From: Joost V. D. <jv...@ul...> - 2005-05-17 20:22:39
|
Hi Bob, mmm, this is not good. I guess that if Jmol always connects close atoms (no matter what the occupancy is), there is no way to read in such a PDB file with several rotamers that are duplicates of one position. It also doesn't matter whether TER between the rotamers is there or not, so it seems. I believe that the only solution would be to tell Jmol not to connect a Tyr ring to another Tyr ring or simply, not to make weird bonds between amino acids. But then again, I'm the one doing something weird to the PDB file. Mmm, pitty ... I'm gonna be stuck on this one for a while ... Thanks for the help already, Bob. And by the way, I reduced the number of rotamers in the PDB link below, just to clear up some things. http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html http://iri-pc87.ulb.ac.be/sample/sample/JOOST1.PDB Joost >Joost, I was playing with your file. Check out: > >http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol.html > >Here's the deal: > >You are using TER to set off those rotomers. This won't work for two reasons. > >First, Jmol is connecting all close atoms, so you are seeing lots of connected >atoms. Not only that, though, there's a limit on number of bonds, and since you >are exceeding that in the basic model, you won't ever be able to see the bonds >the way you expect. > >Second, Jmol can't read "TER" anything more than "termination" > >My fiddling suggests that you need to reconsider how you create this file. >One problem is that the different "TER" block tyrosine residues are duplicates >of Tyr A 155. So it's not clear how you would remove that group and show the >others. (In the animation above, I removed it manually.) > >So I think it's up to you to create a model file with more standard format. > >Bob Hanson > > > >Joost Van Durme wrote: > >> Hello! >> >> I'm investigating rotamer distributions of residues and I write a new PDB file including the found rotamers for one position. These are written at the end of the PDB file. >> The result is that multiple rotamers of one residue are displayed in the molecule. >> Unfortunately, Jmol starts to make bonds between those rotamer atoms, and that's not really what I want. It gets pretty messy that way. >> >> Is there a way to get this fixed? Or a workaround somewhere? >> >> you can view the model here: >> http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html >> >> and download the PDB file here: >> http://iri-pc87.ulb.ac.be/sample/sample/JOOST.PDB >> >> For info, you see the rotamers of a Tyrosine. ;-) >> >> Joost >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by Oracle Space Sweepstakes >> Want to be the first software developer in space? >> Enter now for the Oracle Space Sweepstakes! >> http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >-- > >Robert M. Hanson, ha...@st..., 507-646-3107 >Professor of Chemistry, St. Olaf College >1520 St. Olaf Ave., Northfield, MN 55057 >mailto:ha...@st... >http://www.stolaf.edu/people/hansonr > >"Imagination is more important than knowledge." - Albert Einstein > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Joost V. D. <jv...@ul...> - 2005-05-18 09:08:26
|
Okay, I think this is the way to go. I tried it on the file with 7 rotamers and it works fine. I have a program that generates the PDB file and I can add anything to the file output I want, so if I tell it to write MODEL1 ... ENDMDL for each model, it should work. Thanks for all the help! Saved again. ;-) cheers, Joost >As Miguel suggests and my demo shows, the thing you need to do is to separate >the different models using > >MODEL >ENDMDL > >as shown, for example, at > >http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html > > 1 2 3 4 5 6 7 8 >12345678901234567890123456789012345678901234567890123456789012345678901234567890 >MODEL 1 >ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N >ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C >... >... >ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H >ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H >TER 295 GLU 18 >ENDMDL > >Of course the catch is that with this you need to duplicate ALL the entries. >A nice benefit of this is that then you can run the animations and watch your >rotomers interconvert. > >With 80+ rotomers that's a BIG file. You might consider doing this in a way I've >done, where the single file is read in, then parsed, then reloaded as a set of >models. The JavaScript sequence for this is really not that bad: > >strModel="" >Model=new Array() > >function mycallback(app,msg){ > var strMsg=msg+"" > if(strMsg.length<1000)return > strModel=strMsg > Model=strModel.split("TER") > strModel="" > for(var i=1;i<=Model.length;i++){ > strModel+="MODEL "+i+"\n"+Model[0]+Model[i]+"ENDMDL\n" > } > setTimeout("document.jmol.loadInline(strModel)",100) >} > > >This is a bit crude, but I think it does the job. (It doesn't rip out the >Tyr A 155, though. If that's really what you need, that's a bit of a problem, I >think. > >One PARTIAL solution, actually a pretty nice one would be an option in Jmol such > as > >set interchainbonding ON/OFF > >This would, I guess, have to be executed BEFORE a "load" command and would >direct the bond-generator to NOT connect atoms that are in separate TER sets. >What this would allow is for you to load your model with all those sets just the >way you have them and then restrict them to separate rotomers by defining groups >of atoms as, for example: > >define mainchain 1-210 and not 155 >define rotomer1 (mainchain or 1210) >define rotomer2 (mainchain or 1211) >define rotomer1 (mainchain or 1212) >... >restrict rotomer1 > >except... How do you "unrestrict"? So that then later you can do: > >restrict rotomer2 > >etc. > >This will ONLY work if Miguel can allow for ignoring interchain bonding. > >Bob > > > > > > > >Joost Van Durme wrote: > >> Hello! >> >> I'm investigating rotamer distributions of residues and I write a new PDB >> file including the found rotamers for one position. These are written at the >> end of the PDB file. The result is that multiple rotamers of one residue are >> displayed in the molecule. Unfortunately, Jmol starts to make bonds between >> those rotamer atoms, and that's not really what I want. It gets pretty messy >> that way. >> >> Is there a way to get this fixed? Or a workaround somewhere? >> >> you can view the model here: >> http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html >> >> and download the PDB file here: >> http://iri-pc87.ulb.ac.be/sample/sample/JOOST.PDB >> >> For info, you see the rotamers of a Tyrosine. ;-) >> >> Joost >> >> >> >> ------------------------------------------------------- This SF.Net email is >> sponsored by Oracle Space Sweepstakes Want to be the first software developer >> in space? Enter now for the Oracle Space Sweepstakes! >> http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >> _______________________________________________ Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >-- > >Robert M. Hanson, ha...@st..., 507-646-3107 >Professor of Chemistry, St. Olaf College >1520 St. Olaf Ave., Northfield, MN 55057 >mailto:ha...@st... >http://www.stolaf.edu/people/hansonr > >"Imagination is more important than knowledge." - Albert Einstein > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ----- ----- Interdisciplinary Research Institute for Human and Molecular Biology (IRIBHM) Faculty of Medicine Free University of Brussels Belgium ----- d(^_^)b |
From: Joost V. D. <jv...@ul...> - 2005-05-18 09:26:51
|
I don't want to brag, but check out this beauty: http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html ;-) Joost >Okay, I think this is the way to go. >I tried it on the file with 7 rotamers and it works fine. >I have a program that generates the PDB file and I can add anything to the file output I want, so if I tell it to write MODEL1 ... ENDMDL for each model, it should work. > >Thanks for all the help! >Saved again. ;-) > >cheers, > >Joost > > >>As Miguel suggests and my demo shows, the thing you need to do is to separate >>the different models using >> >>MODEL >>ENDMDL >> >>as shown, for example, at >> >>http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html >> >> 1 2 3 4 5 6 7 8 >>12345678901234567890123456789012345678901234567890123456789012345678901234567890 >>MODEL 1 >>ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N >>ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C >>... >>... >>ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H >>ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H >>TER 295 GLU 18 >>ENDMDL >> >>Of course the catch is that with this you need to duplicate ALL the entries. >>A nice benefit of this is that then you can run the animations and watch your >>rotomers interconvert. >> >>With 80+ rotomers that's a BIG file. You might consider doing this in a way I've >>done, where the single file is read in, then parsed, then reloaded as a set of >>models. The JavaScript sequence for this is really not that bad: >> >>strModel="" >>Model=new Array() >> >>function mycallback(app,msg){ >> var strMsg=msg+"" >> if(strMsg.length<1000)return >> strModel=strMsg >> Model=strModel.split("TER") >> strModel="" >> for(var i=1;i<=Model.length;i++){ >> strModel+="MODEL "+i+"\n"+Model[0]+Model[i]+"ENDMDL\n" >> } >> setTimeout("document.jmol.loadInline(strModel)",100) >>} >> >> >>This is a bit crude, but I think it does the job. (It doesn't rip out the >>Tyr A 155, though. If that's really what you need, that's a bit of a problem, I >>think. >> >>One PARTIAL solution, actually a pretty nice one would be an option in Jmol such >> as >> >>set interchainbonding ON/OFF >> >>This would, I guess, have to be executed BEFORE a "load" command and would >>direct the bond-generator to NOT connect atoms that are in separate TER sets. >>What this would allow is for you to load your model with all those sets just the >>way you have them and then restrict them to separate rotomers by defining groups >>of atoms as, for example: >> >>define mainchain 1-210 and not 155 >>define rotomer1 (mainchain or 1210) >>define rotomer2 (mainchain or 1211) >>define rotomer1 (mainchain or 1212) >>... >>restrict rotomer1 >> >>except... How do you "unrestrict"? So that then later you can do: >> >>restrict rotomer2 >> >>etc. >> >>This will ONLY work if Miguel can allow for ignoring interchain bonding. >> >>Bob >> >> >> >> >> >> >> >>Joost Van Durme wrote: >> >>> Hello! >>> >>> I'm investigating rotamer distributions of residues and I write a new PDB >>> file including the found rotamers for one position. These are written at the >>> end of the PDB file. The result is that multiple rotamers of one residue are >>> displayed in the molecule. Unfortunately, Jmol starts to make bonds between >>> those rotamer atoms, and that's not really what I want. It gets pretty messy >>> that way. >>> >>> Is there a way to get this fixed? Or a workaround somewhere? >>> >>> you can view the model here: >>> http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html >>> >>> and download the PDB file here: >>> http://iri-pc87.ulb.ac.be/sample/sample/JOOST.PDB >>> >>> For info, you see the rotamers of a Tyrosine. ;-) >>> >>> Joost >>> >>> >>> >>> ------------------------------------------------------- This SF.Net email is >>> sponsored by Oracle Space Sweepstakes Want to be the first software developer >>> in space? Enter now for the Oracle Space Sweepstakes! >>> http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >>> _______________________________________________ Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >>-- >> >>Robert M. Hanson, ha...@st..., 507-646-3107 >>Professor of Chemistry, St. Olaf College >>1520 St. Olaf Ave., Northfield, MN 55057 >>mailto:ha...@st... >>http://www.stolaf.edu/people/hansonr >> >>"Imagination is more important than knowledge." - Albert Einstein >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by Oracle Space Sweepstakes >>Want to be the first software developer in space? >>Enter now for the Oracle Space Sweepstakes! >>http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > >----- >----- >Interdisciplinary Research Institute >for Human and Molecular Biology (IRIBHM) >Faculty of Medicine >Free University of Brussels >Belgium >----- >d(^_^)b > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ----- ----- Interdisciplinary Research Institute for Human and Molecular Biology (IRIBHM) Faculty of Medicine Free University of Brussels Belgium ----- d(^_^)b |
From: timothy d. <mol...@ma...> - 2005-05-18 12:37:46
|
On 2005-05-18 (11:26) Joost Van Durme wrote: >I don't want to brag, but check out this beauty: > >http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html > >;-) > very sweet! and I think Egon's idea of 'translucent' atom spheres would look nice here = too. regards, tim --=20 Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:raleigh "Reality is merely an illusion, albeit a very persistent one." - Albert Ein= stein |
From: Miguel <mi...@jm...> - 2005-05-18 12:42:48
|
> I don't want to brag, but check out this beauty: > > http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html > > ;-) > > Joost *Very* nice=21 Miguel |
From: Joost V. D. <jv...@ul...> - 2005-05-18 11:31:10
|
>Joost seems pleased with seeing the rotomer by itself without >the rest of the protein. >Joost is not creating standard PDB files. Nonetheless, was it ever made >possible to display two specific models at the same time? If so, that would >obviously be a solution, but >I can't remember if you can do that. Mmm, I think you're missing something, Bob. I do see all rotamers and the rest of the protein. I just do "select *, model all; wireframe on;" Everything is there .... Don't you see it nicely at http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html ? Joost |
From: Bob H. <ha...@st...> - 2005-05-18 12:45:25
|
Ah, OK, I missed that. You actually WANT to see all the rotomers. Sure. I was just using model 1 model 2 etc. so I was just seeing the individual parts. I thought maybe you wanted to see the individual rotomers one by one; maybe animate them to see them sequentially, that sort of thing. That, it seemed to me, would require something like model 1,2; select not 155; The reason I asked if this were possible is that I thought I remembered a discussion about this some time back -- the desire to be able to compare two specific models of a larger set simultaneously. Obviously if we can do "model all" then in principle we could do "model 1,2", but I don't know if that was ever implemented. Or requested. Bob Joost Van Durme wrote: >>Joost seems pleased with seeing the rotomer by itself without >>the rest of the protein. >>Joost is not creating standard PDB files. Nonetheless, was it ever made >>possible to display two specific models at the same time? If so, that would >obviously be a solution, but >>I can't remember if you can do that. > > > Mmm, I think you're missing something, Bob. > I do see all rotamers and the rest of the protein. > I just do "select *, model all; wireframe on;" > Everything is there .... > > Don't you see it nicely at http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html ? > > Joost > > > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Bob H. <ha...@st...> - 2005-05-18 13:09:22
|
quick question: How do I "unrestrict"? That is, if I say: restrict (model=2 or model=1 and not 133) how do I then later do: restrict (model=3 or model=1 and not 133) ? Bob Hanson Joost Van Durme wrote: >>Joost seems pleased with seeing the rotomer by itself without >>the rest of the protein. >>Joost is not creating standard PDB files. Nonetheless, was it ever made >>possible to display two specific models at the same time? If so, that would >obviously be a solution, but >>I can't remember if you can do that. > > > Mmm, I think you're missing something, Bob. > I do see all rotamers and the rest of the protein. > I just do "select *, model all; wireframe on;" > Everything is there .... > > Don't you see it nicely at http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html ? > > Joost > > > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Miguel <mi...@jm...> - 2005-05-18 13:19:40
|
> quick question: > > How do I =22unrestrict=22? > > That is, if I say: > > restrict (model=3D2 or model=3D1 and not 133) > > how do I then later do: > > restrict (model=3D3 or model=3D1 and not 133) > Sorry, no way to 'unrestrict' :-( 'restrict' is a RasMol command. It is essentially implemented as: select =21selected spacefill off wireframe off cartoons off ribbons off rockets off severalOtherThings off select =21selected So, it explicitly turns off lots of things ... it is not a 'mask' or 'filter' that is applied over the top. I don't think we can change this behavior because of compatibility issues= . We could consider adding a another command that would behave in a filter/mask-like manner, but we would want to think it through carefully.= Miguel |
From: Bob H. <ha...@st...> - 2005-05-18 23:02:16
|
OK, so MODEL/ENDMDL, although its use violates standard PDB format, is the way to go. Here's an attempt at animation using select and NOT using restrict: http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol1.html Fun! -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Miguel <mi...@jm...> - 2005-05-18 23:15:38
|
> OK, so MODEL/ENDMDL, although its use violates standard PDB format, I must be missing something ... Q: In what way is the PDB format being violated? Miguel |
From: Bob H. <ha...@st...> - 2005-05-19 00:56:47
|
Oh, it's just from what Jan, I think, proffered. That MODEL/ENDMDL must contain the entire model, not scraps of it. Not a big deal, I think. Maybe I read that wrong.... <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_67.html> list use= s the following general rules: - In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry. - In the case of a whole macromolecular chain, or significant portion of a chain, having alternate sites, the atoms for each alternate position are listed together. The two conformers are delineated by MODEL/ENDMDL <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_68.html> records. In this case each MODEL must represent the entire molecula= r assemblage, including any heterogen group which is not necessarily disordered. Such is the case when DNA molecules are placed in UP an= d DOWN positions. Miguel wrote: >>OK, so MODEL/ENDMDL, although its use violates standard PDB format, >=20 >=20 > I must be missing something ... >=20 > Q: In what way is the PDB format being violated? >=20 >=20 > Miguel >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_idt12&alloc_id=16344&op=CCk > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users --=20 Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, = MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Miguel <mi...@jm...> - 2005-05-19 02:31:12
|
> Oh, it's just from what Jan, I think, proffered. That MODEL/ENDMDL > must contain the entire model, not scraps of it. > Not a big deal, I think. > Maybe I read that wrong.... > > <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_67.html> list u= ses > the following general rules: =5Bsnip=5D No, I agree with you ... per this pdb definition it is an incorrect use o= f MODEL/ENDMDL. It probably would be better to support alternate conformations. Unfortunately, Jmol does not currently have a mechanism to deal with alternate conformations ... although I think it does a better job than RasMol/Chime. Miguel |
From: Jeremy J Y. <jj...@ey...> - 2005-06-06 22:18:09
|
Hi All, Sorry for the delayed response to this thread. But I wanted to register an amen with respect to the feature request for arbitrary multiple model display. That is, as indicated by Bob Hanson, some command syntax such as model 1,2,[4-7],14 whereby a specific arbitray list of models from among a larger loaded set can be simultaneously displayed. The use case for me is display of a bound protein ligand complex, in some cases including energy-minimized and un-minimized models for each. Visualization of the geometry optimization would be greatly enhanced by this kind of control. -Jeremy. Jeremy J. Yang VP, Support Openeye Scientific Software On Wed, 18 May 2005, Bob Hanson wrote: > Ah, OK, I missed that. You actually WANT to see all the rotomers. > Sure. I was just using > > model 1 > model 2 > etc. > > so I was just seeing the individual parts. > > I thought maybe you wanted to see the individual rotomers one by one; > maybe animate them to see them sequentially, that sort of thing. > That, it seemed to me, would require something like > > model 1,2; select not 155; > > The reason I asked if this were possible is that I thought I remembered > a discussion about this some time back -- the desire to be able to > compare two specific models of a larger set simultaneously. Obviously > if we can do "model all" then in principle we could do "model 1,2", but I > don't know if that was ever implemented. Or requested. > > Bob > > > Joost Van Durme wrote: > > >>Joost seems pleased with seeing the rotomer by itself without > >>the rest of the protein. > >>Joost is not creating standard PDB files. Nonetheless, was it ever made > >>possible to display two specific models at the same time? If so, that would >obviously be a solution, but > >>I can't remember if you can do that. > > > > > > Mmm, I think you're missing something, Bob. > > I do see all rotamers and the rest of the protein. > > I just do "select *, model all; wireframe on;" > > Everything is there .... > > > > Don't you see it nicely at http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html ? > > > > Joost > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by Oracle Space Sweepstakes > > Want to be the first software developer in space? > > Enter now for the Oracle Space Sweepstakes! > > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > > _______________________________________________ > > Jmol-users mailing list > > Jmo...@li... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > Robert M. Hanson, ha...@st..., 507-646-3107 > Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 > mailto:ha...@st... http://www.stolaf.edu/people/hansonr > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Miguel <mi...@jm...> - 2005-06-06 22:37:08
|
> Hi All, > > Sorry for the delayed response to this thread. But I wanted to > register an amen with respect to the feature request for > arbitrary multiple model display. That is, as indicated > by Bob Hanson, some command syntax such as > > model 1,2,=5B4-7=5D,14 > > whereby a specific arbitray list of models from among a larger > loaded set can be simultaneously displayed. Unfortunately, this is non-trivial to implement. Working within the structure of the current rendering engine, I cannot think of an easy way to implement it without having a negative impact on performance ... we want to have an arbitrary set selected from an arbitrarily large set of models. It could be done efficiently with some restructuring of the rendering engine, but that is going to require some work ... and is not going to happen any time soon. For the time-being I think you need to do this using the RasMol method: restrict model=3D1,model=3D2,model=3D4,model=3D5,model=3D6,model=3D7,mode= l=3D14 As you probably know, the downside of this technique is that you lose all= the attributes associated with your other atoms. Miguel |
From: Joost V. D. <jv...@ul...> - 2005-05-19 07:48:49
|
>OK, so MODEL/ENDMDL, although its use violates standard PDB format, >is the way to go. Here's an attempt at animation using select and >NOT using restrict: > >http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol1.html > >Fun! Beautiful animation, Bob! I might implement this on my site when I have all the essentials finished. However, I don't understand where I violate PDB rules here. But anyway, Jmol does exactly what I want, so I'm happy with it. :) Q: what's up with the translucent atoms Egon whas talking about? Is this implemented in Jmol? Joost >-- > >Robert M. Hanson, ha...@st..., 507-646-3107 >Professor of Chemistry, St. Olaf College >1520 St. Olaf Ave., Northfield, MN 55057 >mailto:ha...@st... >http://www.stolaf.edu/people/hansonr > >"Imagination is more important than knowledge." - Albert Einstein > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ----- ----- Interdisciplinary Research Institute for Human and Molecular Biology (IRIBHM) Faculty of Medicine Free University of Brussels Belgium ----- d(^_^)b |
From: Bob H. <ha...@st...> - 2005-05-19 11:07:34
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Joost, apparently the PDB rules state that MODEL/ENDMDL is to contain the entire molecule, not pieces thereof. That's all. Unless you are planning to PUBLISH these as PDB files, it's no big deal. I think it's a great idea to do it just the way you do. It saves loads of space. A comment in the header might be nice that indicates which residue is being modeled and how many models there are. Then you could use "show pdbheader" at the end of the applet script parameter to grab that information on the fly. All you would need is the PDB file itself to produce the whole page. There are lots of interesting things you could do with the header that could be helpful. Bob Joost Van Durme wrote: >> OK, so MODEL/ENDMDL, although its use violates standard PDB format, is the >> way to go. Here's an attempt at animation using select and NOT using >> restrict: >> >> http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol1.html >> >> Fun! > > > Beautiful animation, Bob! I might implement this on my site when I have all > the essentials finished. However, I don't understand where I violate PDB > rules here. But anyway, Jmol does exactly what I want, so I'm happy with it. > :) > > Q: what's up with the translucent atoms Egon whas talking about? Is this > implemented in Jmol? > > Joost > > >> -- >> >> Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, >> St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 >> mailto:ha...@st... http://www.stolaf.edu/people/hansonr >> >> "Imagination is more important than knowledge." - Albert Einstein >> >> >> ------------------------------------------------------- This SF.Net email >> is sponsored by Oracle Space Sweepstakes Want to be the first software >> developer in space? Enter now for the Oracle Space Sweepstakes! >> http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >> _______________________________________________ Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > ----- ----- Interdisciplinary Research Institute for Human and Molecular > Biology (IRIBHM) Faculty of Medicine Free University of Brussels Belgium > ----- d(^_^)b > > > ------------------------------------------------------- This SF.Net email is > sponsored by Oracle Space Sweepstakes Want to be the first software developer > in space? Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click > _______________________________________________ Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Miguel <mi...@jm...> - 2005-05-19 11:47:11
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> Q: what's up with the translucent atoms Egon whas talking about? Is thi= s > implemented in Jmol? Joost, I am still struggling with the translucent atoms. Hope to have it out within the next few days. Miguel |