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run chimera in terminal on mac os x
by ylei＠ecs.umass.edu 24 Feb '10

24 Feb '10

Dear all Could somebody tell me how to run Chimera in terminal on the system of mac? Thanks. Yang

2 1

No glue!
by Jean Didier Pie Marechal 17 Feb '10

17 Feb '10

Dear all, I'd like to add an atom at the mass center of each aromatic fragment of my ligand (I always want to add an atom don't I?). I know how to calculate cm, put an atom or point, select aromatic ring BUT I am banging my head against the wall to define one entity of each ring separately. Would it be a lot more complicate to do so for any cyclic moeity. Thanks for any help! best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Gener 28, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 9 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. ribbon for circular molecule (Volodymyr Babin) > 2. Re: ribbon for circular molecule (Thomas Goddard) > 3. Re: ribbon for circular molecule (Thomas Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 27 Jan 2010 23:48:46 -0500 (EST) > From: "Volodymyr Babin" <vbabin(a)ncsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] ribbon for circular molecule > Message-ID: <53249.152.1.53.169.1264654126.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Sirs, > > I am writing to ask for the chimera sources -- I would like to > visualize a circular molecule using ribbons. As far as I can tell, > with the current code ribbons always have ends (cannot be closed) > because of the following snipped from > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > 696 Molecule::updateRibbonData() > 697 { > 698 clearRibbonData(); > 699 > 700 // > 701 // For each residue, find the residues before > and after. 702 > // Note that only residues with valid guide and plane atoms > 703 > // may be used as the prev/next residue in a ribbon. > 704 // > 705 std::map<Residue *, RibbonResidue> rrMap; > 706 Residue *prev = NULL; > ^^^^^^^^^^^^^^^^^^^^^ > > Could you please allow me to check out the svn version of the > chimera or get (easily compilable) sources of a recent release. > > Thank you, > > Volodymyr > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 28 Jan 2010 10:58:34 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61DE5A.6050907(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Volodymyr, > > Chimera is not easy to compile because it requires about 40 > third-party libraries as described on the Chimera source code page > (link > is on the Chimera download page). > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > Also there is a bit of third-party surface calculation code which > we are > not allowed to distribute. All the source code is viewable with > the web > interface to the SVN repository. We also have a ticket active for > allowing public access to check-out the entire Chimera SVN tree > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > but that has not been done yet. > > If your purpose is to make a figure that doesn't have a gap in > the > circular molecule then the following trick might achieve that. You > could make a new molecule that is not closed and has the two > starting > residues duplicated at the end (with increasing residue numbers). > Then > when you show the ribbon there will be an overlapping stretch. > Because > the overlap will not be perfect you can hide the ribbon for one of > each > duplicated residue. If you add a couple duplicate residues the > ribbon > should come into exact alignment with itself. > > I've added your request for circular ribbons to our feature > request list. > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > If you can live with circular cross-section tube a command like > > shape tube :1-125.A@CA:1.A@CA radius 1 > > could do it but it does not close nicely -- different tangent > vector and > coloring and selection is not as flexible -- the tube is just a > surface > model. > > Tom > > > > Dear Sirs, > > > > I am writing to ask for the chimera sources -- I would like to > > visualize a circular molecule using ribbons. As far as I can tell, > > with the current code ribbons always have ends (cannot be closed) > > because of the following snipped from > > > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > > > 696 Molecule::updateRibbonData() > > 697 { > > 698 clearRibbonData(); > > 699 > > 700 // > > 701 // For each residue, find the residues before > and after. 702 > > // Note that only residues with valid guide and plane atoms > 703 > > // may be used as the prev/next residue in a ribbon. > > 704 // > > 705 std::map<Residue *, RibbonResidue> rrMap; > > 706 Residue *prev = NULL; > > ^^^^^^^^^^^^^^^^^^^^^ > > > > Could you please allow me to check out the svn version of the > > chimera or get (easily compilable) sources of a recent release. > > > > Thank you, > > > > Volodymyr > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > ------------------------------ > > Message: 3 > Date: Thu, 28 Jan 2010 11:38:01 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61E799.3070708(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Volodymyr, > > I will try to get public SVN download of Chimera source working. > It > would be great if you learned about programming Chimera. This > particular part of the code is especially difficult though because > the > ribbon class is produced by an antiquated in-house C++ code > generation > tool called OTF (Object Technology Framework). I'll add you to the > notification list for the SVN access ticket. > > Tom > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Volodymyr Babin > To: Thomas Goddard > Date: 1/28/10 11:16 AM > > > Hi Thomas, > > > > thank you for a very detailed reply. > > > >> Also there is a bit of third-party surface calculation code > which we are > >> not allowed to distribute. > > > > I understand that. I probably was imprecise: it would be nice to be > > able to compute everything but the non-distributable code. > > > >> If your purpose is to make a figure that doesn't have a gap > in the > >> circular molecule then the following trick might achieve that. You > >> could make a new molecule that is not closed and has the two > starting>> residues duplicated at the end (with increasing residue > numbers). Then > >> when you show the ribbon there will be an overlapping stretch. > Because>> the overlap will not be perfect you can hide the ribbon > for one of each > >> duplicated residue. If you add a couple duplicate residues the > ribbon>> should come into exact alignment with itself. > > > > Thank you. I tried this before looking at the sources. I have not > tried> it with the circular cross-section tube though ... thanks. > > > >> I've added your request for circular ribbons to our feature request > >> list. > > > > Thank you. I am not sure this is something of general interest and > > therefore ruled out this option (feature request) deciding to play > > with it myself. I am new to chimera and must admit that its > visualization> capabilities are absolutely outstanding ... which is > another reason > > I would prefer to learn it through. > > > > Thank you & best regards, > > > > Volodymyr > > > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Thomas Goddard > To: Volodymyr Babin > Date: 1/28/10 10:58 AM > > > Hi Volodymyr, > > > > Chimera is not easy to compile because it requires about 40 > > third-party libraries as described on the Chimera source code > page (link > > is on the Chimera download page). > > > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > > > Also there is a bit of third-party surface calculation code which > we are > > not allowed to distribute. All the source code is viewable with > the web > > interface to the SVN repository. We also have a ticket active > for > > allowing public access to check-out the entire Chimera SVN tree > > > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > > > but that has not been done yet. > > > > If your purpose is to make a figure that doesn't have a gap in > the > > circular molecule then the following trick might achieve that. > You > > could make a new molecule that is not closed and has the two > starting > > residues duplicated at the end (with increasing residue numbers). > Then > > when you show the ribbon there will be an overlapping stretch. > Because > > the overlap will not be perfect you can hide the ribbon for one > of each > > duplicated residue. If you add a couple duplicate residues the > ribbon > > should come into exact alignment with itself. > > > > I've added your request for circular ribbons to our feature > request list. > > > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > > > If you can live with circular cross-section tube a command like > > > > shape tube :1-125.A@CA:1.A@CA radius 1 > > > > could do it but it does not close nicely -- different tangent > vector and > > coloring and selection is not as flexible -- the tube is just a > surface > > model. > > > > Tom > > > > > >> Dear Sirs, > >> > >> I am writing to ask for the chimera sources -- I would like to > >> visualize a circular molecule using ribbons. As far as I can tell, > >> with the current code ribbons always have ends (cannot be closed) > >> because of the following snipped from > >> > >> libs/_chimera/Chimera.toolkit/Ribbon.implementation > >> > >> 696 Molecule::updateRibbonData() > >> 697 { > >> 698 clearRibbonData(); > >> 699 > >> 700 // > >> 701 // For each residue, find the residues before and > >> after. 702 // Note that only residues with valid guide > and > >> plane atoms 703 // may be used as the prev/next > residue in a > >> ribbon. > >> 704 // > >> 705 std::map<Residue *, RibbonResidue> rrMap; > >> 706 Residue *prev = NULL; > >> ^^^^^^^^^^^^^^^^^^^^^ > >> > >> Could you please allow me to check out the svn version of the > >> chimera or get (easily compilable) sources of a recent release. > >> > >> Thank you, > >> > >> Volodymyr > >> > >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > End of Chimera-dev Digest, Vol 72, Issue 9 > ****************************************** >

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Re: [chimera-dev] No glue!
by Jean Didier Pie Marechal 15 Feb '10

15 Feb '10

Hi Elaine, yes the centroid option is what I would like to do for each aromatic ring. The thing is that I have a small database to screen regarding relative position of this centroids. My main problem is how could I generate automatically a unique group of atoms for each ring and then calculate the centroid afterwards. I have no idea. Thanks for the help, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dissabte, Febrer 13, 2010 8:31 pm Assumpte: Re: [chimera-dev] No glue! > Hi JD, > I can't answer in terms of programming, but thought I would mention > > that in recent daily builds (version 1.5), "Axes/Planes" (under > Tools... Structure Analysis) has been extended to "Axes/Planes/ > Centroids." With this tool, or with the command "define," you can > create a sphere at the optionally mass-weighted centroid of any set > of > atoms. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> > > These centroid objects, although not atoms, can be used in distance > > measurements via the "Axes/Planes/Centroids" GUI or with the > command > "distance." > > Perhaps these centroid objects will meet your needs, so you don't > need > to write this code to create atoms. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Feb 13, 2010, at 6:25 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > I'd like to add an atom at the mass center of each aromatic > fragment > > of my ligand (I always want to add an atom don't I?). > > > > I know how to calculate cm, put an atom or point, select aromatic > > > ring BUT I am banging my head against the wall to define one > entity > > of each ring separately. > > > > Would it be a lot more complicate to do so for any cyclic moeity. > > Thanks for any help! > > best, > > JD >

1 0

getting nuts with aromatic
by Jean Didier Pie Marechal 13 Feb '10

13 Feb '10

Dear all, I'd like to add an atom at the mass center of each aromatic ring of my ligand (I always want to add an atom, don't I?). I know how to calculate cm, put an atom or point, select aromatic ring BUT I am banging my head against the wall to define one entity of each ring separately. I played a while with bonds properties but I can't see the light (Caroline...). If there is a way to do so for aromatic rings, how complicated would it be to do the same for any kind of cyclic moeity. Thanks for any help! best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Gener 28, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 9 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. ribbon for circular molecule (Volodymyr Babin) > 2. Re: ribbon for circular molecule (Thomas Goddard) > 3. Re: ribbon for circular molecule (Thomas Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 27 Jan 2010 23:48:46 -0500 (EST) > From: "Volodymyr Babin" <vbabin(a)ncsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] ribbon for circular molecule > Message-ID: <53249.152.1.53.169.1264654126.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Sirs, > > I am writing to ask for the chimera sources -- I would like to > visualize a circular molecule using ribbons. As far as I can tell, > with the current code ribbons always have ends (cannot be closed) > because of the following snipped from > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > 696 Molecule::updateRibbonData() > 697 { > 698 clearRibbonData(); > 699 > 700 // > 701 // For each residue, find the residues before > and after. 702 > // Note that only residues with valid guide and plane atoms > 703 > // may be used as the prev/next residue in a ribbon. > 704 // > 705 std::map<Residue *, RibbonResidue> rrMap; > 706 Residue *prev = NULL; > ^^^^^^^^^^^^^^^^^^^^^ > > Could you please allow me to check out the svn version of the > chimera or get (easily compilable) sources of a recent release. > > Thank you, > > Volodymyr > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 28 Jan 2010 10:58:34 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61DE5A.6050907(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Volodymyr, > > Chimera is not easy to compile because it requires about 40 > third-party libraries as described on the Chimera source code page > (link > is on the Chimera download page). > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > Also there is a bit of third-party surface calculation code which > we are > not allowed to distribute. All the source code is viewable with > the web > interface to the SVN repository. We also have a ticket active for > allowing public access to check-out the entire Chimera SVN tree > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > but that has not been done yet. > > If your purpose is to make a figure that doesn't have a gap in > the > circular molecule then the following trick might achieve that. You > could make a new molecule that is not closed and has the two > starting > residues duplicated at the end (with increasing residue numbers). > Then > when you show the ribbon there will be an overlapping stretch. > Because > the overlap will not be perfect you can hide the ribbon for one of > each > duplicated residue. If you add a couple duplicate residues the > ribbon > should come into exact alignment with itself. > > I've added your request for circular ribbons to our feature > request list. > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > If you can live with circular cross-section tube a command like > > shape tube :1-125.A@CA:1.A@CA radius 1 > > could do it but it does not close nicely -- different tangent > vector and > coloring and selection is not as flexible -- the tube is just a > surface > model. > > Tom > > > > Dear Sirs, > > > > I am writing to ask for the chimera sources -- I would like to > > visualize a circular molecule using ribbons. As far as I can tell, > > with the current code ribbons always have ends (cannot be closed) > > because of the following snipped from > > > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > > > 696 Molecule::updateRibbonData() > > 697 { > > 698 clearRibbonData(); > > 699 > > 700 // > > 701 // For each residue, find the residues before > and after. 702 > > // Note that only residues with valid guide and plane atoms > 703 > > // may be used as the prev/next residue in a ribbon. > > 704 // > > 705 std::map<Residue *, RibbonResidue> rrMap; > > 706 Residue *prev = NULL; > > ^^^^^^^^^^^^^^^^^^^^^ > > > > Could you please allow me to check out the svn version of the > > chimera or get (easily compilable) sources of a recent release. > > > > Thank you, > > > > Volodymyr > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > ------------------------------ > > Message: 3 > Date: Thu, 28 Jan 2010 11:38:01 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61E799.3070708(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Volodymyr, > > I will try to get public SVN download of Chimera source working. > It > would be great if you learned about programming Chimera. This > particular part of the code is especially difficult though because > the > ribbon class is produced by an antiquated in-house C++ code > generation > tool called OTF (Object Technology Framework). I'll add you to the > notification list for the SVN access ticket. > > Tom > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Volodymyr Babin > To: Thomas Goddard > Date: 1/28/10 11:16 AM > > > Hi Thomas, > > > > thank you for a very detailed reply. > > > >> Also there is a bit of third-party surface calculation code > which we are > >> not allowed to distribute. > > > > I understand that. I probably was imprecise: it would be nice to be > > able to compute everything but the non-distributable code. > > > >> If your purpose is to make a figure that doesn't have a gap > in the > >> circular molecule then the following trick might achieve that. You > >> could make a new molecule that is not closed and has the two > starting>> residues duplicated at the end (with increasing residue > numbers). Then > >> when you show the ribbon there will be an overlapping stretch. > Because>> the overlap will not be perfect you can hide the ribbon > for one of each > >> duplicated residue. If you add a couple duplicate residues the > ribbon>> should come into exact alignment with itself. > > > > Thank you. I tried this before looking at the sources. I have not > tried> it with the circular cross-section tube though ... thanks. > > > >> I've added your request for circular ribbons to our feature request > >> list. > > > > Thank you. I am not sure this is something of general interest and > > therefore ruled out this option (feature request) deciding to play > > with it myself. I am new to chimera and must admit that its > visualization> capabilities are absolutely outstanding ... which is > another reason > > I would prefer to learn it through. > > > > Thank you & best regards, > > > > Volodymyr > > > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Thomas Goddard > To: Volodymyr Babin > Date: 1/28/10 10:58 AM > > > Hi Volodymyr, > > > > Chimera is not easy to compile because it requires about 40 > > third-party libraries as described on the Chimera source code > page (link > > is on the Chimera download page). > > > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > > > Also there is a bit of third-party surface calculation code which > we are > > not allowed to distribute. All the source code is viewable with > the web > > interface to the SVN repository. We also have a ticket active > for > > allowing public access to check-out the entire Chimera SVN tree > > > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > > > but that has not been done yet. > > > > If your purpose is to make a figure that doesn't have a gap in > the > > circular molecule then the following trick might achieve that. > You > > could make a new molecule that is not closed and has the two > starting > > residues duplicated at the end (with increasing residue numbers). > Then > > when you show the ribbon there will be an overlapping stretch. > Because > > the overlap will not be perfect you can hide the ribbon for one > of each > > duplicated residue. If you add a couple duplicate residues the > ribbon > > should come into exact alignment with itself. > > > > I've added your request for circular ribbons to our feature > request list. > > > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > > > If you can live with circular cross-section tube a command like > > > > shape tube :1-125.A@CA:1.A@CA radius 1 > > > > could do it but it does not close nicely -- different tangent > vector and > > coloring and selection is not as flexible -- the tube is just a > surface > > model. > > > > Tom > > > > > >> Dear Sirs, > >> > >> I am writing to ask for the chimera sources -- I would like to > >> visualize a circular molecule using ribbons. As far as I can tell, > >> with the current code ribbons always have ends (cannot be closed) > >> because of the following snipped from > >> > >> libs/_chimera/Chimera.toolkit/Ribbon.implementation > >> > >> 696 Molecule::updateRibbonData() > >> 697 { > >> 698 clearRibbonData(); > >> 699 > >> 700 // > >> 701 // For each residue, find the residues before and > >> after. 702 // Note that only residues with valid guide > and > >> plane atoms 703 // may be used as the prev/next > residue in a > >> ribbon. > >> 704 // > >> 705 std::map<Residue *, RibbonResidue> rrMap; > >> 706 Residue *prev = NULL; > >> ^^^^^^^^^^^^^^^^^^^^^ > >> > >> Could you please allow me to check out the svn version of the > >> chimera or get (easily compilable) sources of a recent release. > >> > >> Thank you, > >> > >> Volodymyr > >> > >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > End of Chimera-dev Digest, Vol 72, Issue 9 > ****************************************** >

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ribbon for circular molecule
by Volodymyr Babin 28 Jan '10

28 Jan '10

Dear Sirs, I am writing to ask for the chimera sources -- I would like to visualize a circular molecule using ribbons. As far as I can tell, with the current code ribbons always have ends (cannot be closed) because of the following snipped from libs/_chimera/Chimera.toolkit/Ribbon.implementation 696 Molecule::updateRibbonData() 697 { 698 clearRibbonData(); 699 700 // 701 // For each residue, find the residues before and after. 702 // Note that only residues with valid guide and plane atoms 703 // may be used as the prev/next residue in a ribbon. 704 // 705 std::map<Residue *, RibbonResidue> rrMap; 706 Residue *prev = NULL; ^^^^^^^^^^^^^^^^^^^^^ Could you please allow me to check out the svn version of the chimera or get (easily compilable) sources of a recent release. Thank you, Volodymyr

2 2

calculate volume major blob
by Jean Didier Pie Marechal 24 Jan '10

24 Jan '10

Dear all, I need to do the work for thousands of structures, so Iam interesting in a scripting solution here. After a surfnet calculation on a given atom selection, my script select the whole surface model and calculates the volume of the all bunch. However, I'd like to have the volume of the major blob only. On the other hand, for a given number of structures, I would like to remove all minor blobs blobs so that only the major one remains on the screen. How could I do this second step? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

2 1

extensions outside the chimera directory
by Jean Didier Pie Marechal 22 Jan '10

22 Jan '10

Dear All, I am preparing a series of practical for a MSc and I'd like a series of extensions I have to be accessible for students. Unfortunately, I do not have write access to the /usr/local/chimera directory of the pcs of the classrom and the OS images the machines boot on are not upgradable easily. Could I locate extensions in a user directory? Sorry for my ignorance.... Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Gener 20, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. StructureSequence.residues change (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 19 Jan 2010 13:22:31 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] StructureSequence.residues change > Message-ID: <BE4EE11C-A560-4D1D-A08B-5ED3AA052CF5(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > I've made a change in the 1.5 build that could affect > script/extension > writers that use the StructureSequence.residues list. That list > can > now contain None values. This is because now the sequence is the > full > sequence if available in SEQRES records even if some of the > corresponding structure is missing. Such missing structure has > None > for the Residue value. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu >

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StructureSequence.residues change
by Eric Pettersen 19 Jan '10

19 Jan '10

I've made a change in the 1.5 build that could affect script/extension writers that use the StructureSequence.residues list. That list can now contain None values. This is because now the sequence is the full sequence if available in SEQRES records even if some of the corresponding structure is missing. Such missing structure has None for the Residue value. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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(no subject)
by Mojie Duan 19 Jan '10

19 Jan '10

Dear Chimera Developers, I needs to calculate the inter-helical angle for thousands of conformations. We know Chimera can calculate the inter-helical angle for one conformation. We are wondering if Chimera can calculate the inter-helical angle for all these conformations at one time? or would you please point out how to write a script to do this? Thanks. Mojie

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Calculating RMSD
by Victor Muñoz 15 Jan '10

15 Jan '10

Hi, I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong? Thanks for your help.

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