Re: [Jmol-users] Calculate structure results
Beta in parentheses may be ok. I was so focused on beta turns that I did not stop and consider what the presence of the parentheses would mean. Another issue with color is with hydrogen bonds of beta sheets. Presently these hydrogen bonds come in two colors. The colors document only shows one. >>> "Angel Herráez" 03/04/11 2:24 PM >>> > OK, bad assumption on my part. I was assuming it was identifying beta turns. The Colors document on the > Jmol site does indicate blue for beta turn. My fault. So we should say just "turns", right? Will do that Aha, that's why I put beta in parentheses last time! * strand [255,200,0] FFC800 (*) turn [96,128,255]6080FF :-) -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Really Ugly Windows Firefox Issue
Angel- Thanks for the information. I'll try to update now. I don't think an update 3.6.15 was expected. I think the next update was supposed to be 4. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: "Angel Herráez" Sent: Friday, March 04, 2011 3:14 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Really Ugly Windows Firefox Issue I just got notice of the latest upgrade: What's New in Firefox 3.6.15 Firefox 3.6.15 fixes the following issues found in previous versions of Firefox 3.6: * Fixed an issue where some Java applets would fail to load in Firefox 3.6.14 It works now! Two page reloads, no problem in the applet. -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Really Ugly Windows Firefox Issue
I just got notice of the latest upgrade: What´s New in Firefox 3.6.15 Firefox 3.6.15 fixes the following issues found in previous versions of Firefox 3.6: * Fixed an issue where some Java applets would fail to load in Firefox 3.6.14 It works now! Two page reloads, no problem in the applet. -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Calculate structure results
> OK, bad assumption on my part. I was assuming it was identifying beta turns. > The Colors document on the > Jmol site does indicate blue for beta turn. My fault. So we should say just "turns", right? Will do that Aha, that's why I put beta in parentheses last time! strand [255,200,0] FFC800 () turn [96,128,255]6080FF :-) -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Calculate structure results
OK, bad assumption on my part. I was assuming it was identifying beta turns. The Colors document on the Jmol site does indicate blue for beta turn. Karl >>> Robert Hanson 03/03/11 8:18 PM >>> Karl, Here's the report for 2mhr according to DSSP, which we are using now for Jmol's standard structure calculation. Wouldn't surprise me at all if a turn is 3, 4, or 5 residues -- that's the nature of them in DSSP. SUMMARY: G : A:12_A:14 H : A:19_A:37 H : A:41_A:64 T : A:65_A:66 T : A:68_A:69 H : A:70_A:85 T : A:86_A:86 H : A:93_A:109 T : A:110_A:110 G : A:111_A:114 T : A:115_A:117 and attached details. The various kinds of turns in DSSP are probably not all beta turns by that definition, because they can be from 4 to 6 residues: >33< >444< >< And if parts of them overlap with other structural forms, they will show up as being shorter than their usual length (see attached listing). I'll be surprised if you can find an error vis-a-vis DSSP. I think we have a very solid implementation of that. Bob On Wed, Mar 2, 2011 at 3:55 PM, Karl Oberholser wrote: Hi All, I have recently discovered what I think is erroneous output for turns when using calculate structure. Beta turns contain four residues, but the segments that are colored blue after using calculate structure are from two to five residues long. Some of the ones that are three and five residues contain a hydrogen bond between the residues expected for a beta turn. It appears that some turns are being marked short by one residue and others are long by a residue. I get these results using the application with 12.0.34 and on Proteopedia by adding '?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar' to the page url. It occurs with myohemerythrin (2mhr.pdb) and domain 2 of chain a of glycogen phosphorylase. Karl Karl M. Oberholser, Ph.D.Phone: Emeritus Professor of Chemistry Voice: 717-766-0512 Chemistry & Biochemistry Dept.Fax: 717-691-6046 Messiah College e-mail: oberh...@messiah.edu P.O. Box 3049 One College Avenue Grantham, Pa 17027 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Calculate structure results
Hi, Furthermore: On Fri, Mar 4, 2011 at 1:15 AM, Robert Hanson wrote: > T : A:65_A:66 An R-L nest that is part of a Schellmann loop > T : A:68_A:69 A type I beta-turn > T : A:86_A:86 A type I turn (also a niche3/4 bound to a water) > T : A:110_A:110 Hmmm. Not a turn. Looks like the helix from 93-113 is being bent out of shape by the metal-binding residues. > T : A:115_A:117 A type II turn overlapping an L-R nest bound to Tyr-18 phenol OH. So, yes, most of these are turns. I would add that I have no doubt Jmol has a correct DSSP implementation, and that DSSP generally gets it right. However, I'm not fond of the idea of 3 and 5 residue beta turns, but that is inevitable when there is overlap between structure, and you have to compress it into a single 'sequence' like "...TT...". gilleain -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
Hi Bob, Actually i didn't generate this .cos files, so i don't know if it was used the .mol file and , therefore, i don't know if they were supposed to match. But i think for my purpouse it would be easier to avoid creating a .jvxl file, since i can use the function loadCosmo and it works. I would like to know how to load those commands of the function without opening the console, i want, once the .mol is loaded, the surface to open along with it, if it is possible. I'm sending the Java class i created attached. JmolTable.java Description: Binary data JmolLoadCompound.java Description: Binary data -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)
Thank you very mucho for your help! > The difficulty is defining the atoms involved in the receptor...showing > bonds and ribbons in the entire protein is quite easy: > > select protein; cartoon on; > > The ligand will display initially as bonds and atoms. I suspect this isn't > what you want :-) Here's script for displaying bonds and atoms only > within, > say, 6 Angstroms of the ligand(s): > > select protein; cartoon only; select within(6.0,ligand);wireframe 60; > spacefill 100; > > and if you're interested only in displaying sidechains: > > select protein; cartoon only; select within(6.0,ligand) and > sidechain;wireframe 60; spacefill 100; > > You can save that script to a .spt file for easy retrieval elsewhere (and > easy updating, if your fancy changes later), or you can just copy and > paste > it in the second argument of jmolApplet, just after "load > 1.1_1.1_1__receptor.pdb." > > Cheers, Mike > > On Wed, Mar 2, 2011 at 10:17 AM, wrote: > >> Hello, i would like to find examples about how to define default values >> for a receptor-ligand model (pdb format). >> >> >>jmolApplet(400, "load 1.1_1.1_1__receptor.pdb"); >> >> >> For us is useful to load the applet showing "ribbons" and "bonds" for >> the >> receptor and "bonds" only for the ligand. >> >> Are any available Jmol example settings with receptor-ligand models? >> Thank you. >> >> >> >> -- >> Free Software Download: Index, Search & Analyze Logs and other IT data >> in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Mike Evans > Organic Chemistry Graduate Student > Moore Group > University of Illinois, Urbana-Champaign > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
