Thu, 05/13/2010 - 23:03
| Time | Name | Message |
|---|---|---|
| 14:02 | infjamc | My main concern is that there is no way to manually upload a solution yet |
| 14:03 | CharlieFortsConscience | the lottery is, you dont know how walked the solns are... you assume walked to death |
| 14:03 | Aotearoa | yes, we need pure ones and walked ones seperate huh |
| 14:03 | Seth_Cooper | what do you mean about not being able to manually upload a solution? |
| 14:04 | Seth_Cooper | can you be more specific? |
| 14:04 | zoran | what we're seeing on our end is that the best candidate solution gets worked more, but there's little exploration with merging insights from multiple solution |
| 14:04 | infjamc | My understanding is that the top solutions are uploaded automatically periodically |
| 14:04 | Aotearoa | i agree zoran |
| 14:04 | infjamc | Allowing for manual uploads could speed up the process |
| 14:05 | infjamc | Zoran: my experience with the latest all hands puzzle is that the top solutions are sufficiently different that direct copying isn't easy |
| 14:05 | Seth_Cooper | manual uploads that are made publicly available to everyone, you mean? |
| 14:05 | infjamc | Seth: Yes |
| 14:05 | infjamc | Zoran: (continued from last message) The ability to do side-by-side, residue-by-residue comparisons between two solutions would be nice |
| 14:06 | zoran | i think we can do that. do you think it would help to avoid all people working exactly on the same (currently best) soln |
| 14:06 | Aotearoa | YES |
| 14:06 | infjamc | I'm thinking about something more advanced than the current method for using one solution to improve another (loading B as a guide to improve A) |
| 14:07 | infjamc | The ability to work on two structures simultaneously might be nice |
| 14:07 | infjamc | ...with a table of side-by-side comparison of the scores of each residue |
| 14:07 | zoran | this is good. btw you can use one structure as a guide for the other. do you use that? |
| 14:08 | infjamc | That's what I currently do, but sometimes I feel that it's not enough when two solutions have similar scores at the margin |
| 14:08 | infjamc | (but very different backbone structures) |
| 14:08 | zoran | so to recap: |
| 14:09 | infjamc | If the side-by-side comparison is too much to implement, I can see one simplification that would work |
| 14:09 | zoran | ability to share saved solutions with all |
| 14:09 | Aotearoa | YES |
| 14:09 | infjamc | Namely, displaying the difference of score at this residue relative to the guide when we use tab to see residue scores |
| 14:09 | zoran | side by side comparison with per-residue score difference |
| 14:10 | infjamc | Even better would be the ability to have the guide show up in full-atom mode, too |
| 14:10 | infjamc | It matters when you're working with hydrogen bonds |
| 14:11 | zoran | ok, i'm sure you have a list of things that would help casp in general. now is the time to make your voice heard |
| 14:12 | infjamc | I'll let other people speak first-- it seems that I'm being the vocal minority here |
| 14:12 | mat747 | dev - will you be adding this chat log to the website |
| 14:13 | zoran | yes, including the summary of the ideas |
| 14:13 | aap2 | minor request: split show sidchains clashes or exposed in two |
| 14:13 | mat747 | thanks - back 50 mins |
| 14:13 | HillObserver | uh, this might sound obvious but it's hard to focus on improving any given puzzle when there are a lot of open puzzles |
| 14:13 | Aotearoa | me too hillobserv |
| 14:14 | Judecca | does anybody else think it would be useful to take say, chunks from different alignments and use them together. |
| 14:14 | spvincent | I imagine everyone has their wish list:unfortunately its different for each player |
| 14:14 | Judecca | lets say alignment #1 is missing the first 20 or so residues but #2 has the first 20. would it work to mix and match |
| 14:14 | infjamc | And while we're on the topic of alignments... |
| 14:14 | Seth_Cooper | Judecca, we have implemented just that |
| 14:14 | zoran | with casp we don't know what we're getting every day. but we realize that having 3 puzzles for the same target is not good. we will not do this from now on |
| 14:15 | CharlieFortsConscience | can you give an idea of the range of puzzles for this casp? my first, but is it generally alignmment as we've seen in this first week? |
| 14:15 | Judecca | Seth_Cooper: sweet :) |
| 14:15 | Seth_Cooper | allowing you to only thread a part from each alignment |
| 14:15 | infjamc | Dev: (I've mentioned this in an Email to Firas earlier) How's the progress on cutpoints? |
| 14:16 | infjamc | The ability to fold a protein as several smaller pieces and then sew them back together is sorely needed when there are large gaps in the alignment |
| 14:16 | Aotearoa | I would like to see the threading aminos have some kind of numbering system for easier location on 3d protein, showing also orange phobic groups and scores, Blue amino groups and scores and even if possible make the threading possible from the actual screen as well as the threading alignment box. |
| 14:16 | zoran | except for the very few ab initio (from scratch) targets all will be alignment. |
| 14:17 | Aotearoa | *then shuffling them back and forth would way more constructive instead of shooting first and what ever we hit calling it the target. |
| 14:17 | Seth_Cooper | infjamc: cutpoints is something we've looked into from time to time but has never made it all the way to a full feature |
| 14:17 | infjamc | Okay |
| 14:18 | Aotearoa | thanks Seth. yeah sometimes its easier to see the protien when all of it is present |
| 14:18 | infjamc | Again, I really hate to ask so much just because I have the "insider information," but since it's a recurring problem I just want to make the alignment tool easier for everyone to use |
| 14:18 | infjamc | ...partly because a common complaint I've heard is that the clashing residues often caused by forcing a bad template can be difficult to fix, especially for less experienced players |
| 14:18 | Seth_Cooper | Aotearoa: you'd like the alignment panel to be numbered, and also show hydrophobiciy as well? |
| 14:18 | zoran | we won't be able to do cutpoints for casp. seth has 2 prototypes but they never made it up to a feature. |
| 14:19 | aap2 | could it be possible have an option to leave aminos strechted while/after threading? |
| 14:19 | rwillett | The alignment already does show hydrophobicity. |
| 14:19 | Seth_Cooper | Aotearoa: as in, color the letters by hydrophobicity rather than the current color scheme? |
| 14:19 | Aotearoa | that would just make it easier for us to see before we thread, where they are in relation to the protein shape, as ive seen proline in a helix which is not normal |
| 14:20 | rwillett | The coloring in the alignment is better how it is. |
| 14:20 | Aotearoa | *no the colours they are are fine, but to add a small extra feature to show just how many are present, for making sheets easier |
| 14:20 | Aotearoa | *diving sheets and helix's* |
| 14:20 | rwillett | Ah. |
| 14:20 | zoran | spvincent: we'd still like to hear everyones wishlist and understand it better. we'll have to prioritize what can be done later |
| 14:20 | rwillett | LIke to click between the two. |
| 14:21 | infjamc | zoran: regarding prioritization-- there's an issue that seems to be present since the alignment tool was introduced |
| 14:21 | infjamc | Often, at least one residue will have a misplaced backbone atom after applying an alignment |
| 14:21 | zoran | aap2: they take the coordinate structure from template |
| 14:21 | Seth_Cooper | infjamc: yes |
| 14:21 | Aotearoa | *dividing sheets |
| 14:21 | spvincent | Written documentattion is something I'd very much like to see,particularly for the alignment tool |
| 14:21 | Seth_Cooper | infjamc: I think we have found why the oxygens were out of place |
| 14:22 | infjamc | Okay |
| 14:22 | Aotearoa | great news Seth ! |
| 14:22 | infjamc | Is there a way to fix it via the rebuild tool, though? |
| 14:22 | infjamc | It really hurts the protein score if that problem means losing a hydrogen bond |
| 14:22 | zoran | Aotearoa: can you provide more details with each bullet. we're not quite sure what you mean |
| 14:22 | Seth_Cooper | no I don't think the rebuild tool will take care of that |
| 14:22 | Seth_Cooper | we have a fix for threading that will prevent it |
| 14:22 | spvincent | And there are a whole bunch of things related to scripting but its more convenient to prepare a wish list for these rather than try and enumerate them here. |
| 14:22 | infjamc | Seth: thanks |
| 14:23 | aap2 | zoran: yes, but now strechted segments are automticaly corrected, i would to fix it myself because it often does things i do not want |
| 14:23 | zoran | spvincent: (and others) send the list to me, just make sure it is clear what you want and how that would help you |
| 14:24 | spvincent | Will do: thanks |
| 14:24 | infjamc | Actually, no to think of it... if aligning part of the template is allowed, there is one step further that might help |
| 14:24 | zoran | aap2: this is the same as cutpoints request then. it will be hard to get that done for this casp |
| 14:25 | infjamc | ...allowing the user to set a custom location to force each residue into |
| 14:25 | infjamc | A self-applied template, essentially |
| 14:25 | infjamc | This could be useful for large gaps |
| 14:25 | infjamc | Again, that's for the long term |
| 14:26 | zoran | we can create a better documentation for the alignment |
| 14:26 | Aotearoa | While we are shuffling the aminos back and forth to match up to templete, its hard for me to know what groups of aminos are being moved, if i would like to seperate them, its hard to know where they will end up on the template. so by just including numbers would mean for a 200 reside protein, i could divide out 20 per sheet, and counting them is hard on the screen. if once grouped they totaled how many aminos were present in the |
| 14:26 | Aotearoa | grouping, *perhaps plus a score* then i would quickly see where to move them to make the protein better set out with the right aminos in their favorite places. perhaps just an orange and blue addition. |
| 14:28 | Aotearoa | do you know what i mean by a score of the total grouped aminos? |
| 14:28 | zoran | Aotearoa: i think the selective threading that we should have out soon might help with this |
| 14:28 | Seth_Cooper | a score of just the ones' youve selected? |
| 14:28 | CharlieFortsConscience | Occasionally, puzzles 'feel' different with wig and shake, some feel 'sticky' and lethargic. Does each puz have wig shk 'thresholds? Rebuilding prolines is currently soul-destroying. Rebuild was jiggered a few updates ago, it's not the power it used to be |
| 14:29 | Aotearoa | yes, between the breaks in the threading box (black area) and compaired to the template |
| 14:30 | Seth_Cooper | no, wiggle and shake use the same parameters for the competitions puzzles |
| 14:30 | Renton | IMAGE: |
| 14:31 | zoran | CharlieFortsConscience: some if this may be due to the initial state of the puzzles. sometimes they are more optimal than other times. i don't think we changed the functionality |
| 14:32 | Seth_Cooper | Renton, what should we look at in that image? |
| 14:32 | Aotearoa | right now i can look at the thread from one of the templates, do a protein_hide_score and see what protein alignment brings back the better score |
| 14:32 | infjamc | zoran: a problem that I've been encountering a lot recently is similar to what CFC has mentioned |
| 14:33 | infjamc | Often, I have to reload a puzzle just to get wiggle to work normally again |
| 14:33 | Seth_Cooper | are there any puzzles in particular? |
| 14:33 | infjamc | the alternative would be getting a slower wiggle that doesn't go to completion |
| 14:33 | infjamc | Seth: EVERY puzzle! |
| 14:33 | CharlieFortsConscience | yes |
| 14:33 | infjamc | I'm not sure if it's because I'm running Foldit on single core |
| 14:34 | zoran | and when you reload the game the wiggle works differently? |
| 14:34 | CharlieFortsConscience | yes |
| 14:34 | infjamc | (running it with both cores would overheat my cpu) |
| 14:34 | HillObserver | inf - I run on a single core and don't seem to have this problem |
| 14:34 | infjamc | zoran: I don't have to reload the game-- I just have to reload the puzzle by going back to the main menu |
| 14:34 | Renton | *i just wanted to show off my puzzle and teams work* |
| 14:35 | zoran | sounds like a clear bug. if you can have a saved solution that you can replicate it with, pls send |
| 14:35 | infjamc | The problem, though, is that it's easily solved by reloading the puzzle |
| 14:35 | infjamc | That's the coping mechanism I have been working with since March |
| 14:35 | infjamc | (or possibly earlier) |
| 14:36 | infjamc | Basically, it's not a major bug that would break the game-- it's just a bit annoying |
| 14:36 | Seth_Cooper | that is odd, i'm not sure what might cause it |
| 14:36 | infjamc | My guess is that it might have something to do with the wiggling procedure |
| 14:36 | zoran | can it be repeatedly generated, or is it random? |
| 14:36 | Seth_Cooper | if there are some steps to reproduce it you can send them to me |
| 14:36 | infjamc | During those slower wiggles, I often get residues with much worse backbone scores |
| 14:36 | Aotearoa | now, my biggest question is: are those templates giving us the right protein shapes possible ? do we know they are Good to work with ? |
| 14:37 | infjamc | So, my guess is that the problem is that the wiggle procedure changes once a threshold is met |
| 14:37 | Aotearoa | *Threading Templates* |
| 14:37 | infjamc | And when that happens, only the local (closer to the worst clash) residues are considered rather than the entire protein |
| 14:37 | Seth_Cooper | since we don't know the answer, we can't be sure of how good the templates are |
| 14:37 | zoran | Aotearoa: yes these the best matches. sometimes there are more, so we give you a b and c puzzles with different set of templates |
| 14:37 | Seth_Cooper | but, we are trying to use the best methods for finding them |
| 14:38 | aap2 | i would like to keep tab pressed without the information screen flickering on and off |
| 14:38 | Aotearoa | I am using them cause I believe it it the future, but on the otherhand, I also want to fold like I used too without them, the random shapes they bring up, do not always look like they would if we folded them ourselves. |
| 14:39 | zoran | aap2: this will have a big effect on the casp outcome :) |
| 14:39 | Aotearoa | *it is the Future* sorry my spelling is terrible today. |
| 14:39 | spvincent | And please turn off the pulsing graphics, or provide an option to do so. |
| 14:39 | Seth_Cooper | the templates are real protein shapes |
| 14:39 | HillObserver | @spvincent: yes, turn off pulsing graphics |
| 14:39 | aap2 | zoran: yes! :P |
| 14:39 | Seth_Cooper | so they are realistic for what a protein would fold into |
| 14:39 | Aotearoa | are the highest scoring templates so far, far from the original thread from the alignment |
| 14:40 | zoran | we can turn off the pulsing (or provide an option) |
| 14:40 | Aotearoa | or are those highest scoring proteins, one's we've made big changes too ? |
| 14:41 | spvincent | Thanks! |
| 14:41 | Seth_Cooper | yes, changes from the initial threading have to be made to get closer to the native |
| 14:41 | Seth_Cooper | that's very important, to improve on the template |
| 14:41 | Aotearoa | Thanks Seth ! |
| 14:42 | aap2 | i dont know if this is fixed yet but i had some issues with threading upon an already threaded protien, it caused unfixable clashes/the segments got very odd |
| 14:42 | Seth_Cooper | otherwise, we could just guess that the template is the answer |
| 14:42 | Aotearoa | *moon walks back to protein 1b* |
| 14:42 | HillObserver | I've had the same double threading problem aap's had |
| 14:42 | Seth_Cooper | This may be related to the problem infjamc brought up |
| 14:43 | Seth_Cooper | which should be fixed in a update soon |
| 14:43 | Seth_Cooper | do you often change the alignments, or just keep the initial alignment? |
| 14:44 | SUCHARD | keep the initial |
| 14:44 | HillObserver | I discovered the problem by accident...usually I don't rethread over an existing thread |
| 14:44 | infjamc | I tend to change them to get a better match, even if that means leaving more gaps |
| 14:44 | aap2 | change it a little bit |
| 14:44 | aap2 | i go for less gaps |
| 14:44 | Aotearoa | just one more quick question, when threading - if i leave two black spaces between my groupings of aminos, what does the alignment treat that as? the spaces on top line. |
| 14:45 | Madde | modify it, thread and forget |
| 14:46 | Seth_Cooper | if you leave spaces in the top line, that is a gap in the alignment that will need to be fixed when threading |
| 14:46 | HillObserver | dev: I've noticed that some rebuilds take a long time but if I band the area to rebuild then the rebuild works very quickly and comes up with very strange solutions (that it wouldn't do if not banded) |
| 14:46 | Seth_Cooper | when it threads, it will have to move those segments a bit to close the gap |
| 14:46 | Seth_Cooper | HillObserver: that's correct |
| 14:46 | Aotearoa | ahhhh ok |
| 14:47 | HillObserver | is this a quirk? |
| 14:47 | Aotearoa | here I am thinking they related to where they are positioned in the proteins shape on the screen. duh. |
| 14:47 | CharlieFortsConscience | Coming back to the notion of no change to functionality of wiggle, why are local and global so different in their 'aggression'? it never used to be that way. Agan, seems skewed towards difficult hydrophobes like pro and met, but it used to be better. Tied to the rebuild amendments in the last few updates? |
| 14:48 | Seth_Cooper | HillObserver: http://fold.it/portal/node/987558 |
| 14:49 | Seth_Cooper | CFC: the two wiggles are different, because to prevent the whole protein from moving, local has to 'cut' the protein chain and reconnect it |
| 14:49 | Seth_Cooper | CFC: global wiggle doesn't need to do that |
| 14:50 | HillObserver | thanks Seth, but it's not the speed of the rebuilds, it's that it rebuilds into really weird shapes and will sometimes embed backbone into other parts of the backbone |
| 14:51 | HillObserver | it doesn't do this if I just run rebuild |
| 14:51 | Seth_Cooper | HillObserver: well, when bands are present it mostly ignores things like the clashing score, in favor of the bands |
| 14:51 | HillObserver | ah, I see, ok |
| 14:51 | Seth_Cooper | HillObserver: perhaps it shoudl take that into account more |
| 14:51 | Aotearoa | any more casp questions ? |
| 14:52 | Seth_Cooper | is it difficult to move the alignments when there are more than two lines? |
| 14:52 | Seth_Cooper | ie several template sequences ? |
| 14:53 | HillObserver | seth, yes. Sometimes I'll band sheets on a rebuilding script to prevent the protein from exploding and it defeats the purpose if it ignores clashing |
| 14:53 | Seth_Cooper | HillObserver: I'll look into that |
| 14:53 | HillObserver | thank you |
| 14:53 | Seth_Cooper | as far as multiple templates go, |
| 14:54 | mimi | going off alignment for a moment, something I would like to see would be an option to do a reset of the absolute best score. So that when you restart a puzzle you don't have to be constrained by a previous high score. It can affect the use of certain scripts |
| 14:54 | infjamc | mimi: you can do this manually |
| 14:54 | Renton | YAY I agree Mimi |
| 14:54 | Seth_Cooper | one reason we have multiple puzzles (like 1a 1b 1c) is that we want to give lots of templates but as we add more to a single puzzle the alignment gets harder and harder to use |
| 14:54 | infjamc | Go to open/share solutions |
| 14:55 | mat747 | mimi - me too |
| 14:55 | infjamc | Check show auto and quick saves |
| 14:55 | infjamc | Then delete your absolute best solution and restart the program |
| 14:55 | infjamc | Problem: too much hassle? |
| 14:55 | mimi | but you may want to keep that solution |
| 14:55 | aap2 | i might still want to use it |
| 14:55 | Renton | looks back at infjam |
| 14:55 | spvincent | Can you keep your best but call it something else |
| 14:56 | infjamc | In that case, load the solution, save a copy, then delete it |
| 14:56 | spvincent | mimim beat me too it |
| 14:56 | Renton | pin a tail on it. |
| 14:56 | HillObserver | seth: I would be in favor of more alignments than (a), (b) and (c) puzzles...don't know about everyone else |
| 14:56 | Seth_Cooper | perhaps "restore absolute best" from a script should really just call "restore recent best"? |
| 14:56 | infjamc | But again, that's another extra step! |
| 14:56 | CharlieFortsConscience | OH.... yes. Development of LUA - is it possible to get reset_best to include quick_save_slots? It'll give SO much more room to manouevre |
| 14:56 | infjamc | And while we're at it: what about the ability to manually set dihedral angles through LUA? |
| 14:57 | spvincent | But then you can't use recent best in the script should you ish to do so. |
| 14:57 | aap2 | also an actualt local wiggle in lua |
| 14:57 | infjamc | Again, that's just me wanting to run Foldit like PyRosetta, so if that's too much I'll shut up now |
| 14:57 | TheGUmmer | and freeze segments in LUA |
| 14:57 | spvincent | right : Quicksave or an equivalent is defintely on the wish list |
| 14:58 | CharlieFortsConscience | It took so long to get LUA in and working, but we need a 2nd level evolution to fulfil our goal of automating us out of the equation... |
| 14:59 | HillObserver | one last bit from me: in the selection interface, the behavior option is not adjustable when a script is running (it hides behind the script "cancel/show output" box. Can you make this box transparent so we can click behind it? |
| 15:00 | Madde | you can press the B key |
| 15:00 | TheGUmmer | you can move it can't you |
| 15:00 | HillObserver | thanks Madde. |
| 15:00 | Madde | I found out accidentally |
| 15:00 | CharlieFortsConscience | ...and and and.... We used to be able to click set recent best mid-recipe or script, as things were happening |
| 15:01 | aap2 | more importance sliders, like an sidechain subscore importance slider |
| 15:01 | infjamc | Oh, and before I forget... |
| 15:01 | Seth_Cooper | okay, so for LUA: quicksave, local wiggle, and freeze? |
| 15:01 | infjamc | It would be nice if there were a quick way to force hydrogen bonds |
| 15:01 | infjamc | Currently, I have to do this 30+ times after applying an alignment: |
| 15:01 | infjamc | Middle click on hydrogen, drag to oxygen |
| 15:02 | infjamc | Right click on band, choose change band length |
| 15:02 | infjamc | Decrease to zero, then click on okay |
| 15:02 | infjamc | Repeat for every hydrogen band until the entire beta sheet is secured |
| 15:02 | infjamc | It would be nice if there's a two-click method for doing this |
| 15:02 | Seth_Cooper | i see, like a 'hydrogen bond band' |
| 15:02 | infjamc | Namely, click atom or residue A and then atom or residue B |
| 15:03 | infjamc | The result is a zero-lengthed band at normal strengthen between them |
| 15:03 | Seth_Cooper | or even just two sheets, and it could find the appropriate backbone atoms |
| 15:03 | infjamc | Again, it's only 2 clicks vs 5, but it really adds up |
| 15:03 | Christoph | automatic lining up of sheets would be very cool, if something like that is possible |
| 15:04 | Aotearoa | A sheet maker too please |
| 15:04 | Madde | http://fold.it/portal/node/987454 |
| 15:04 | mat747 | seth - we need change band strength in Lua |
| 15:04 | CharlieFortsConscience | One more thing.... cys-cys bonding as routine? given their importance in vivo, could it be reflected in Foldo? |
| 15:04 | infjamc | Aot: same for helices? |
| 15:05 | Aotearoa | for the newbies yes. |
| 15:05 | Seth_Cooper | tweak has methods for making sheets and helices as well |
| 15:05 | TheGUmmer | tweak in |L|UA would be nice |
| 15:05 | infjamc | The problem is that it works by messing up the loops next to them |
| 15:05 | Aotearoa | its just hard to align them using the good old U bend |
| 15:05 | infjamc | And the loops have to be long enoguh |
| 15:06 | infjamc | *enough |
| 15:06 | Seth_Cooper | i see |
| 15:06 | Seth_Cooper | okay, I wanted to ask about the multiple templates, because beta_helix and I were talking about how to make it more usable to have many templates in one puzzle |
| 15:06 | Renton | Im watching you CFC ! |
| 15:06 | CharlieFortsConscience | :) |
| 15:07 | HillObserver | I'm all for more multiple templates |
| 15:07 | infjamc | Renton: what happened? Oh, 299? |
| 15:07 | Renton | come on give us ONE puzzle ! |
| 15:07 | aap2 | 2 puzzles (a and b) with more templates sounds good |
| 15:07 | Seth_Cooper | basically what we were thinking was instead of aligning them all at once, basically align 1 template at a time |
| 15:07 | Christoph | maybe only show one line in the aligments window and have the ability to exchange that line with the different aligments |
| 15:07 | Aotearoa | I agree aap2 |
| 15:08 | Seth_Cooper | and the rest go into a "reserve" that you can swap in |
| 15:08 | Aotearoa | nice idea !!! |
| 15:08 | infjamc | It's like forming an all-star team in sports :-) |
| 15:08 | Seth_Cooper | something like this: |
| 15:08 | HillObserver | the problem with multiple puzzles is that the really good players will eventually use the best alignment from one of the two puzzles and just replicate it in the other puzzle |
| 15:09 | TheGUmmer | like pop up with a list of alignments to choose from |
| 15:09 | infjamc | Seth: I figured out the URL on my own, but it's cut off |
| 15:09 | Renton | omg 12264 finally. *thank you "Aotearoa's Romance"* |
| 15:09 | CharlieFortsConscience | Well... I've learned that alignment is basically a head-start, the end-score derives from your 'processing' I dont waste time threading a better score unless there are obvious mismatches |
| 15:09 | infjamc | Everyone else: the file extension is png |
| 15:09 | Christoph | seth: yup, looks good |
| 15:09 | Seth_Cooper | basically the blue arrows would cycle through templates |
| 15:10 | Seth_Cooper | the green would move them up into what is now the current alignment window |
| 15:10 | Seth_Cooper | and the red move them out |
| 15:10 | Aotearoa | looks good to me Seth ! |
| 15:11 | aap2 | if it remembers the player made changes it would be good |
| 15:12 | Seth_Cooper | yes, the idea is if you take a template out then put it back in it will remember where it was |
| 15:12 | Seth_Cooper | by where it was, i mean the alignment |
| 15:12 | Aotearoa | YAY ! |
| 15:12 | HillObserver | btw: we were sent the fold it table to document our puzzle moves. Is it not possible for the program to just simply create a puzzle log file that documents each script run? |
| 15:12 | CharlieFortsConscience | ...yes - extend the remember cache, it's very short atm |
| 15:13 | Renton | I have to go, thanks Zoran and Seth ! look forward to seeing you again soon. |
| 15:13 | Aotearoa | See you guys ! |
| 15:13 | HillObserver | yes, must run too. Thank you folks for listening. |
| 15:13 | Seth_Cooper | HillObserver: you should ask beta_helix about that |
| 15:14 | HillObserver | @seth: ok, will do |
| 15:14 | Seth_Cooper | okay, I think that's good feedback for today! thanks for chatting |
| 15:14 | TheGUmmer | thanks you for listening |
| 15:14 | Seth_Cooper | and thanks for playing! |
| 15:15 | CharlieFortsConscience | Cheers Seth |
| 15:15 | Madde | will the next chat start an hour earlier, too? |
| 15:15 | infjamc | Madde: technically, PST on the website should read PDT |
| 15:15 | Aotearoa | my goat makes three stomps |
| 15:15 | infjamc | The UTC times are correct, though |
| 15:16 | Madde | I was looking at the GMT times |
| 15:16 | infjamc | Please correct me if I'm wrong, but I thought it started on time? |
| 15:16 | Seth_Cooper | yes, we mean for them to start at 2pm today |
| 15:16 | mat747 | no |
| 15:16 | Seth_Cooper | and 11 am tomorrow |
| 15:17 | Seth_Cooper | it looks like the UTC was off by an hour |
| 15:17 | CharlieFortsConscience | Madde, where are you? |
| 15:17 | Madde | Germany |
| 15:17 | mimi | that is so Seth |
| 15:17 | infjamc | Madde: summer time? |
| 15:17 | Seth_Cooper | I'll fix that in the blog post |
| 15:17 | Madde | yes |
| 15:17 | Madde | it's GMT+2 here |
| 15:18 | Madde | and GMT+1 in winter |
| 15:18 | infjamc | So it started at midnight for you? |
| 15:18 | infjamc | (the chat) |
| 15:18 | Madde | it should have |
| 15:18 | mat747 | GMT +9.5 here |
| 15:19 | CharlieFortsConscience | .5??? |
| 15:19 | Madde | but it did at 11pm |
| 15:19 | infjamc | Hmmm |
| 15:19 | infjamc | That's strange... |
| 15:19 | Seth_Cooper | Does the blog post look correct now? |
| 15:20 | infjamc | The time offset was correct for my time zone (U.S. Eastern Daylight time = -4) |
| 15:20 | CharlieFortsConscience | *you're an extra 30 mins in the future mat?* |
| 15:20 | TheGUmmer | like newfoundland |
| 15:20 | mat747 | http://alturl.com/t7oe |
| 15:21 | infjamc | Ah, I see what's going on |
| 15:21 | infjamc | Pacific daylight time = -7 |
| 15:21 | infjamc | Not -8!!! |
| 15:22 | Seth_Cooper | You can always check the clock on the top of the Foldit page |
| 15:22 | Madde | Seth: yes, it looks correct now |
| 15:22 | Seth_Cooper | well I should get started implementing this feedback |
| 15:22 | mat747 | cfc - ? |
| 15:23 | Seth_Cooper | talk to everyone tomorrow! |
| 15:23 | aap2 | cya |
| 15:23 | Madde | bye |
| 15:23 | BletchleyPark | whoa did I miss the chat ? |
| 15:24 | infjamc | The UTC time on the website was off by one hour... it's fixed now |
| 15:24 | aap2 | yep |
| 15:24 | BletchleyPark | yeah great |
| 15:25 | BletchleyPark | Is the quake bug being worked on ? |
| 15:25 | Renton | you missed out on seth and zorans autographs on an exclusive fold.it card with their photos on it |
| 15:25 | BletchleyPark | I could care less |
| 15:25 | Renton | collectors items ! |
| 15:25 | BletchleyPark | is the quake bug being worked oon |
| 15:25 | aap2 | i dont remember it being mentioned in the chat |
| 15:26 | Madde | it seems you are the only one with this bug |
| 15:26 | Renton | not unless you feedback it |
| 15:26 | infjamc | That depends whether the Irani clerics agree (sorry, bad joke) |
| 15:26 | BletchleyPark | no, I seem to be the only one mentioning it |
| 15:26 | mat747 | infjamc - forward or back ? |
| 15:26 | infjamc | mat747: my guess is that someone got PST and PDT confused |
| 15:27 | infjamc | The former is UTC-8, while the latter (which is what the US west coast is running on right now) is -7 |
| 15:27 | Madde | I'm using Quake a lot and I never had this problem |
| 15:27 | Renton | omg you guys are geeks |
| 15:27 | infjamc | So 2 PM on the west coast is UTC 2100 |
| 15:27 | infjamc | Which is when it actually started |
| 15:27 | zoran | ok, i'm back. are there more questions/suggestions? |
| 15:28 | Renton | bletchypark go man gooo |
| 15:28 | aap2 | lol |
| 15:28 | zoran | the time being off was actually my fault |
| 15:28 | BletchleyPark | off global, ciao |
| 15:28 | Renton | ZORAN is here BP |
| 15:28 | --- findow is away (Auto away) | |
| 15:29 | zoran | it looks like the quake has been discussed already. is it deterministically reproducable? |
| 15:30 | BletchleyPark | Hi zoran, yes it is |
| 15:30 | infjamc | zoran: I think I might have mentioned this last year |
| 15:30 | BletchleyPark | on two different machines |
| 15:30 | BletchleyPark | qith quake with a lot of bands |
| 15:30 | BletchleyPark | with |
| 15:30 | infjamc | If you try to band every residue when the protein is more than ~80 residues long, the program crashes |
| 15:30 | BletchleyPark | this problem did not exist before |
| 15:30 | infjamc | So the upper limit is around 3000 or 4000 bands? |
| 15:31 | BletchleyPark | I don't think it uses even that many |
| 15:31 | zoran | we can do that easly, but is that what BP wants just a bound on the # of bands? |
| 15:31 | BletchleyPark | the problem was not in the debug version |
| 15:31 | BletchleyPark | I tried to revert back to the one on the server but I got a 404 |
| 15:31 | BletchleyPark | NO ! :) |
| 15:32 | Renton | only one hour left cfc |
| 15:32 | BletchleyPark | no bound on those bands, I just do not want the program to crash on me |
| 15:32 | BletchleyPark | please |
| 15:32 | zoran | seth said he looked into it but he couldn't reproduce it on 2 machines he tried |
| 15:33 | BletchleyPark | well, I can positively reproduce it every time on two machines I tried it on |
| 15:33 | zoran | windows? |
| 15:33 | BletchleyPark | yes, XP64 bit and W2K 32 bit |
| 15:34 | zoran | any way you can try it on the more recent os? |
| 15:35 | zoran | we don't have these oses |
| 15:35 | BletchleyPark | it worked before on both OS'es so it is not an OS issue |
| 15:35 | BletchleyPark | and it also worked fine on XP32 |
| 15:35 | zoran | it now does not work on xp32? |
| 15:36 | BletchleyPark | that machine is currently not available |
| 15:36 | Madde | I'm using Quake on XP SP3 32bit and Win7 64bit w/o problems |
| 15:36 | BletchleyPark | I am referring to a variant of quake with many bands |
| 15:36 | BletchleyPark | original quake does not use many bands |
| 15:37 | Madde | oh, ok. I'm using the original |
| 15:37 | zoran | is there a way others can try to do exactly what you're doing and see if they can replicate the crash? |
| 15:37 | zoran | do we have that exact script. we thought you were talking about the quake script |
| 15:37 | BletchleyPark | I could share the recipe with seth ? |
| 15:37 | zoran | plese do |
| 15:37 | BletchleyPark | it is a variant on quake |
| 15:38 | zoran | as well as a saved puzzle on which it verifyably crashes |
| 15:38 | BletchleyPark | is there a simple way to share it with seth only ? |
| 15:39 | zoran | message it to him on the web site |
| 15:39 | Madde | I could try our group's mega quake |
| 15:39 | BletchleyPark | it is a recipe, how can I message a recipe ? |
| 15:39 | zoran | it seems something specific to that script. |
| 15:40 | BletchleyPark | Please try it Madde, see what happens |
| 15:40 | BletchleyPark | I can make screenshots and save them as jpgs ? |
| 15:41 | zoran | message seth, and he'll give you instructions. |
| 15:41 | BletchleyPark | ok, thanks |
| 15:42 | zoran | anything else we should know regarding improving casp outcomes? |
| 15:43 | BletchleyPark | not that I can think of now, thanks |
| 15:44 | vakobo | variant of overnight script i use works fine on XP32 and crashes on W2K and Linux 64bit (ubuntu 10.4). On W2K with error message and w/o any message on linux |
| 15:44 | BletchleyPark | interesting |
| 15:44 | BletchleyPark | which error message ? |
| 15:45 | zoran | vakobo: pls message seth on fold.it site with the script. and the description of failure |
| 15:45 | vakobo | ok |
| 15:46 | vakobo | simple message or feedback? |
| 15:46 | zoran | message |
| 15:47 | mat747 | zoran - i would like Steven Pletsch suggestion for Lua |
| 15:47 | mat747 | http://fold.it/portal/node/987105 |
| 15:51 | zoran | all of it? |
| 15:51 | mat747 | if you like |
| 15:52 | mat747 | "sidechain to the specified position " would help via lua |
| 15:53 | CharlieFortsConscience | ...but we'll settle for quicksave slot options when running scripts... |
| 15:53 | zoran | you mean to one of the discrete things it can snap to? |
| 15:54 | zoran | we'll have quicksave slots |
| 15:54 | CharlieFortsConscience | more than 3? |
| 15:55 | zoran | how many? |
| 15:55 | Renton | as many as amino acids on protein? |
| 15:55 | mat747 | zoran - yep |
| 15:56 | CharlieFortsConscience | aim for 10. I'd settle for 5. |
| 15:57 | zoran | ok we'll have 5 quicksaves in lua |
| 15:58 | CharlieFortsConscience | :) 6 would be better... |
| 15:59 | zoran | we can have 20 and only the first 5 have key shortcuts. way too many could be a memory consumption issue |
| 16:00 | Madde | who needs shortcuts in LUA? |
| 16:00 | smith92clone | define shortcut |
| 16:00 | zoran | are people sharing their recipes or is it the case that most people work with private ones? |
| 16:00 | zoran | hotkey |
| 16:01 | smith92clone | I run recipes with high vote count, read it, then start making changes. |
| 16:01 | CharlieFortsConscience | If you implement 5, scripting will reach another level. We desperately need a way to circumvent the gulf between abs_best and recent |
| 16:01 | SUCHARD | I work with others |
| 16:01 | aap2 | share with team |
| 16:01 | Renton | 1b 12265 omg wooohooo |
| 16:02 | vakobo | it wold be nice if script execution terminates automaticaly on puzzle expiration |
| 16:02 | Madde | I share some with public, some with team and use slightly modified ones private |
| 16:02 | vakobo | *would |
| 16:02 | --- makedon is away (Auto away) | |
| 16:02 | Renton | 30 stinking minutes left before I can summersault through the house ending in a splits. |
| 16:03 | keypad5 | <-- 30 minutes to find 60 points... hmmm |
| 16:03 | Renton | come and fold with us then silly. hahaha |
| 16:04 | Renton | hard to find the last points though |
| 16:04 | zoran | ok, must leave now. thank you all. we'll be here tomorrow as well. |
| 16:04 | mat747 | zoran - a replay to sidechain to the specified position - we can move a selected segment sidechain to different positions in the newinterface now with Shift + arrow keys , it would good if we could do that via LUA |
| 16:05 | BletchleyPark | night Zoran |
| 16:05 | BletchleyPark | BP is off global |
| 16:05 | vakobo | bye, Zoran |
| 16:05 | Renton | hi Vakobo ! |
| 16:06 | vakobo | hi |
| 16:08 | Renton | great team work CG |
| 16:08 | Renton | oh gone already |