it pretty impressive). Definitly a must-have from now on, in fact how could I even live without it;) Martin On 20.09.12 19:38, Tsjerk Wassenaar wrote: > Hi :) > > You can also add > > cmd.disable('all') > cmd.enable(cur_obj) > > To have all other objects turned off. This is one I'm definitely going to use :) > > Cheers, > > Tsjerk > > On Thu, Sep 20, 2012 at 6:32 PM, Jason Vertrees > <jas...@sc...> wrote: >> Hi Martin, >> >>> Is it possible to somehow assign "page up" or "page down" keys to switch >>> from one loaded model to the next one in the PyMOL models list? >>> This would be useful because I often have several similar models listed >>> and in doing so it would be easier and convenient to identify changes >>> within them. >> How about something like http://pymolwiki.org/index.php/ObjectFocus. >> It's cool what you can do with PyMOL and 8 minutes of coding. >> >> Two changes to the script you might want: >> * replace 'orient' with 'zoom' >> * don't animate the change, remote ',animate=1' from the orient command. >> >> Cheers, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrödinger, Inc. >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://ad.doubleclick.net/clk;258768047;13503038;j? >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > |