From: Robert H. <ha...@st...> - 2015-01-28 17:21:53
|
The idea of a MUTATE command has been rattling around in my brain for a while, and last night it hit me that we have all the pieces to do this right -- structural comparison using Jmol bioSMARTS, flexible fit using compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very serviceable MINIMIZE command. A few added tweaks, and nine hours work, and what do you know? Jmol has a new command today! Do try it out! Bob http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.28.zip Jmol.___JmolVersion="14.3.12_2015.01.28" new feature: MUTATE command -- operates only on last model present if multiple models are loaded -- replaces one amino acid group with another -- can read from RCSB or from user-specified file -- examples: mutate 33 lys // uses last occurrence of resno=33 mutate @3 arg // replaces group of atom 3 mutate @r @fname // replaces resno in variable r with file data (use "==XXX" for RCSB) mutate {r} his // same as above; r must be an atom selection mutate 22 "myfile.cif" // user-defined replacement bug fix: write "t.pdb" now correctly sequences groups and atoms, even after mutation new feature: resno is user settable -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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: Angel H. <ang...@ua...> - 2015-01-28 17:58:20
|
Bob, that sounds terrific! Many people were expecting this tool. If the results prove realistic enough, it will make for a great teaching resource. I probably do not have the time now, but will put this for testing in my to-do list Thanks for those 9 hours! ;-) buying you a handful of beers is suitable to celebrate this -- remind me! |
From: Jim Hu <jim...@gm...> - 2015-01-28 20:18:24
|
Cool! After a long period of not having time, I just started looking again at getting the jsmol2wp Wordpress plugin into wordpress.org. How does this fit with jsmol? I'm assuming that some of the stuff requires Jmol to do the processing. Jim On Jan 28, 2015, at 11:21 AM, Robert Hanson <ha...@st...> wrote: > The idea of a MUTATE command has been rattling around in my brain for a while, and last night it hit me that we have all the pieces to do this right -- structural comparison using Jmol bioSMARTS, flexible fit using compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very serviceable MINIMIZE command. A few added tweaks, and nine hours work, and what do you know? Jmol has a new command today! > > Do try it out! > > Bob > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.28.zip > > Jmol.___JmolVersion="14.3.12_2015.01.28" > > new feature: MUTATE command > -- operates only on last model present if multiple models are loaded > -- replaces one amino acid group with another > -- can read from RCSB or from user-specified file > -- examples: > mutate 33 lys // uses last occurrence of resno=33 > mutate @3 arg // replaces group of atom 3 > mutate @r @fname // replaces resno in variable r with file data (use "==XXX" for RCSB) > mutate {r} his // same as above; r must be an atom selection > mutate 22 "myfile.cif" // user-defined replacement > > bug fix: write "t.pdb" now correctly sequences groups and atoms, even after mutation > > new feature: resno is user settable > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department 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 > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users ===================================== Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 |
From: Robert H. <ha...@st...> - 2015-01-28 20:30:25
|
MUTATION works the same in JavaScript as Java. Just mutate 20 ARG like that. Done. No special minimization going on here, though. That's the next phase. Bob On Wed, Jan 28, 2015 at 2:18 PM, Jim Hu <jim...@gm...> wrote: > Cool! > > After a long period of not having time, I just started looking again at > getting the jsmol2wp Wordpress plugin into wordpress.org. How does this > fit with jsmol? I'm assuming that some of the stuff requires Jmol to do the > processing. > > Jim > > On Jan 28, 2015, at 11:21 AM, Robert Hanson <ha...@st...> wrote: > > The idea of a MUTATE command has been rattling around in my brain for a > while, and last night it hit me that we have all the pieces to do this > right -- structural comparison using Jmol bioSMARTS, flexible fit using > compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE > TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very > serviceable MINIMIZE command. A few added tweaks, and nine hours work, and > what do you know? Jmol has a new command today! > > Do try it out! > > Bob > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.28.zip > > Jmol.___JmolVersion="14.3.12_2015.01.28" > > new feature: MUTATE command > -- operates only on last model present if multiple models are loaded > -- replaces one amino acid group with another > -- can read from RCSB or from user-specified file > -- examples: > mutate 33 lys // uses last occurrence of resno=33 > mutate @3 arg // replaces group of atom 3 > mutate @r @fname // replaces resno in variable r with file > data (use "==XXX" for RCSB) > mutate {r} his // same as above; r must be an atom selection > mutate 22 "myfile.cif" // user-defined replacement > > bug fix: write "t.pdb" now correctly sequences groups and atoms, even > after mutation > > new feature: resno is user settable > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department 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 > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. > http://goparallel.sourceforge.net/_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ===================================== > Jim Hu > Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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: Rolf H. <rh...@fl...> - 2015-01-30 11:28:23
|
On 01/28/2015 06:21 PM, Robert Hanson wrote: > The idea of a MUTATE command has been rattling around in my brain for a > while, and last night it hit me that we have all the pieces to do this > right -- structural comparison using Jmol bioSMARTS, flexible fit using > compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE > TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very > serviceable MINIMIZE command. A few added tweaks, and nine hours work, and > what do you know? Jmol has a new command today! > > Do try it out! > > Bob > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.28.zip > When I try to run this Jmol version within the 'Jena3D Viewer' the HTML5 version freezes almost completely without error message (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=html5&JMOLVERSION=14.3.12_2015.01.28) and the Java version (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=java&JMOLVERSION=14.3.12_2015.01.28) using 'IcedTea Java' doesn't freeze but stops in the middle of the initializing script with the following error message: script ERROR: java.lang.NoSuchMethodError: org.jmol.script.SV.oValue(Lorg/jmol/script/SV;)Ljava/lang/Object; I could identify the following commands from the initializing script that result in the same error message: ca2 = {1:A.CA/1}.xyz + {1:A.CA/1}.xyz - {2:A.CA/1}.xyz; draw boundary_1_A PLANE PERP 180 @ca2 (1:A.CA/1) translucent 0.2 red; Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Rolf H. <rh...@fl...> - 2015-01-30 11:49:08
|
On 01/28/2015 06:21 PM, Robert Hanson wrote: > The idea of a MUTATE command has been rattling around in my brain for a > while, and last night it hit me that we have all the pieces to do this > right -- structural comparison using Jmol bioSMARTS, flexible fit using > compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE > TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very > serviceable MINIMIZE command. A few added tweaks, and nine hours work, and > what do you know? Jmol has a new command today! > > Do try it out! > Q: Would it be possible to add an option to the new command to add the mutated residues as spearate models instead of changing the original model? We use this in the 'Jena3D Viewer' (e.g.: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=html5&VIEW=variant) to visualize (crude models of) SNPs/SAPs side by side with the original residues. For the mutation we currently use an external program that mutates a single residue (per chain). We then cut out the mutated residues and add them as a new model to the original PDB file and repeat this for all SNPs/SAPs. This minimizes the amount of data, which is especially relevant for proteins like hemoglobin where about 400 SNPs/SAPs are available. And it enables multiple mutations at the same position. A drawback is that it doesn't work for NMR structures which already have multiple models. But this might be overcome by adding the new models to a separate second file that is loaded together with the original file. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Angel H. <ang...@ua...> - 2015-01-30 12:15:51
|
Rolf, wouldn't the idea of "alternate (PDB format's "altLoc") be better suited to this mutations than adding them in a new model? > Q: Would it be possible to add an option to the new command to add the > mutated residues as spearate models instead of changing the original model? > > We use this in the 'Jena3D Viewer' > For the mutation we currently use an external program that mutates a > single residue (per chain). We then cut out the mutated residues and add > them as a new model to the original PDB file and repeat this for all |
From: Rolf H. <rh...@fl...> - 2015-01-30 12:20:09
|
On 01/30/2015 01:15 PM, Angel Herráez wrote: > Rolf, wouldn't the idea of "alternate (PDB format's "altLoc") be > better suited to this mutations than adding them in a new model? > As far as I know 'altloc' is only suitable for different positions of existing atoms and not for adding new atoms. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Rolf H. <rh...@fl...> - 2015-01-30 12:31:27
|
On 01/30/2015 01:20 PM, Rolf Huehne wrote: > On 01/30/2015 01:15 PM, Angel Herráez wrote: >> Rolf, wouldn't the idea of "alternate (PDB format's "altLoc") be >> better suited to this mutations than adding them in a new model? >> > As far as I know 'altloc' is only suitable for different positions of > existing atoms and not for adding new atoms. > Another problem would be the limitation by a single letter for the 'altloc' ID. How would you get 400 (or more) different IDs into a single letter? And there might also be problems displaying all at once. (I havn't worked with 'altloc' yet so I am not sure about this.) Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Angel H. <ang...@ua...> - 2015-01-30 13:48:59
|
Hi Rolf > And there might also be problems displaying all at once. (I havn't > worked with 'altloc' yet so I am not sure about this.) I'm quite sure that may be easily controlled, but you are right on the other points. > > As far as I know 'altloc' is only suitable for different positions of > > existing atoms and not for adding new atoms. That's right, I did not realize a new residue will have different atom names and so altloc is not suitable |
From: Robert H. <ha...@st...> - 2015-01-30 15:30:18
|
alt-loc should be fine; the entire group is being replaced, so there is no problem with names. Can't help with the 400 -- even if you could do that, you would not want to using Jmol, I think. Better tools for that. But for small numbers, we could add mutations as alt-loc. Actually, that's a lot easier that creating a whole new group. Way before 400 you will run into the problem that the allowed number of bonds that link residues will be exceeded (20? something like that). |
From: Rolf H. <rh...@fl...> - 2015-01-30 16:14:10
|
On 01/30/2015 04:30 PM, Robert Hanson wrote: > alt-loc should be fine; the entire group is being replaced, so there is no > problem with names. Can't help with the 400 -- even if you could do that, > you would not want to using Jmol, I think. Better tools for that. But for > small numbers, we could add mutations as alt-loc. Actually, that's a lot > easier that creating a whole new group. Way before 400 you will run into > the problem that the allowed number of bonds that link residues will be > exceeded (20? something like that). > One advantage of adding the mutated residues is that there are no such limits. Bob, why do you think that Jmol wouldn't be suitable for doing 400 independent single residue mutations? If it is suitable for doing each of them individually, why shouldn't it be suitable for all of them consecutively (all done on the original structure)? Maybe performance could be a problem but we will have to see how performance will be after sidechain positioning optimizations have been added. And the two specialized programs we are using to precompute the mutations can also take several minutes for one PDB entry. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Robert H. <ha...@st...> - 2015-01-30 16:17:59
|
I think 400 protein models in a single multi-model PDB file is problematic. 30,000 x 400 = 12,000,000 atoms. On Fri, Jan 30, 2015 at 10:14 AM, Rolf Huehne <rh...@fl...> wrote: > On 01/30/2015 04:30 PM, Robert Hanson wrote: > > alt-loc should be fine; the entire group is being replaced, so there is > no > > problem with names. Can't help with the 400 -- even if you could do that, > > you would not want to using Jmol, I think. Better tools for that. But for > > small numbers, we could add mutations as alt-loc. Actually, that's a lot > > easier that creating a whole new group. Way before 400 you will run into > > the problem that the allowed number of bonds that link residues will be > > exceeded (20? something like that). > > > One advantage of adding the mutated residues is that there are no such > limits. > > Bob, why do you think that Jmol wouldn't be suitable for doing 400 > independent single residue mutations? > > If it is suitable for doing each of them individually, why shouldn't it > be suitable for all of them consecutively (all done on the original > structure)? > Maybe performance could be a problem but we will have to see how > performance will be after sidechain positioning optimizations have been > added. And the two specialized programs we are using to precompute the > mutations can also take several minutes for one PDB entry. > > Regards, > Rolf > > > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rh...@fl... > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph > Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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: Rolf H. <rh...@fl...> - 2015-01-30 16:25:48
|
On 01/30/2015 05:17 PM, Robert Hanson wrote: > I think 400 protein models in a single multi-model PDB file is problematic. > 30,000 x 400 = 12,000,000 atoms. > That is why I proposed not to copy the whole model but just the mutated residues. So for a protein with 30,000 atoms and an average of 20 atoms per residue this would mean 38,000 atoms afterwards. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Robert H. <ha...@st...> - 2015-01-30 16:37:20
|
Oh, so you mean, model 1 --- original protein ---- model 2 ...mutation 1... model 3 ...mutation 2... model 4 ...mutation 3... like that? On Fri, Jan 30, 2015 at 10:25 AM, Rolf Huehne <rh...@fl...> wrote: > On 01/30/2015 05:17 PM, Robert Hanson wrote: > > I think 400 protein models in a single multi-model PDB file is > problematic. > > 30,000 x 400 = 12,000,000 atoms. > > > That is why I proposed not to copy the whole model but just the mutated > residues. > So for a protein with 30,000 atoms and an average of 20 atoms per > residue this would mean 38,000 atoms afterwards. > > Regards, > Rolf > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rh...@fl... > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph > Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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: Rolf H. <rh...@fl...> - 2015-01-30 16:52:42
|
On 01/30/2015 05:37 PM, Robert Hanson wrote: > Oh, so you mean, > > model 1 > --- original protein ---- > model 2 > ...mutation 1... > model 3 > ...mutation 2... > model 4 > ...mutation 3... > > like that? > Yes, exactly. And to avoid the problem with NMR structures or other multi-model files it might be wiser to build the new models in a second file, at least optionally: file 1 model 1 --- original protein --- file 2 model 1 ... mutation 1 of file 1 model 1... file 2 model 2 ... mutation 2 of file 1 model 1... For mutations in the second original model one could add another file and so on. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Robert H. <ha...@st...> - 2015-01-30 16:16:14
|
OK, some adjustments. http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.30.zip Jmol.___JmolVersion="14.3.12_2015.01.30" new feature: MUTATE command -- operates only on last model present if multiple models are loaded -- replaces one *or more *amino acids group with others -- can read from RCSB or from user-specified file -- examples: mutate 33 lys // replace resno=33 with lysine mutate @3 arg // replaces group of atom 3 with arginine mutate @r gly // replaces groups in variable r with glycine mutate 22 "myfile.cif" // user-defined replacement mutate {1-3} ala // replace first three residues with alanine mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with gly-leu-val-ala-gly mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3 with leu-tyr-ser mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2 mutate {within(sequence, "GAT")} GYT // replace locations of GAT with GYT (needs testing) mutate 35 @fname // replaces resno=35 with file data (use "==ALA" or "~A" for RCSB) mutate {r} his // same as above; r must be an atom selection bug fix: code fixes relating to calculate structure in 01.29 On Fri, Jan 30, 2015 at 9:30 AM, Robert Hanson <ha...@st...> wrote: > alt-loc should be fine; the entire group is being replaced, so there is no > problem with names. Can't help with the 400 -- even if you could do that, > you would not want to using Jmol, I think. Better tools for that. But for > small numbers, we could add mutations as alt-loc. Actually, that's a lot > easier that creating a whole new group. Way before 400 you will run into > the problem that the allowed number of bonds that link residues will be > exceeded (20? something like that). > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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: Rolf H. <rh...@fl...> - 2015-01-30 17:01:29
|
On 01/30/2015 05:52 PM, Rolf Huehne wrote: > On 01/30/2015 05:37 PM, Robert Hanson wrote: >> Oh, so you mean, >> >> model 1 >> --- original protein ---- >> model 2 >> ...mutation 1... >> model 3 >> ...mutation 2... >> model 4 >> ...mutation 3... >> >> like that? >> > Yes, exactly. > Here is an example from the 'Jena3D Viewer': http://jenalib.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1DEH&MODE=asymmetricSNP Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Robert H. <ha...@st...> - 2015-01-30 22:01:58
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The limitation here is simply that constructs such as chains, "polymers", groups, atoms, and bonds, secondary structure are attributes of a model on an N:1 basis. The basic structure in all Jmol sessions is: ModelSet Model[] Atom[] Bond[] (more arrays of various sorts) Model->Chain[]->Group[]-> (pointers to a subset of atoms, pointer to its chain) BioModel (extends Model) adds: BioPolymer[](a set of linearly covalently connected monomers)->Monomer[] (extends Group) So you can't have chains that cross model boundaries, nor bonds. That's pretty much written in stone. The mutation business is marking a set of atoms for deletion, adding a new set of atoms at the end of the atom array, moving those atoms into position, and then doing some careful patching to get the pointers correct. Officially what we are doing is moving a group to a new Chain within the same model. Jmol is actually running a script to do this. That script looks like something like this: atoms0 = {*} res0 = ({26:32}) set appendNew false load append "==GLY" set appendNew true res1 = {!atoms0};r1 = res1[1];r0 = res1[0] if ({r1 & within(group, r0)}){ // test for only one group haveHs = ({_H and connected(res0)} != 0) if (!haveHs) {delete _H and res1} // bioSMILES-based search for backbone in new structure sm = '[*.N][*.CA][*.C][*.O]' keyatoms = res1.find(sm) // construction of a dihedral difference map x = compare(res1,res0,sm,'BONDS') if(x){ print 'mutating ' + res0[1].label('%n%r') + ' to ' + "==GLY".trim('=') // matching the backbone and moving it into place using the "flex-fit" idea rotate branch @x compare res1 res0 SMARTS @sm rotate translate 0 // patching in the new bonds; deleting the old N2 = {*.N and !res0 && connected(res0)} C0 = {*.C and !res0 && connected(res0)} delete res0 if (N2) { delete *.OXT and res1 connect {N2} {res1 & *.C} } if (C0) { connect {C0} {res1 & *.N} } } } Then the new chain is established. I think I could write a little adapter that "reads" atoms from another model, not from a file. This would allow mixing and matching pieces of models to create a new one, leaving the "libary" of pieces still intact. That certainly could be interesting. Bob |