[Jmol-users] Jmol error in Firefox/Windows only
Hi, I have a figure that is working in Firefox on Mac but broken in FF/Win Vista. It works fine in Mac/Safari and Win/Internet Explorer. The error message in the Java console is as follows: script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) eval ERROR: line 1 command 2 of file null: script 3d/centerS1Abox.spt FileManager opening http://moleculesinmotion.com/3Dfigure_schumacher/3d/sidechains.spt script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) Can anyone tell me how to get around this? If this is a file placement issue - I thought that was only a problem with local files? Thanks, Frieda PS - Jmol 11.5.27 // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol error in Firefox/Windows only
I should have mentioned more about the problem - the Jmol loads just fine on the page and responds to the mouse, but the problem occurs when a script is called from a radio button, checkbox, etc. (Buttons that do not call scripts work fine.) Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol error in Firefox/Windows only
what happens when you go to that page and then plug this into the URL
address line?
javascript:void(jmolScript('script 3d/sidechains.spt'))
?
Frieda Reichsman wrote:
I should have mentioned more about the problem - the Jmol loads just
fine on the page and responds to the mouse, but the problem occurs
when a script is called from a radio button, checkbox, etc. (Buttons
that do not call scripts work fine.)
Frieda
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Jmol error in Firefox/Windows only
There is no change in the button behavior, nor any discernible change
in FF.
On Apr 21, 2008, at 8:15 AM, Bob Hanson wrote:
what happens when you go to that page and then plug this into the URL
address line?
javascript:void(jmolScript('script 3d/sidechains.spt'))
?
Frieda Reichsman wrote:
I should have mentioned more about the problem - the Jmol loads just
fine on the page and responds to the mouse, but the problem occurs
when a script is called from a radio button, checkbox, etc. (Buttons
that do not call scripts work fine.)
Frieda
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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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
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Re: [Jmol-users] Jmol error in Firefox/Windows only
Placing all the files in the same directory (and changing all the file calls) still results in a security error when a script is called by a button: script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:06 AM, Frieda Reichsman wrote: I should have mentioned more about the problem - the Jmol loads just fine on the page and responds to the mouse, but the problem occurs when a script is called from a radio button, checkbox, etc. (Buttons that do not call scripts work fine.) Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol error in Firefox/Windows only
CORRECTION - the pdb file does not load into the applet when all files are placed into the same directory. SO the breakage is even worse in this case. script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) Sent previously, incorrect: Placing all the files in the same directory (and changing all the file calls) still results in a security error when a script is called by a button: // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:06 AM, Frieda Reichsman wrote: I should have mentioned more about the problem - the Jmol loads just fine on the page and responds to the mouse, but the problem occurs when a script is called from a radio button, checkbox, etc. (Buttons that do not call scripts work fine.) Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol error in Firefox/Windows only
Hi Eran - I thought this sounded a lot like the problem that you folks are having. Thank you for confirming the domain name aspect of it. Question - So, i assume there is no problem as long as the DNS reverse lookup IP address resolves to the domain name of the URL-- for example, published figures at Biochemical Journal work perfectly (requires subscription): http://www.biochemj.org/bj/410/0439/bj4100439add2.htm --can you do a reverse lookup on that URL (I'm assuming you have a subscription from the Weizmann...) and confirm that -- or tell me how to do a reverse lookup myself? Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:51 AM, Eran Hodis wrote: Hi Frieda, This is a issue we are dealing with in Proteopedia as well. The combination of Firefox version 2 and Java version 1.6.0_03+ (latest stable release is 1.6.0_05) is more sensitive to security issues. When I do a reverse DNS lookup on the IP address you gave (64.95.78.91) I get permaculture.gaiahost.coop. I'm guessing that this name does not match the domain name of the website where you are having these problems. This mismatch causes the combination of FF2 and Java 1.6.0_03+. At least that is how I understand it at the moment, and if anyone wants to correct me I'll be glad to be corrected. Regular commands seem to be passed ok to the Jmol applet, but scripts or files stored on the server throw the error when you try to execute or load them. The odd part is that any script or load file commands inside the original definition of the applet works fine. Rolf pointed out a message board dealing with the issue in one of his previous messages I've copied below: This looks like a problem we are also facing with our JenaLib Jmol Viewer and Firefox. It started with Java version 1.6.0_03. Since Egon uses 1.6.0_05 I would expect that he will also have the same java.security.AccessControlException problem with the following URL: http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh I tried other Jmol sites and they worked fine with Java 1.6.0_03. But I couldn't figure out what makes the difference. The following thread in the Java forum http://forum.java.sun.com/thread.jspa?threadID=5230759; seems to refer to this problem. It is suggested there that the problem could be avoided by connecting back to the server before any liveconnect calls are made. But removing any callbacks didn't help with our viewer and I couldn't detect any other liveconnect calls before loading the PDB file and script from our server. As explanation for the difference between InternetExplorer and Firefox I found the suggestion that the more stringent default security policy of Firefox is responsible for it. Regards, Rolf Best regards, Eran On Mon, Apr 21, 2008 at 3:43 PM, Frieda Reichsman [EMAIL PROTECTED] wrote: CORRECTION - the pdb file does not load into the applet when all files are placed into the same directory. SO the breakage is even worse in this case. script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) Sent previously, incorrect: Placing all the files in the same directory (and changing all the file calls) still results in a security error when a script is called by a button: // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:06 AM, Frieda Reichsman wrote: I should have mentioned more about the problem - the Jmol loads just fine on the page and responds to the mouse, but the problem occurs when a script is called from a radio button, checkbox, etc. (Buttons that do not call scripts work fine.) Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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.
Re: [Jmol-users] Jmol error in Firefox/Windows only
Hi Frieda, I'm not sure what the IP address of that website is, does anyone know how to get an IP address from a domain name? http://remote.12dt.com/ allows you to do a reverse DNS lookup which you can also do on a Mac terminal by doing nslookup followed by a space and then the IP address. Best, Eran On Mon, Apr 21, 2008 at 4:42 PM, Frieda Reichsman [EMAIL PROTECTED] wrote: Hi Eran - I thought this sounded a lot like the problem that you folks are having. Thank you for confirming the domain name aspect of it. Question - So, i assume there is no problem as long as the DNS reverse lookup IP address resolves to the domain name of the URL-- for example, published figures at Biochemical Journal work perfectly (requires subscription): http://www.biochemj.org/bj/410/0439/bj4100439add2.htm --can you do a reverse lookup on that URL (I'm assuming you have a subscription from the Weizmann...) and confirm that -- or tell me how to do a reverse lookup myself? Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:51 AM, Eran Hodis wrote: Hi Frieda, This is a issue we are dealing with in Proteopedia as well. The combination of Firefox version 2 and Java version 1.6.0_03+ (latest stable release is 1.6.0_05) is more sensitive to security issues. When I do a reverse DNS lookup on the IP address you gave (64.95.78.91) I get permaculture.gaiahost.coop. I'm guessing that this name does not match the domain name of the website where you are having these problems. This mismatch causes the combination of FF2 and Java 1.6.0_03+. At least that is how I understand it at the moment, and if anyone wants to correct me I'll be glad to be corrected. Regular commands seem to be passed ok to the Jmol applet, but scripts or files stored on the server throw the error when you try to execute or load them. The odd part is that any script or load file commands inside the original definition of the applet works fine. Rolf pointed out a message board dealing with the issue in one of his previous messages I've copied below: This looks like a problem we are also facing with our JenaLib Jmol Viewer and Firefox. It started with Java version 1.6.0_03. Since Egon uses 1.6.0_05 I would expect that he will also have the same java.security.AccessControlException problem with the following URL: http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh I tried other Jmol sites and they worked fine with Java 1.6.0_03. But I couldn't figure out what makes the difference. The following thread in the Java forum http://forum.java.sun.com/thread.jspa?threadID=5230759; seems to refer to this problem. It is suggested there that the problem could be avoided by connecting back to the server before any liveconnect calls are made. But removing any callbacks didn't help with our viewer and I couldn't detect any other liveconnect calls before loading the PDB file and script from our server. As explanation for the difference between InternetExplorer and Firefox I found the suggestion that the more stringent default security policy of Firefox is responsible for it. Regards, Rolf Best regards, Eran On Mon, Apr 21, 2008 at 3:43 PM, Frieda Reichsman [EMAIL PROTECTED] wrote: CORRECTION - the pdb file does not load into the applet when all files are placed into the same directory. SO the breakage is even worse in this case. script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) Sent previously, incorrect: Placing all the files in the same directory (and changing all the file calls) still results in a security error when a script is called by a button: // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Apr 21, 2008, at 8:06 AM, Frieda Reichsman wrote: I should have mentioned more about the problem - the Jmol loads just fine on the page and responds to the mouse, but the problem occurs when a script is called from a radio button, checkbox, etc. (Buttons that do not call scripts work fine.) Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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.
Re: [Jmol-users] Improvement for select sequence range
Bob Hanson wrote: Better idea -- this is in Jmol 11.5.30 unless I hear complaints. PROPOSED JMOL DEFAULT CHANGE - set sequenceRangePhysical (default FALSE) NOTE: The default FALSE behavior for this setting is a change from previous Jmol versions because it was argued that the default behavior is unexpected, nonintuitive, and generally not useful. The issue is with PDB/mmCIF files that contain insertion codes or residue numbers that are out of order and the effect that has on selecting ranges of residues. Setting sequenceRangePhysical TRUE forces select 1-3 to select residues physically located in the file between and including residues 1 and 3 on any chain. In the case that a chain does not contain either residue 1 or residue 3, no atoms are returned for that chain. This is Jmol behavior through Jmol 11.5.29. Setting sequenceRangePhysical FALSE (proposed default behavior starting in Jmol 11.5.30) translates select 1-3 to select resno = 1 and resno = 3, ignoring physical location in the file, and not requiring that either residue 1 nor residue 3 exist on any chain. In the case where the residue numbers include insertion codes, the behavior when sequenceRangePhysical is set TRUE is the same as above. So select 1^A-3^B selects for all residues in the file between and including those two codes. Both must exist on any given chain for which atoms are returned. When sequenceRangePhysical is set FALSE, the behavior is to logically AND the resno range with the insertion code. The command select 1^A-3 is the same as select 1-3^A and returns the same as select resno =1 and resno =3 and *^A. The selection select 1^A-3^B does not make sense in this context and is simply interpreted as select 1-3^B. Maybe I havn't understood the insertion code part correctly, but for me it looks like there will be no range selected in the above example 1-3^A. Suppose the sequence would be 1,2,3,3A. Then the only residue selected would be 3A because it is the only one that matches all three conditions. Bob, you havn't commented yet on my last proposal (use = / = notation only if one of the border residues is missing). I still think this is the best solution that was mentioned yet. Of course the physical range selection is the only way to cope reliably with numbering irregularities like insertion codes. So any = / = based method will fail at least in some cases. And this is also true for the solution of Jmol 11.5.30 (if I understood it correctly). But it has 2 additional disadvantages: 1) some people have to change scripts/sites to revert to a correct selection 2) one has to decide principally which method should be used My proposal lacks both of these disadvantages and still reduces the selection failure rate. 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol error in Firefox/Windows only
Hi Frieda, I'm not sure what the IP address of that website is, does anyone know how to get an IP address from a domain name? Maybe: http://www.dnswatch.info/ - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Improvement for select sequence range
Rolf, first, these are just development versions (11.5.x), so we can
undo anything. I did see your suggestion, but I don't think it is really
workable. You can't have an algorithm that sometimes does one thing and
sometimes another in such an unpredictable fashion. (And, remember, this
is chain-specific.)
The logic here is that (a) we can have it the way we always did -- using
that flag, and (b) we can have it the way a user would expect as well.
That's the general solution to this. So the real question is whether we
want the default for sequenceRangePhysical to be TRUE or FALSE.
I'm hearing you say you want it TRUE, so that there are no changes to
current scripts. That's certainly the way I usually lean, but in this
case I thought Eric made a significant argument for changing the default
behavior to one that is far more logical to the user. (The user
generally doesn't care what the physical layout of the file is -- they
just want to know about residue numbers, and since the proposed change
is consistent with Rasmol behavior, one could argue that what we have
now is a bug, in fact.)
As for Insertion codes
Rolf Huehne wrote:
Maybe I havn't understood the insertion code part correctly, but for me
it looks like there will be no range selected in the above example
1-3^A. Suppose the sequence would be 1,2,3,3A. Then the only residue
selected would be 3A because it is the only one that matches all three
conditions.
Basically, I propose that what 1-3^A means is within range 1-3, all
inserted residues of type A. That's easy to explain. Certainly in some
cases there could be a string of these, so it could amount to a range.
So, for example, with 2by9, we get (old/your) way:
load =2by9
select 182-183
$ select 182-183 and *.N
$ print {selected}.label()
[CYS]182:X.N #1269
[ALA]183:X.N #1275
but 183-184:
$ select 183-184
$ print {selected}.label()
[ALA]183:X.N #1275
[GLY]183^A:X.N #1280
[TYR]184:X.N #1284
That seems strange and rather unexpected to me. It's because the
inserted item is after the original in the file. I would rather see (I
think):
$ select 182-183 and *.N
$ print {selected}.label()
[CYS]182:X.N #1269
[ALA]183:X.N #1275
[GLY]183^A:X.N #1280
$ select 183-184
$ print {selected}.label()
[ALA]183:X.N #1275
[GLY]183^A:X.N #1280
[TYR]184:X.N #1284
(Actually, I have some question as to whether the alternative locations
should be included. I think so.)
Eric, if you select 183 do you expect to select it and the inserted
code next to it? How about 183-184 -- what would you expect there?
183, 183^A, 184, 184^A
or
183, 183^A, 184
or
183, 184
?
Bob, you havn't commented yet on my last proposal (use = / =
notation only if one of the border residues is missing). I still think
this is the best solution that was mentioned yet. Of course the physical
range selection is the only way to cope reliably with numbering
irregularities like insertion codes. So any = / = based method will
fail at least in some cases.
Don't worry about my committing it or not -- let's arrive at a consensus
view if we can. I have to say I don't like the minimize the failure
rate idea. Let's get this fixed.
And this is also true for the solution of Jmol 11.5.30 (if I understood
it correctly). But it has 2 additional disadvantages:
1) some people have to change scripts/sites to revert to a correct selection
I'm not convinced that will be a problem. I just don't see how we can
have it behave one way and then another simply based on knowledge the
user doesn't have (whether groups are present or not in a specific chain).
2) one has to decide principally which method should be used
If it's a serious concern, all we need to do is have the default
behavior be
set sequenceRangePhysical TRUE
and let Eric be sure to set sequenceRangePhysical FALSE for his pages.
My proposal lacks both of these disadvantages and still reduces the
selection failure rate.
my goal is to eliminate the failure rate.
Bob
Regards,
Rolf
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Re: [Jmol-users] Improvement for select sequence range
OK, upon rereading this thread, especially Rolf's earliest post, and thinking more about what SELECT a-b should mean, and what insertions are, and all that, I do agree that the first solution I had in mind and put into 11.5.30 is not a good idea. What if we just went with Eric's initial idea, but not in the sense of resno =/=. I agree with Rolf that that will really mess up scripts, and I agree with Eric that what we have now is not intuitive. But I disagree with Rolf that the behavior should be different depending upon what the file is like. That to me seems like it would be totally opaque behavior to a user. It seems to me what we have now is just about right, except we should allow for missing end groups. Then no scripts will be affected, because surely no one has a script that selects 0 atoms (11.5.29 behavior) or expects that. Taking Eric's example (2rd0): (505,528,529,530) Do we all agree that select 520-530 should select 3 groups (as Rasmol)? Taking Rolf's example with 1ak4: (27,1027,2027,3027,4027,5027,28) Do we all agree that select 27-28 should select all of these? select 27-2027 should select just the first three? select 5027-28 should select the last two? And insertions (1jgq): (1031,1032,1032^A,1032^B,1033) Do we all agree that select 1031-1033 should select all? select 1031-1032^A should select just the first 3? select 1031-1032^C should select... what? perhaps the first 4? If so, I will just make Jmol do that, that's all. Bob -- 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 - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Improvement for select sequence range
nevermind. The proposed algorithm is: For each model... For each chain in the model... While not done... Given two sequence+insertion codes A and B... 1) look for (another) A. 2) if A is not found... 2a) find the code numerically closest to it and larger 2b) if no such code exists, return DONE 2c) set INEXACT 3) if B is missing (select 1-) 3a) select the last group of the chain 3b) set INEXACT else 3c) look for B at or after A in the file 3d) if B is not found... 4a) find the code numerically closest to it and smaller 4b) if no such code exists, return DONE 4c) set INEXACT 5) select all atoms physically between and including codes A and B 6) if INEXACT, return DONE, else return NOT DONE Bob Hanson wrote: In addition, I note that if there are two blocks of groups having the same group numbers (as in the old 1t0n or 1blu files) in the same chain (in my observation, protein and water), then the first matching range (the protein) is selected. Bob Bob Hanson wrote: I have committed this for testing as 11.5.31_dev. It turns out the original rewrite of the sequence range code was done by Miguel in Sept/2005 in response to a request by Rolf relating to a strange PDB file (1t0n) that had duplicate numbering and no chain designations. As far as I can see, that particular PDB file has been fixed, and the problem is a non-issue. So the way the (proposed) code works now, is this: Given two sequence+insertion codes A and B... For each chain... 1) look for A. 2) if A is not found, find the code numerically closest to it and larger 3) if no such code exists, return 0 atoms 4) if B is missing (select 1-) select the last group of the chain else look for B at or after A in the file 5) if B is not found, find the code numerically closest to it and smaller 6) if no such code exists, return 0 atoms 7) return all atoms physically between and including codes A and B How does that sound? Bob -- 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 - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
