From: kanika s. <ksh...@gm...> - 2011-02-25 12:46:08
|
Hi, i am working to generate a dimer of my protein..I have made a duplicate of my protein....Can any one tell me how to rotate my molecule to get maximum stability..??? Regards.. Kanika |
From: Hongbo Z. <hon...@bi...> - 2011-02-25 13:10:25
|
Hi, Kanika, are you looking for biological units of proteins when you say stable dimer? If this is the case, I recommend the page: http://pdbwiki.org/index.php/Biological_unit at the bottom of the page you can find four very useful servers for the determination of biological units of proteins (PQS is not updated anymore): The Protein Quaternary Structure Server (PQS) [2] or [3] The Macro-Molecular Structure Database (MSD) [4] or [5] The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] Protein quaternary structure investigation (PiQSi) [7] As a matter of fact, the PDB also provides the biological assembly of each PDB entry for download. More information can be found at: http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html If your protein is not from the PDB, you can still try pisa ( http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein coordinate files uploaded by the users and determines the "stable dimer" or else-mer of your protein. hope these help! hongbo On 02/25/2011 01:46 PM, kanika sharma wrote: > Hi, > i am working to generate a dimer of my protein..I have made a duplicate > of my protein....Can any one tell me how to rotate my molecule to get > maximum stability..??? > > > Regards.. > Kanika > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search& Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel.: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu@biotec.tu-dresden Webpage: www.biotec.tu-dresden.de |
From: kanika s. <ksh...@gm...> - 2011-02-28 11:20:50
|
I have a dimeric protein 3HHZ.....to generate the dimer foll transformations have to be made....the problem is that this is an identity matrix,so will not change anything...can anyone help with this?? how can i get the asymmetric unit to generate dimer?? REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu <hon...@bi... > wrote: > Hi, Kanika, > > are you looking for biological units of proteins when you say stable dimer? > If this is the case, I recommend the page: > > http://pdbwiki.org/index.php/Biological_unit > at the bottom of the page you can find four very useful servers for the > determination of biological units of proteins (PQS is not updated anymore): > The Protein Quaternary Structure Server (PQS) [2] or [3] > The Macro-Molecular Structure Database (MSD) [4] or [5] > The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] > Protein quaternary structure investigation (PiQSi) [7] > > As a matter of fact, the PDB also provides the biological assembly of each > PDB entry for download. More information can be found at: > > http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html > > If your protein is not from the PDB, you can still try pisa ( > http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts > protein coordinate files uploaded by the users and determines the "stable > dimer" or else-mer of your protein. > > hope these help! > hongbo > > > On 02/25/2011 01:46 PM, kanika sharma wrote: > >> Hi, >> i am working to generate a dimer of my protein..I have made a duplicate >> of my protein....Can any one tell me how to rotate my molecule to get >> maximum stability..??? >> >> >> Regards.. >> Kanika >> >> >> >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search& Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> >> >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > -- > Hongbo ZHU > Postdoctoral Researcher > Structural Bioinformatics > > Technische Universität Dresden > Biotechnology Center > Tatzberg 47/49 > 01307 Dresden, Germany > > Tel.: +49 (0) 351 463-40083 > Fax: +49 (0) 351 463-40087 > E-Mail: hongbo.zhu@biotec.tu-dresden > Webpage: www.biotec.tu-dresden.de > |
From: Chad D. <cha...@gm...> - 2011-02-28 12:06:31
|
I thought symexp() would accomplish this, no? From: http://pymol.sourceforge.net/newman/user/S0400xtal.html Something like: fetch 3hhz symexp mysymm, 3hhz, (3hhz), 2.75 (I came up with 2.75 by trail-and-error as 2.5 generates no symmetry mates and 3.0 generated too many) In the case of 3m2m, the header you pasted shows there are 12 potential biological assemblies, 1 through 8 are all monomeric, however. 9 through 12 are the dimeric assemblies. If you need a dimer, you need to download any one of 9 through 12, which are probably all equivalent to one another. Note that PISA seems to believe that this is a monomer. I would be sure that you have other evidence that this is a dimer, as there are other crystal contacts in the deposited 3m2m. These might also help http://www.pymolwiki.org/index.php/Symexp http://www.pymolwiki.org/index.php/BiologicalUnit -Chad On Mon, Feb 28, 2011 at 12:20, kanika sharma <ksh...@gm...> wrote: > I have a dimeric protein 3HHZ.....to generate the dimer foll transformations > have to be made....the problem is that this is an identity matrix,so will > not change anything...can anyone help with this?? > how can i get the asymmetric unit to generate dimer?? > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu > <hon...@bi...> wrote: >> >> Hi, Kanika, >> >> are you looking for biological units of proteins when you say stable >> dimer? If this is the case, I recommend the page: >> >> http://pdbwiki.org/index.php/Biological_unit >> at the bottom of the page you can find four very useful servers for the >> determination of biological units of proteins (PQS is not updated anymore): >> The Protein Quaternary Structure Server (PQS) [2] or [3] >> The Macro-Molecular Structure Database (MSD) [4] or [5] >> The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] >> Protein quaternary structure investigation (PiQSi) [7] >> >> As a matter of fact, the PDB also provides the biological assembly of each >> PDB entry for download. More information can be found at: >> >> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html >> >> If your protein is not from the PDB, you can still try pisa ( >> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein >> coordinate files uploaded by the users and determines the "stable dimer" or >> else-mer of your protein. >> >> hope these help! >> hongbo >> >> On 02/25/2011 01:46 PM, kanika sharma wrote: >>> >>> Hi, >>> i am working to generate a dimer of my protein..I have made a duplicate >>> of my protein....Can any one tell me how to rotate my molecule to get >>> maximum stability..??? >>> >>> >>> Regards.. >>> Kanika >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> >>> >>> >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> Hongbo ZHU >> Postdoctoral Researcher >> Structural Bioinformatics >> >> Technische Universität Dresden >> Biotechnology Center >> Tatzberg 47/49 >> 01307 Dresden, Germany >> >> Tel.: +49 (0) 351 463-40083 >> Fax: +49 (0) 351 463-40087 >> E-Mail: hongbo.zhu@biotec.tu-dresden >> Webpage: www.biotec.tu-dresden.de > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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: kanika s. <ksh...@gm...> - 2011-02-28 12:20:57
|
the symexp data may not always be consistent with the biomt transformations..although they turn out to be.. considering the case of 3hh7...the biological unit and asymm unit are same...to form a dimer of this protein...i cannot find a clue by biomt data REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
From: Tsjerk W. <ts...@gm...> - 2011-02-28 12:22:17
|
Hi Chad, Kanika, Symexp is for generating symmetry mates, not for (re)constructing biological assemblies. If the BIOMT record gives an identity matrix, it means that there is no further information for building a biological unit. The biological unit is most likely contained in the PDB file. Note that it may be part of the structure in the PDB file, as those may contain an asymmetric crystallographic unit. Kanika, You come up with a different protein every time, which makes it a bit confusing for us, but probably also for yourself. Maybe it's good to first get to understand the basics, the file formats, biological units, pymol, etc. Otherwise, provide a more full account of what you're trying to do, what you've tried to do yourself getting there and where you got stuck. Cheers, Tsjerk On Mon, Feb 28, 2011 at 1:06 PM, Chad Davis <cha...@gm...> wrote: > I thought symexp() would accomplish this, no? > From: > http://pymol.sourceforge.net/newman/user/S0400xtal.html > > Something like: > > fetch 3hhz > symexp mysymm, 3hhz, (3hhz), 2.75 > > (I came up with 2.75 by trail-and-error as 2.5 generates no symmetry > mates and 3.0 generated too many) > > In the case of 3m2m, the header you pasted shows there are 12 > potential biological assemblies, 1 through 8 are all monomeric, > however. 9 through 12 are the dimeric assemblies. If you need a dimer, > you need to download any one of 9 through 12, which are probably all > equivalent to one another. Note that PISA seems to believe that this > is a monomer. I would be sure that you have other evidence that this > is a dimer, as there are other crystal contacts in the deposited 3m2m. > > These might also help > http://www.pymolwiki.org/index.php/Symexp > http://www.pymolwiki.org/index.php/BiologicalUnit > > -Chad > > > On Mon, Feb 28, 2011 at 12:20, kanika sharma <ksh...@gm...> wrote: >> I have a dimeric protein 3HHZ.....to generate the dimer foll transformations >> have to be made....the problem is that this is an identity matrix,so will >> not change anything...can anyone help with this?? >> how can i get the asymmetric unit to generate dimer?? >> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B >> >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 >> >> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 >> >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 >> On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu >> <hon...@bi...> wrote: >>> >>> Hi, Kanika, >>> >>> are you looking for biological units of proteins when you say stable >>> dimer? If this is the case, I recommend the page: >>> >>> http://pdbwiki.org/index.php/Biological_unit >>> at the bottom of the page you can find four very useful servers for the >>> determination of biological units of proteins (PQS is not updated anymore): >>> The Protein Quaternary Structure Server (PQS) [2] or [3] >>> The Macro-Molecular Structure Database (MSD) [4] or [5] >>> The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] >>> Protein quaternary structure investigation (PiQSi) [7] >>> >>> As a matter of fact, the PDB also provides the biological assembly of each >>> PDB entry for download. More information can be found at: >>> >>> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html >>> >>> If your protein is not from the PDB, you can still try pisa ( >>> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein >>> coordinate files uploaded by the users and determines the "stable dimer" or >>> else-mer of your protein. >>> >>> hope these help! >>> hongbo >>> >>> On 02/25/2011 01:46 PM, kanika sharma wrote: >>>> >>>> Hi, >>>> i am working to generate a dimer of my protein..I have made a duplicate >>>> of my protein....Can any one tell me how to rotate my molecule to get >>>> maximum stability..??? >>>> >>>> >>>> Regards.. >>>> Kanika >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>>> data >>>> generated by your applications, servers and devices whether physical, >>>> virtual >>>> or in the cloud. Deliver compliance at lower cost and gain new business >>>> insights. http://p.sf.net/sfu/splunk-dev2dev >>>> >>>> >>>> >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> -- >>> Hongbo ZHU >>> Postdoctoral Researcher >>> Structural Bioinformatics >>> >>> Technische Universität Dresden >>> Biotechnology Center >>> Tatzberg 47/49 >>> 01307 Dresden, Germany >>> >>> Tel.: +49 (0) 351 463-40083 >>> Fax: +49 (0) 351 463-40087 >>> E-Mail: hongbo.zhu@biotec.tu-dresden >>> Webpage: www.biotec.tu-dresden.de >> >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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...> - 2011-03-01 12:44:45
|
Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh # remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow *color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin |
From: Tsjerk W. <ts...@gm...> - 2011-03-01 15:40:41
|
Hi Martin, The wiki way should work. The only thing I can think of is that you're not doing what you think you're doing :S Did you copy paste the commands from the wiki? Did you get an error? What version are you using? > but, the selection kind of does not work for me (I'm assuming the operator > for the logical AND is 'and'). That's correct, 'and' gives the intersection. > What is it that I need to do differently? Can you provide an example that works using fetch and such? Just a simple script we can try. Cheers, Tsjerk -- 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: David R. <dav...@gm...> - 2011-03-01 15:54:23
|
Hi Martin, Try the following: color tv_red, resn asp+glu or color tv_red, resn asp or resn glu Cheers, 2011/3/1 Martin Hediger <ma...@bl...> > Dear all > What is the selection syntax to select all GLU and ASP residues within an > object? > > I'm trying it the way its written on the wiki: > > remove resn hoh # remove water > h_add # add hydrogens > > as surface > color grey90 > > color slate, resn lys # lysines in light blue > color paleyellow, resn cys # cysteines in light yellow*color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* > > but, the selection kind of does not work for me (I'm assuming the operator > for the logical AND is 'and'). > What is it that I need to do differently? > > Kind regards > Martin > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Santiago de Compostela (Spain) http://webspersoais.usc.es/persoais/david.rodriguez.diaz <http://webspersoais.usc.es/persoais/david.rodriguez.diaz> |
From: Jason V. <jas...@sc...> - 2011-03-01 16:49:46
|
Hi Martin, To select all ASPs and GLUs just type, select resn GLU+ASP or select resn GLU or resn ASP or, if you need parentheses, select ((resn GLU) or (resn ASP)) Maybe this will help: # fetch a test protein fetch 1rsy, async=0 # color all ASPs and GLUs red color tv_red, (resn ASP or resn GLU) While the boolean 'and' works, the following will fail to select and color any atoms: color tv_red, (resn ASP and resn GLU) because there will be no _single atom_ in both an ASP and a GLU. The boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in any ASP _and_ in any GLU--which is impossible. Cheers, -- Jason On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger <ma...@bl...> wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within an > object? > > I'm trying it the way its written on the wiki: > > remove resn hoh # remove water > h_add # add hydrogens > > as surface > color grey90 > > color slate, resn lys # lysines in light blue > color paleyellow, resn cys # cysteines in light yellow > color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light > red > > but, the selection kind of does not work for me (I'm assuming the operator > for the logical AND is 'and'). > What is it that I need to do differently? > > Kind regards > Martin > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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: Hongbo Z. <hon...@bi...> - 2011-03-02 10:06:22
|
I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead of AND in such situation. The expression: select resn GLU or resn ASP actually means select (resn == GLU) or (resn == ASP) The reason of using Boolean operator *or* is very clean when the two operands are stated completely. But when the operands are simplified, our first reaction is to use *and* because it is very natural to say "I want GLU *and* ASP" if you want both GLU and ASP. And it is even more confusing in Jmol : select 110 or 112 (select resno==110 or resn==112) if want you really want is 110 *and* 112 :) hongbo On 03/01/2011 05:43 PM, Jason Vertrees wrote: > Hi Martin, > > To select all ASPs and GLUs just type, > > select resn GLU+ASP > > or > > select resn GLU or resn ASP > > or, if you need parentheses, > > select ((resn GLU) or (resn ASP)) > > > Maybe this will help: > > # fetch a test protein > > fetch 1rsy, async=0 > > # color all ASPs and GLUs red > > color tv_red, (resn ASP or resn GLU) > > > While the boolean 'and' works, the following will fail to select and > color any atoms: > > color tv_red, (resn ASP and resn GLU) > > because there will be no _single atom_ in both an ASP and a GLU. The > boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in > any ASP _and_ in any GLU--which is impossible. > > Cheers, > > -- Jason > > > > On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...> wrote: >> Dear all >> What is the selection syntax to select all GLU and ASP residues within an >> object? >> >> I'm trying it the way its written on the wiki: >> >> remove resn hoh # remove water >> h_add # add hydrogens >> >> as surface >> color grey90 >> >> color slate, resn lys # lysines in light blue >> color paleyellow, resn cys # cysteines in light yellow >> color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light >> red >> >> but, the selection kind of does not work for me (I'm assuming the operator >> for the logical AND is 'and'). >> What is it that I need to do differently? >> >> Kind regards >> Martin >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search& Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de |
From: Martin H. <ma...@bl...> - 2011-03-02 21:03:51
|
Hey Hongbo, good way of putting it. Indeed, I think thats what seemed most intuetively to me in the beginning, and so I ended up trying to figure out why 'AND' was not giving me the expected selection. Remembering my boolean algebra lecture from back in the days, I suddendly realized that it has to be 'OR', right now I'm wondering why this is not expressed as 'v' (as opposed to 'AND', which then would of course be '^'). But you're right, the Jmol example is really making the point of how weird this can appear to be. Martin Am 02.03.11 11:06, schrieb Hongbo Zhu: > I believe the confusion is caused by the simplified selection expression > in PyMOL (and some other visualization tools as well). I remember that > one of my colleagues once questioned strongly the reason of using OR > instead of AND in such situation. > > The expression: > > select resn GLU or resn ASP > > actually means > > select (resn == GLU) or (resn == ASP) > > The reason of using Boolean operator *or* is very clean when the two > operands are stated completely. But when the operands are simplified, > our first reaction is to use *and* because it is very natural to say > > "I want GLU *and* ASP" > > if you want both GLU and ASP. > > And it is even more confusing in Jmol : > > select 110 or 112 (select resno==110 or resn==112) > > if want you really want is 110 *and* 112 :) > > hongbo > > On 03/01/2011 05:43 PM, Jason Vertrees wrote: >> Hi Martin, >> >> To select all ASPs and GLUs just type, >> >> select resn GLU+ASP >> >> or >> >> select resn GLU or resn ASP >> >> or, if you need parentheses, >> >> select ((resn GLU) or (resn ASP)) >> >> >> Maybe this will help: >> >> # fetch a test protein >> >> fetch 1rsy, async=0 >> >> # color all ASPs and GLUs red >> >> color tv_red, (resn ASP or resn GLU) >> >> >> While the boolean 'and' works, the following will fail to select and >> color any atoms: >> >> color tv_red, (resn ASP and resn GLU) >> >> because there will be no _single atom_ in both an ASP and a GLU. The >> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in >> any ASP _and_ in any GLU--which is impossible. >> >> Cheers, >> >> -- Jason >> >> >> >> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...> wrote: >>> Dear all >>> What is the selection syntax to select all GLU and ASP residues within an >>> object? >>> >>> I'm trying it the way its written on the wiki: >>> >>> remove resn hoh # remove water >>> h_add # add hydrogens >>> >>> as surface >>> color grey90 >>> >>> color slate, resn lys # lysines in light blue >>> color paleyellow, resn cys # cysteines in light yellow >>> color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light >>> red >>> >>> but, the selection kind of does not work for me (I'm assuming the operator >>> for the logical AND is 'and'). >>> What is it that I need to do differently? >>> >>> Kind regards >>> Martin >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> _______________________________________________ >>> 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: Tsjerk W. <ts...@gm...> - 2011-03-02 21:07:48
|
Hey :) It's good to note that programs are written by programmers, using programmer's logic.The confusion is not so much caused by the simplified expression, but by users with little background in mathematics/logic assessing 'and' and 'or' from a linguistic background. In computer science and mathematics OR := union, AND := intersection. It's covered quite well in http://www.pymolwiki.org/index.php/Selection_Algebra Cheers, Tsjerk On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu <hon...@bi...> wrote: > I believe the confusion is caused by the simplified selection expression > in PyMOL (and some other visualization tools as well). I remember that > one of my colleagues once questioned strongly the reason of using OR > instead of AND in such situation. > > The expression: > > select resn GLU or resn ASP > > actually means > > select (resn == GLU) or (resn == ASP) > > The reason of using Boolean operator *or* is very clean when the two > operands are stated completely. But when the operands are simplified, > our first reaction is to use *and* because it is very natural to say > > "I want GLU *and* ASP" > > if you want both GLU and ASP. > > And it is even more confusing in Jmol : > > select 110 or 112 (select resno==110 or resn==112) > > if want you really want is 110 *and* 112 :) > > hongbo > > On 03/01/2011 05:43 PM, Jason Vertrees wrote: >> Hi Martin, >> >> To select all ASPs and GLUs just type, >> >> select resn GLU+ASP >> >> or >> >> select resn GLU or resn ASP >> >> or, if you need parentheses, >> >> select ((resn GLU) or (resn ASP)) >> >> >> Maybe this will help: >> >> # fetch a test protein >> >> fetch 1rsy, async=0 >> >> # color all ASPs and GLUs red >> >> color tv_red, (resn ASP or resn GLU) >> >> >> While the boolean 'and' works, the following will fail to select and >> color any atoms: >> >> color tv_red, (resn ASP and resn GLU) >> >> because there will be no _single atom_ in both an ASP and a GLU. The >> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in >> any ASP _and_ in any GLU--which is impossible. >> >> Cheers, >> >> -- Jason >> >> >> >> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...> wrote: >>> Dear all >>> What is the selection syntax to select all GLU and ASP residues within an >>> object? >>> >>> I'm trying it the way its written on the wiki: >>> >>> remove resn hoh # remove water >>> h_add # add hydrogens >>> >>> as surface >>> color grey90 >>> >>> color slate, resn lys # lysines in light blue >>> color paleyellow, resn cys # cysteines in light yellow >>> color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light >>> red >>> >>> but, the selection kind of does not work for me (I'm assuming the operator >>> for the logical AND is 'and'). >>> What is it that I need to do differently? >>> >>> Kind regards >>> Martin >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> > > -- > Hongbo ZHU > Postdoctoral Researcher > Structural Bioinformatics > > Technische Universität Dresden > Biotechnology Center > Tatzberg 47/49 > 01307 Dresden, Germany > > Tel: +49 (0) 351 463-40083 > Fax: +49 (0) 351 463-40087 > E-Mail: hongbo.zhu at biotec > Webpage: www.biotec.tu-dresden.de > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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: Hongbo Z. <hon...@bi...> - 2011-03-02 21:36:57
|
On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: > Hey :) > > It's good to note that programs are written by programmers, using > programmer's logic. First of all, I was not complaining about the logic of the PyMOL programmers. I tried to help find out the reason that might cause Martin's script to break based on the similar complains I had received. It is true that programs are written by programmers. But I guess many users actually hate that fact so much because they see again and again that some programmers just presume that all users will think the same way as they think. (Of course after these users become programmers they start to do the same ;) The confusion is not so much caused by the > simplified expression, but by users with little background in > mathematics/logic assessing 'and' and 'or' from a linguistic > background.In computer science and mathematics OR := union, AND := > intersection. It's covered quite well in > http://www.pymolwiki.org/index.php/Selection_Algebra I disagree. I think it is caused by the simplified expression to the users who think intuitively instead of immediately mathematically when they try to write down the first line of selection script, no matter how much mathematics/logic they have (the colleague I mentioned is a computer scientist). After staring at the unexpected outcome for a while, they will try to think mathematically or google-ly ;). I can not think of a good way to address this small issue for new users. Maybe a more informative hint to the users is helpful rather than just print "0 atoms selected". For example, PyMOL can print the selection result of each operand, or print the complete selection expression translated from the the simplified selection expression. > > Cheers, > > Tsjerk > > On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu > <hon...@bi...> wrote: >> I believe the confusion is caused by the simplified selection expression >> in PyMOL (and some other visualization tools as well). I remember that >> one of my colleagues once questioned strongly the reason of using OR >> instead of AND in such situation. >> >> The expression: >> >> select resn GLU or resn ASP >> >> actually means >> >> select (resn == GLU) or (resn == ASP) >> >> The reason of using Boolean operator *or* is very clean when the two >> operands are stated completely. But when the operands are simplified, >> our first reaction is to use *and* because it is very natural to say >> >> "I want GLU *and* ASP" >> >> if you want both GLU and ASP. >> >> And it is even more confusing in Jmol : >> >> select 110 or 112 (select resno==110 or resn==112) >> >> if want you really want is 110 *and* 112 :) >> >> hongbo >> >> On 03/01/2011 05:43 PM, Jason Vertrees wrote: >>> Hi Martin, >>> >>> To select all ASPs and GLUs just type, >>> >>> select resn GLU+ASP >>> >>> or >>> >>> select resn GLU or resn ASP >>> >>> or, if you need parentheses, >>> >>> select ((resn GLU) or (resn ASP)) >>> >>> >>> Maybe this will help: >>> >>> # fetch a test protein >>> >>> fetch 1rsy, async=0 >>> >>> # color all ASPs and GLUs red >>> >>> color tv_red, (resn ASP or resn GLU) >>> >>> >>> While the boolean 'and' works, the following will fail to select and >>> color any atoms: >>> >>> color tv_red, (resn ASP and resn GLU) >>> >>> because there will be no _single atom_ in both an ASP and a GLU. The >>> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in >>> any ASP _and_ in any GLU--which is impossible. >>> >>> Cheers, >>> >>> -- Jason >>> >>> >>> >>> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...> wrote: >>>> Dear all >>>> What is the selection syntax to select all GLU and ASP residues within an >>>> object? >>>> >>>> I'm trying it the way its written on the wiki: >>>> >>>> remove resn hoh # remove water >>>> h_add # add hydrogens >>>> >>>> as surface >>>> color grey90 >>>> >>>> color slate, resn lys # lysines in light blue >>>> color paleyellow, resn cys # cysteines in light yellow >>>> color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light >>>> red >>>> >>>> but, the selection kind of does not work for me (I'm assuming the operator >>>> for the logical AND is 'and'). >>>> What is it that I need to do differently? >>>> >>>> Kind regards >>>> Martin >>>> >>>> ------------------------------------------------------------------------------ >>>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>>> data >>>> generated by your applications, servers and devices whether physical, >>>> virtual >>>> or in the cloud. Deliver compliance at lower cost and gain new business >>>> insights. http://p.sf.net/sfu/splunk-dev2dev >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >>> >>> >> >> -- >> Hongbo ZHU >> Postdoctoral Researcher >> Structural Bioinformatics >> >> Technische Universität Dresden >> Biotechnology Center >> Tatzberg 47/49 >> 01307 Dresden, Germany >> >> Tel: +49 (0) 351 463-40083 >> Fax: +49 (0) 351 463-40087 >> E-Mail: hongbo.zhu at biotec >> Webpage: www.biotec.tu-dresden.de >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search& Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT data >> generated by your applications, servers and devices whether physical, virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de |
From: Martin H. <ma...@bl...> - 2011-03-02 22:21:34
|
yeah, its true. We should work out a tutorial for this kind of things. Something where there is only one line of instruction and one line of command, like: 1) Download a file fetch pdb1.pdb 2) Select all ASP or GLU residues: select acids, resn ASP+GLU 3) Suggestions? Am 02.03.11 22:36, schrieb Hongbo Zhu: > On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: >> Hey :) >> >> It's good to note that programs are written by programmers, using >> programmer's logic. > First of all, I was not complaining about the logic of the PyMOL > programmers. I tried to help find out the reason that might cause > Martin's script to break based on the similar complains I had received. > > It is true that programs are written by programmers. But I guess many > users actually hate that fact so much because they see again and again > that some programmers just presume that all users will think the same > way as they think. (Of course after these users become programmers they > start to do the same ;) > > The confusion is not so much caused by the >> simplified expression, but by users with little background in >> mathematics/logic assessing 'and' and 'or' from a linguistic >> background.In computer science and mathematics OR := union, AND := >> intersection. It's covered quite well in >> http://www.pymolwiki.org/index.php/Selection_Algebra > I disagree. I think it is caused by the simplified expression to the > users who think intuitively instead of immediately mathematically when > they try to write down the first line of selection script, no matter how > much mathematics/logic they have (the colleague I mentioned is a > computer scientist). After staring at the unexpected outcome for a > while, they will try to think mathematically or google-ly ;). > > I can not think of a good way to address this small issue for new users. > Maybe a more informative hint to the users is helpful rather than just > print "0 atoms selected". For example, PyMOL can print the selection > result of each operand, or print the complete selection expression > translated from the the simplified selection expression. > >> Cheers, >> >> Tsjerk >> >> On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu >> <hon...@bi...> wrote: >>> I believe the confusion is caused by the simplified selection expression >>> in PyMOL (and some other visualization tools as well). I remember that >>> one of my colleagues once questioned strongly the reason of using OR >>> instead of AND in such situation. >>> >>> The expression: >>> >>> select resn GLU or resn ASP >>> >>> actually means >>> >>> select (resn == GLU) or (resn == ASP) >>> >>> The reason of using Boolean operator *or* is very clean when the two >>> operands are stated completely. But when the operands are simplified, >>> our first reaction is to use *and* because it is very natural to say >>> >>> "I want GLU *and* ASP" >>> >>> if you want both GLU and ASP. >>> >>> And it is even more confusing in Jmol : >>> >>> select 110 or 112 (select resno==110 or resn==112) >>> >>> if want you really want is 110 *and* 112 :) >>> >>> hongbo >>> >>> On 03/01/2011 05:43 PM, Jason Vertrees wrote: >>>> Hi Martin, >>>> >>>> To select all ASPs and GLUs just type, >>>> >>>> select resn GLU+ASP >>>> >>>> or >>>> >>>> select resn GLU or resn ASP >>>> >>>> or, if you need parentheses, >>>> >>>> select ((resn GLU) or (resn ASP)) >>>> >>>> >>>> Maybe this will help: >>>> >>>> # fetch a test protein >>>> >>>> fetch 1rsy, async=0 >>>> >>>> # color all ASPs and GLUs red >>>> >>>> color tv_red, (resn ASP or resn GLU) >>>> >>>> >>>> While the boolean 'and' works, the following will fail to select and >>>> color any atoms: >>>> >>>> color tv_red, (resn ASP and resn GLU) >>>> >>>> because there will be no _single atom_ in both an ASP and a GLU. The >>>> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in >>>> any ASP _and_ in any GLU--which is impossible. >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> >>>> >>>> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...> wrote: >>>>> Dear all >>>>> What is the selection syntax to select all GLU and ASP residues within an >>>>> object? >>>>> >>>>> I'm trying it the way its written on the wiki: >>>>> >>>>> remove resn hoh # remove water >>>>> h_add # add hydrogens >>>>> >>>>> as surface >>>>> color grey90 >>>>> >>>>> color slate, resn lys # lysines in light blue >>>>> color paleyellow, resn cys # cysteines in light yellow >>>>> color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light >>>>> red >>>>> >>>>> but, the selection kind of does not work for me (I'm assuming the operator >>>>> for the logical AND is 'and'). >>>>> What is it that I need to do differently? >>>>> >>>>> Kind regards >>>>> Martin >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>>>> data >>>>> generated by your applications, servers and devices whether physical, >>>>> virtual >>>>> or in the cloud. Deliver compliance at lower cost and gain new business >>>>> insights. http://p.sf.net/sfu/splunk-dev2dev >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> >>> -- >>> Hongbo ZHU >>> Postdoctoral Researcher >>> Structural Bioinformatics >>> >>> Technische Universität Dresden >>> Biotechnology Center >>> Tatzberg 47/49 >>> 01307 Dresden, Germany >>> >>> Tel: +49 (0) 351 463-40083 >>> Fax: +49 (0) 351 463-40087 >>> E-Mail: hongbo.zhu at biotec >>> Webpage: www.biotec.tu-dresden.de >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data >>> generated by your applications, servers and devices whether physical, virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> _______________________________________________ >>> 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: Sampson, J. <Jar...@ny...> - 2011-03-01 18:02:25
|
Hi Martin - ** Short answer: Use `resn asp+glu` (although your original command actually works for me). ** Not-so-short answer, with a bonus question about comment syntax: The Asp/Glu line of your script can be condensed slightly using a plus sign, but the original syntax of that line actually works fine for me (PyMOL v.1.3, Fink/X11 build on Mac OS 10.6.6). However, for me, the lines to remove waters and add hydrogens fail. To elaborate, I've found that, with certain commands (but oddly not all of them -- for example, the `color` statements in your original script handle this just fine), adding a comment on the same line returns a "Malformed selection" error. I don't know if this is by design or an "unintended feature." I would expect these comments to be handled the same way as in Python code, but for whatever reason, they are not. (Query for the developers: Is there a specific reason some PyMOL functions attempt to include the hash mark and comment in the selection, rather than ignoring everything after the #? Perhaps it has something to do with the number of arguments--both the commands below that fail with an inline comment take only a single selection argument.) If you really want to keep the comment on the same line, add a semicolon between the command and the comment. The other option, of course, is to place the comment on the previous line. Also, you can use `remove solvent` to cover all the different ways of describing water (HOH, WAT, H2O). Try this: # remove water remove solvent; # or put the comment on the same line after a semicolon # add hydrogens h_add; # this one also requires a semicolon # basic view as surface color grey90 # color lys blue, cys yellow, asp/glu red color slate, resn lys # comments here seem to work without the semicolon color paleyellow, resn cys color tv_red, resn asp+glu Hope that helps, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Mar 1, 2011, at 7:44 AM, Martin Hediger wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh # remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= |
From: Robert C. <rob...@qu...> - 2011-03-01 16:37:21
|
Hi Martin, On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger <ma...@bl...> wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within > an object? > > I'm trying it the way its written on the wiki: > > remove resn hoh # remove water > h_add # add hydrogens > > as surface > color grey90 > > color slate, resn lys # lysines in light blue > color paleyellow, resn cys # cysteines in light yellow > *color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* The easier way to write that is: color tv_red, resn asp+glu You can string several sorts of selections together that way, for example: select actsite, resi 105+262+286 select aliphatic, resn ala+val+leu+ile Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Maia C. <ch...@ua...> - 2011-03-01 16:21:02
|
For me, color red, resn asp+glu works. Maia Martin Hediger wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within > an object? > > I'm trying it the way its written on the wiki: > remove resn hoh # remove water > h_add # add hydrogens > > as surface > color grey90 > > color slate, resn lys # lysines in light blue > color paleyellow, resn cys # cysteines in light yellow > *color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* > > > but, the selection kind of does not work for me (I'm assuming the > operator for the logical AND is 'and'). > What is it that I need to do differently? > > Kind regards > Martin > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ------------------------------------------------------------------------ > > _______________________________________________ > 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: Tim T. <tst...@gm...> - 2011-03-01 22:32:16
|
Hi, Seems to work fine for me. I'm using version 1.3, although I doubt that this could be a version compatibility problem. Could you give more specifics on how it doesn't work for you (ASPs not colored red or GLUs not colored red, etc.) ? Note that the parenthesis around 'resn glu' aren't needed. Tim On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger <ma...@bl...> wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within an > object? > > I'm trying it the way its written on the wiki: > > remove resn hoh # remove water > h_add # add hydrogens > > as surface > color grey90 > > color slate, resn lys # lysines in light blue > color paleyellow, resn cys # cysteines in light yellow*color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* > > but, the selection kind of does not work for me (I'm assuming the operator > for the logical AND is 'and'). > What is it that I need to do differently? > > Kind regards > Martin > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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: Tsjerk W. <ts...@gm...> - 2011-02-28 11:31:59
|
Hi Kanika, In 3HHZ.pdb, I find: REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N, REMARK 350 AND CHAINS: O, R REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 So there are two BIOMT records. One identity, indicating that the coordinates as the are are also part of the biological assembly, and one giving the transformation to be applied to a copy. From the previous posts, you should already know how to do that... Cheers, Tsjerk On Mon, Feb 28, 2011 at 12:20 PM, kanika sharma <ksh...@gm...> wrote: > I have a dimeric protein 3HHZ.....to generate the dimer foll transformations > have to be made....the problem is that this is an identity matrix,so will > not change anything...can anyone help with this?? > how can i get the asymmetric unit to generate dimer?? > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu > <hon...@bi...> wrote: >> >> Hi, Kanika, >> >> are you looking for biological units of proteins when you say stable >> dimer? If this is the case, I recommend the page: >> >> http://pdbwiki.org/index.php/Biological_unit >> at the bottom of the page you can find four very useful servers for the >> determination of biological units of proteins (PQS is not updated anymore): >> The Protein Quaternary Structure Server (PQS) [2] or [3] >> The Macro-Molecular Structure Database (MSD) [4] or [5] >> The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] >> Protein quaternary structure investigation (PiQSi) [7] >> >> As a matter of fact, the PDB also provides the biological assembly of each >> PDB entry for download. More information can be found at: >> >> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html >> >> If your protein is not from the PDB, you can still try pisa ( >> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein >> coordinate files uploaded by the users and determines the "stable dimer" or >> else-mer of your protein. >> >> hope these help! >> hongbo >> >> On 02/25/2011 01:46 PM, kanika sharma wrote: >>> >>> Hi, >>> i am working to generate a dimer of my protein..I have made a duplicate >>> of my protein....Can any one tell me how to rotate my molecule to get >>> maximum stability..??? >>> >>> >>> Regards.. >>> Kanika >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> >>> >>> >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> Hongbo ZHU >> Postdoctoral Researcher >> Structural Bioinformatics >> >> Technische Universität Dresden >> Biotechnology Center >> Tatzberg 47/49 >> 01307 Dresden, Germany >> >> Tel.: +49 (0) 351 463-40083 >> Fax: +49 (0) 351 463-40087 >> E-Mail: hongbo.zhu@biotec.tu-dresden >> Webpage: www.biotec.tu-dresden.de > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > 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: kanika s. <ksh...@gm...> - 2011-02-28 11:55:53
|
my protein is 3m2m..iv downloaded the biological assembly 1 for this.. http://www.rcsb.org/pdb/explore/explore.do?structureId=3M2M to generate dimer for this the BIOMT data is like this from the pdb file....i dont know how will this work if its an identity matrix.. REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 7 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 8 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 9 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 10 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 11 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 12 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |