From: Mauricio C. T. <tr...@sc...> - 2008-04-29 18:51:13
|
This is great Bob, and is exactly what I was after last month ( http://www.mail-archive.com/jmo...@li.../msg10041.html), my apologies if I was not clear enough then ;) Now, as for an spherical capsids 'user' at VIPERdb, I would like to be able to: 1) have the option to show/hide any of the biomolecules in the PDB file, in spherical capsids there's always 60. This doesn't mean all 60 biomolecules should be loaded initially by default, but only when the user chooses to. The default will always be to load and show biomolecule number one. As I understand it, every time the user wants to display another biomolecule in the biounit, the PDB file needs to be (down)loaded again and read using a different filter? If so, I think it would be more practical (but perhaps more trouble to implement) to load the PDB file once, save all the biomats corresponding to all the biomolecules in the biounit, and then use them latter as needed? (this might save a lot of HTTP requests ;) I'm thinking about buttons to show 1/4, 1/2 or full capsid. But also an option to show biomols 1,6 and 7 (or any combination), to present an specific interface. 2) have the option to apply symmetry to any number of chains in the ASU (many capsids have more than one chain in the ASU), I believe one can do that with the filter as is, right? I'm thinking of the option to show chain A of biomol 1 and chain C of biomol 7 (or any combination), again, to present an specific interface. 3) have the option to apply symmetry just to a segment of an specific chain in the ASU, I believe one can do that with the filter as is, right? I'm thinking about the option to show only the residues involved in an specific quaternary structure, beta annulus for example, around an icosahedral symmetry axis, comprised from a few residues of chain B of biomol 1, a few from chain C of biomol 6, and so on ... I'm thinking on implementing an ad hoc UI for the above, so I don't know about the Jmol menu. Although I guess for other systems it would be nice to have a list of all biomols available. 4) have all the biomolecules (as whole or parts, as explained above) as different model/frame to apply different representations to them. So, "load append" works? Some, or all, of the points above might be valid for other systems too. As you said Bob, this is huge, and I'm very exited about it, will certainly simplify the scripts we use, and more importantly, the way people interact with these structures and learn from them. Thanks again for the great work! Date: Tue, 29 Apr 2008 09:34:25 -0500 From: Bob Hanson <ha...@st...> Subject: [Jmol-users] Jmol load FILTER "SELECT *.CA; BIOMOLECULE n; APPLY SYMMETRY" To: jmo...@li... Message-ID: <481...@st...> Content-Type: text/plain; charset=ISO-8859-1; format=flowed biomolecule oriented Jmol users: OK, I'm convinced by my colleagues here at St. Olaf and Carleton that this is HUGE. Just playing with it a bit, I'm totally excited. You can now load a subset of the atoms in a PDB file into Jmol (a limited SELECT sort of filter to the LOAD command that works at the file-reading level for PDB files) and then also select one of the BIOMOLECULE specifications in the "REMARK 350" biological unit section of the header and apply the symmetry described in that header. Thank you to Eric, Rolf, and Dan for suggesting this. I believe that the next version of Jmol you see, 11.5.32, will have this working correctly. I've done a navigation mode fly-through of the entire 60-unit simian virus (1sva.pdb) looking at helices and sheets as I flew, and I'm sold. On my 1.2Gb-memory laptop Jmol rotates 124,000 atoms with cartoons like nothing in real time. So I think we are onto something. Now, interface. What do you want? I presume a menu entry under the main "symmetry" entry should be the place to start. What options do you need? -- option to replace or append? -- option to apply symmetry? -- list of biomolecules available (with # of atoms involved if symmetry is applied?) anything else on that menu? I suspect as people play with this more, they will want me to expand on that load filter select option. What else? Bob -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | tr...@sc... 0 | http://viperdb.scripps.edu/ ** Aut tace aut loquere meliora silentio ** |
From: Mauricio C. T. <tr...@sc...> - 2008-04-30 16:12:32
|
So the balance here will be with what Jmol will do and what people want > to customize it to do (at web pages, for example). that sounds OK to me (I'm mostly interested in web pages) > > > Mauricio Carrillo Tripp wrote: > > > This is great Bob, and is exactly what I was after last month > > ( > http://www.mail-archive.com/jmo...@li.../msg10041.html > ), > > my apologies if I was not clear enough then ;) > > Now, as for an spherical capsids 'user' at VIPERdb, I would like to be > > able to: > > > > 1) have the option to show/hide any of the biomolecules in the PDB > > file, in spherical capsids there's always 60. This doesn't mean all 60 > > biomolecules should be loaded initially by default, but only when the > > user chooses to. The default will always be to load and show > > biomolecule number one. As I understand it, every time the user wants > > to display another biomolecule in the biounit, the PDB file needs to > > be (down)loaded again and read using a different filter? If so, I > > think it would be more practical (but perhaps more trouble to > > implement) to load the PDB file once, save all the biomats > > corresponding to all the biomolecules in the biounit, and then use > > them latter as needed? (this might save a lot of HTTP requests ;) I'm > > thinking about buttons to show 1/4, 1/2 or full capsid. But also an > > option to show biomols 1,6 and 7 (or any combination), to present an > > specific interface. > > > By default, Jmol will simply load the coordinates -- that's not > negotiable. We could imagine a script "set" flag, though, that would > direct Jmol to some other behavior. > > The PDB file does not need to be downloaded again in terms of a browser > -- the browser will cache the file, and it will load very fast from the > hard drive. Right now the biomolecules (each including biomt matrix > array and chain list) are being saved, and in principle they could be > accessed later. We can look into this option. In the mean time you will > need to do a re-load. But we have load APPEND, and it is very fast with > reasonably sized systems, so that might work better than you think. > OK > > Buttons to show "1/4, 1/2, or full capsid" would have to be set up by a > user (you). There are ways to customize the Jmol popup menu -- with a > simple small file on disk that expands a menu item. Or if using a web > page, it would be an HTML button, perhaps. yes, that's what I meant, building (us) an ad hoc UI for the Jmol applet, all we need is the functionality and the API ;) > The different sets of atoms > created by individual BIOMT transformations are selectable using the > "symop" selection option: > > select symop=3 > select symop<6 > > etc. (There is a bug there -- symop=1 specifically is not selectable in > 11.5.32) OK, so for example, if I want to display 1/2 capsid, I will have to load the PDB file 30 times, each time using a different select in the loading filter. By using the append option in the load command, all 30 biomolecules will 'live' on different frames, which can be independently selected by frame, OR the symop operator. correct? > > > > 2) have the option to apply symmetry to any number of chains in the > > ASU (many capsids have more than one chain in the ASU), I believe one > > can do that with the filter as is, right? I'm thinking of the option > > to show chain A of biomol 1 and chain C of biomol 7 (or any > > combination), again, to present an specific interface. > > > So tell me more about what it means when there are multiple > biomolecules. What would that indicate? The spherical virus capsid (biounit) is made up of 60 identical copies of the ASU (biomol 1). The ASU in itself can be made up of one or more independent chains, which in general terms corresponds to the triangulation number value (T). So for example, a T=3 capsid has 3 independent chains (A,B,C) forming the ASU, which in turn will give 180 (3x60) chains forming the full capsid. The PDB file contains coordinates for the first copy of the ASU, and also the 60 transformations (biomat 1...60) that need to be applied to those coordinates in order to generate the full capsid (usually the first transformation is the identity). So each PDB file, in essence, contains a full capsid (functional biounit), in a very reduced space (file size). In addition to the intra-unit interfaces (protein-protein interactions between the chains that form the ASU), one is also interested in seeing/studying the inter-unit interfaces (protein-protein interactions between the chains of different copies of the ASU). Some of these inter-unit interfaces are formed by up to six copies of the ASU, all sharing a common symmetry axis (in this case, a 6-fold symmetry axis). > The way you would do this > currently would be to load biomolecule 1 into one Jmol frame and > biomolecule 7 into another frame. Sounds like you would like to be able > to display these independently or together - not a problem. I'm thinking > this would be a menu option to load or to load APPEND. > > 3) have the option to apply symmetry just to a segment of an specific > > chain in the ASU, I believe one can do that with the filter as is, > > right? I'm thinking about the option to show only the residues > > involved in an specific quaternary structure, beta annulus for > > example, around an icosahedral symmetry axis, comprised from a few > > residues of chain B of biomol 1, a few from chain C of biomol 6, and > > so on ... > > > Is your interest the applet? This sounds like what Jmol.js is for. yes, I agree. > > > > I'm thinking on implementing an ad hoc UI for the above, so I don't > > know about the Jmol menu. Although I guess for other systems it would > > be nice to have a list of all biomols available. > > > > 4) have all the biomolecules (as whole or parts, as explained above) > > as different model/frame to apply different representations to them. > > So, "load append" works? > > > oh, yes. load append is great. Well tested. The big issue is going to be > memory. In most cases there is no need to generate a full capsid (it looks pretty awesome though ;). Because of symmetry, ~1/4 capsid contains all interfaces of interest. > > > > Some, or all, of the points above might be valid for other systems > > too. As you said Bob, this is huge, and I'm very exited about it, will > > certainly simplify the scripts we use, and more importantly, the way > > people interact with these structures and learn from them. > > > > Thanks again for the great work! > > > my pleasure! > -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | tr...@sc... 0 | http://viperdb.scripps.edu/ |
From: Rolf H. <rh...@fl...> - 2008-04-30 17:02:37
|
Mauricio Carrillo Tripp wrote: > Bob Hanson wrote: >> The different sets of atoms >> created by individual BIOMT transformations are selectable using the >> "symop" selection option: >> >> select symop=3 >> select symop<6 >> >> etc. (There is a bug there -- symop=1 specifically is not selectable in >> 11.5.32) > > > OK, so for example, if I want to display 1/2 capsid, I will have to load > the PDB file 30 times, each time using a different select in the loading > filter. > By using the append option in the load command, all 30 biomolecules > will 'live' on different frames, which can be independently selected by > frame, OR the symop operator. correct? > We must be careful not to mix up terms here. As far as I understood the "biomolecule" is always a whole biologically active unit. In the case of Mauricio's virus capsid there is only a single biomolecule and it consists of the asymmetric unit plus 59 copies generated by symmetry operations. In the case of PDB entry '4otb' there are 6 different biomolecules which all look very similar. Each biomolecule consists of different sets of 2 chains (out of 12) from the asymmetric unit plus 2 copies of these chains generated by symmetry operations. So in the end you will have 6 slightly different hexamers if you generate all biomolecules. As far as Bob has described the filter options yet, I don't think that it is currently possible to apply only a subset of the symmetry operations of a specific biomolecule. So with the virus capsid you would always get 60 copies of whatever you selected by the filter (e.g. only 1 chain out of 3) into a single model/frame. And if you wanted to display only only one half of the capsid you could use for example the following command: display symop<=30 How this half would really look like would of course depend on the order of the symmetry operations (e.g.: a ball might look afterwards like a ball with holes and not like one half of a ball). Regards, Rolf |
From: Bob H. <ha...@st...> - 2008-04-30 17:11:42
|
Mauricio Carrillo Tripp wrote: > The different sets of atoms > created by individual BIOMT transformations are selectable using the > "symop" selection option: > > select symop=3 > select symop<6 > > etc. (There is a bug there -- symop=1 specifically is not > selectable in > 11.5.32) > > > OK, so for example, if I want to display 1/2 capsid, I will have to load > the PDB file 30 times, each time using a different select in the > loading filter. heavens, no. You just load it once, then display only the parts of the capsid you want (if you can settle for just *.CA atoms). If you want all the atoms, I think you probably can't load 1/2 the capsid anyway. > By using the append option in the load command, all 30 biomolecules > will 'live' on different frames, which can be independently selected by > frame, OR the symop operator. correct? you just select and display them in the sets you want. Maybe display symop=2 or symop=3 or .... and that would display whatever part of the capsid you want to display. > > > > > > 2) have the option to apply symmetry to any number of chains in the > > ASU (many capsids have more than one chain in the ASU), I > believe one > > can do that with the filter as is, right? I'm thinking of the option > > to show chain A of biomol 1 and chain C of biomol 7 (or any > > combination), again, to present an specific interface. > > > So tell me more about what it means when there are multiple > biomolecules. What would that indicate? > > > The spherical virus capsid (biounit) is made up of 60 identical copies > of the ASU (biomol 1). > The ASU in itself can be made up of one or more independent chains, > which in general > terms corresponds to the triangulation number value (T). So for > example, a T=3 capsid has > 3 independent chains (A,B,C) forming the ASU, which in turn will give > 180 (3x60) chains forming the > full capsid. I understand. > The PDB file contains coordinates for the first copy of the ASU, and > also the 60 > transformations (biomat 1...60) that need to be applied to those > coordinates in order to generate the full > capsid (usually the first transformation is the identity). So each PDB > file, in essence, contains a full > capsid (functional biounit), in a very reduced space (file size). Yes. > In addition to the intra-unit interfaces (protein-protein interactions > between the chains that form the > ASU), one is also interested in seeing/studying the inter-unit > interfaces (protein-protein interactions > between the chains of different copies of the ASU). Some of these > inter-unit interfaces are formed by > up to six copies of the ASU, all sharing a common symmetry axis (in > this case, a 6-fold symmetry axis). > Right, so probably what we want to add to the filter is the capability of selecting specific BIOMT records. > > In most cases there is no need to generate a full capsid (it looks > pretty awesome > though ;). Because of symmetry, ~1/4 capsid contains all interfaces of > interest. Still a lot of atoms if you want all of them. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Bob H. <ha...@st...> - 2008-04-30 18:13:27
|
Rolf Huehne wrote: > >In the case of PDB entry '4otb' there are 6 different biomolecules which > all look very similar. Each biomolecule consists of different sets of 2 >chains (out of 12) from the asymmetric unit plus 2 copies of these >chains generated by symmetry operations. So in the end you will have 6 >slightly different hexamers if you generate all biomolecules. > > > And would you want to generate them all at the same time? Where do these different hexamers come from? >As far as Bob has described the filter options yet, I don't think that >it is currently possible to apply only a subset of the symmetry >operations of a specific biomolecule. So with the virus capsid you would >always get 60 copies of whatever you selected by the filter (e.g. only 1 >chain out of 3) into a single model/frame. And if you wanted to display >only only one half of the capsid you could use for example the following >command: > > > Right, but this could be extended to include only specific BIOMT records. > display symop<=30 > >How this half would really look like would of course depend on the order >of the symmetry operations (e.g.: a ball might look afterwards like a >ball with holes and not like one half of a ball). > >Regards, >Rolf > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: <rh...@fl...> - 2008-04-30 22:39:51
|
Quoting Bob Hanson <ha...@st...>: > Rolf Huehne wrote: > >> >> In the case of PDB entry '4otb' there are 6 different biomolecules which >> all look very similar. Each biomolecule consists of different sets of 2 >> chains (out of 12) from the asymmetric unit plus 2 copies of these >> chains generated by symmetry operations. So in the end you will have 6 >> slightly different hexamers if you generate all biomolecules. >> >> >> > And would you want to generate them all at the same time? Where do these > different hexamers come from? > No, I would only generate one at a time. As far as I understand it they are the result of imperfect packing in the crystal. As a consequence it is not possible to reduce the asymmetric unit to less than 12 chains for '4otb'. Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Mauricio C. T. <tr...@sc...> - 2008-04-30 21:17:43
|
From: Rolf Huehne <rh...@fl...> > > We must be careful not to mix up terms here. As far as I understood the > "biomolecule" is always a whole biologically active unit. > > In the case of Mauricio's virus capsid there is only a single > biomolecule and it consists of the asymmetric unit plus 59 copies > generated by symmetry operations. > > I might have been using terms in a bad way then. I've been thinking of the whole capsid as a biounit, which is the one biologically active, and each copy of the ASU as biomolecules, which by themselves have no biological activity. Now I see both (biounit, biomolecule) are interchangeable ( http://pdbwiki.org/index.php/Biological_unit). Thanks for the correction. > > As far as Bob has described the filter options yet, I don't think that > it is currently possible to apply only a subset of the symmetry > operations of a specific biomolecule. So with the virus capsid you would > always get 60 copies of whatever you selected by the filter (e.g. only 1 > chain out of 3) into a single model/frame. And if you wanted to display > only only one half of the capsid you could use for example the following > command: > > display symop<=30 > > How this half would really look like would of course depend on the order > of the symmetry operations (e.g.: a ball might look afterwards like a > ball with holes and not like one half of a ball). Good point. Although we take care in producing the transformation matrices always in the same order and sequentially when processing the original PDB file (we discard all biomat info, re-orient the ASU to a standard location and generate all the new 60 biomats -in the VIPERdb standard orientation these are the same for all capsids actually-) So I think 'display symop<=30' should work. > > > Regards, > Rolf > > > From: Bob Hanson <ha...@st...> > > > OK, so for example, if I want to display 1/2 capsid, I will have to load > > the PDB file 30 times, each time using a different select in the > > loading filter. > > heavens, no. You just load it once, then display only the parts of the > capsid you want (if you can settle for just *.CA atoms). If you want all > the atoms, I think you probably can't load 1/2 the capsid anyway. > I see. That's what we're using for the duplicates method in our current implementation (*.CA atoms) > > > In addition to the intra-unit interfaces (protein-protein interactions > > between the chains that form the > > ASU), one is also interested in seeing/studying the inter-unit > > interfaces (protein-protein interactions > > between the chains of different copies of the ASU). Some of these > > inter-unit interfaces are formed by > > up to six copies of the ASU, all sharing a common symmetry axis (in > > this case, a 6-fold symmetry axis). > > > > Right, so probably what we want to add to the filter is the capability > of selecting specific BIOMT records. > That would be great. How complex the selection on the filter can be? Could I select, for example, residues 5-20 from chain A and res 41-50 from chain B, and then apply BIOMT 1,6 and 7? > > > > > In most cases there is no need to generate a full capsid (it looks > > pretty awesome > > though ;). Because of symmetry, ~1/4 capsid contains all interfaces of > > interest. > > Still a lot of atoms if you want all of them. Right. For that kind of display only CA will have to do. But when we have a few residues per chain (see above) that need to be transformed/copied, all atoms shouldn't be a problem. -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | tr...@sc... 0 | http://viperdb.scripps.edu/ <http://www.scripps.edu/%7Etrippm> |
From: Bob H. <ha...@st...> - 2008-04-29 22:35:39
|
So the balance here will be with what Jmol will do and what people want to customize it to do (at web pages, for example). Mauricio Carrillo Tripp wrote: > This is great Bob, and is exactly what I was after last month > (http://www.mail-archive.com/jmo...@li.../msg10041.html), > my apologies if I was not clear enough then ;) > Now, as for an spherical capsids 'user' at VIPERdb, I would like to be > able to: > > 1) have the option to show/hide any of the biomolecules in the PDB > file, in spherical capsids there's always 60. This doesn't mean all 60 > biomolecules should be loaded initially by default, but only when the > user chooses to. The default will always be to load and show > biomolecule number one. As I understand it, every time the user wants > to display another biomolecule in the biounit, the PDB file needs to > be (down)loaded again and read using a different filter? If so, I > think it would be more practical (but perhaps more trouble to > implement) to load the PDB file once, save all the biomats > corresponding to all the biomolecules in the biounit, and then use > them latter as needed? (this might save a lot of HTTP requests ;) I'm > thinking about buttons to show 1/4, 1/2 or full capsid. But also an > option to show biomols 1,6 and 7 (or any combination), to present an > specific interface. > By default, Jmol will simply load the coordinates -- that's not negotiable. We could imagine a script "set" flag, though, that would direct Jmol to some other behavior. The PDB file does not need to be downloaded again in terms of a browser -- the browser will cache the file, and it will load very fast from the hard drive. Right now the biomolecules (each including biomt matrix array and chain list) are being saved, and in principle they could be accessed later. We can look into this option. In the mean time you will need to do a re-load. But we have load APPEND, and it is very fast with reasonably sized systems, so that might work better than you think. Buttons to show "1/4, 1/2, or full capsid" would have to be set up by a user (you). There are ways to customize the Jmol popup menu -- with a simple small file on disk that expands a menu item. Or if using a web page, it would be an HTML button, perhaps. The different sets of atoms created by individual BIOMT transformations are selectable using the "symop" selection option: select symop=3 select symop<6 etc. (There is a bug there -- symop=1 specifically is not selectable in 11.5.32) > 2) have the option to apply symmetry to any number of chains in the > ASU (many capsids have more than one chain in the ASU), I believe one > can do that with the filter as is, right? I'm thinking of the option > to show chain A of biomol 1 and chain C of biomol 7 (or any > combination), again, to present an specific interface. > So tell me more about what it means when there are multiple biomolecules. What would that indicate? The way you would do this currently would be to load biomolecule 1 into one Jmol frame and biomolecule 7 into another frame. Sounds like you would like to be able to display these independently or together - not a problem. I'm thinking this would be a menu option to load or to load APPEND. > 3) have the option to apply symmetry just to a segment of an specific > chain in the ASU, I believe one can do that with the filter as is, > right? I'm thinking about the option to show only the residues > involved in an specific quaternary structure, beta annulus for > example, around an icosahedral symmetry axis, comprised from a few > residues of chain B of biomol 1, a few from chain C of biomol 6, and > so on ... > Is your interest the applet? This sounds like what Jmol.js is for. > I'm thinking on implementing an ad hoc UI for the above, so I don't > know about the Jmol menu. Although I guess for other systems it would > be nice to have a list of all biomols available. > > 4) have all the biomolecules (as whole or parts, as explained above) > as different model/frame to apply different representations to them. > So, "load append" works? > oh, yes. load append is great. Well tested. The big issue is going to be memory. > Some, or all, of the points above might be valid for other systems > too. As you said Bob, this is huge, and I'm very exited about it, will > certainly simplify the scripts we use, and more importantly, the way > people interact with these structures and learn from them. > > Thanks again for the great work! > my pleasure! -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |