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MUD transcript:  19-01-00

Protein Geometry & Protein Synthesis

Course room(s): PPS 

15:56:46  ClareS connects.

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15:56:56  CharafB says "wow, it's going to be a long day for you!"
15:57:11  ClareS says "Hi"
15:57:32  ClareS says "good to see you all, and it's not even (quite) 16:00 yet ;)"
15:57:39  RobertO says "yes especially since I didnt get to sleep until 3am"
15:57:42  CharafB says "hello!"
15:58:02  RobertO says "Hi Clare"
15:58:12  ClareS says "we'll be starting properly in a few minutes -- to give a few more people a chance to be on time"
15:58:54  RobertO rubs sand out of his eyes and os glad people cant see him
15:59:19  ClareS says (to charafb) "thanks for your questions, it's great to have something to start the discussion with"
16:00:18  SpyrosS connects.
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16:00:52  CharafB says (to clar) "I find it easier..."
16:01:00  SarahL says "hello everyone, my computer is't behaving itself this afternoon, glad to you Robert"
16:01:34  SpyrosS says "hello everyone"
16:01:54  RobertO says (to sarahl) "good to see you again to...had to miss the last time and it seems ages"
16:02:50  ClareS says (to spyros) "hi"
16:03:18  CharafB says (to Spy) "Hi"
16:03:37  ClareS says (to roberto) "even the last MUD was held last century ;)"
16:03:55  RobertO says (to clares) "Sorry I couldnt make it last time and thanks for getting the MUD transcripts, hope you had a good holiday, mine was hectic"
16:04:12  ClareS says "seriously, I hope you all had a merry Christmas, a happy New Year and a bug-free Millennium"
16:04:43  ClareS says (to roberto) "sorry I took so long to put the transcripts up"
16:05:13  ClareS will just wait a couple more minutes..
16:05:27  SarahL says "i have to leave at 4.45 to collect my children"
16:05:41  RobertO says (to clares) "dont worry I was very busy with the y2k since I am responsible for over 50 computers for our group"
16:06:14  ClareS says (to sarah) "that sounds like a good reason to start now... shall we start with Charaf's questions on torsion angles?"
16:06:41  SarahL says "thanks"
16:06:42  CharafB says (to clar) "yes, tell us!"
16:06:45  RobertO says (to Sarahl) "thats right you have kids....how old are they and boys or girls...I have a daughter myself from a previous marriage"
16:07:14  ClareS says "you have probably all seen Charaf's message to the list concerning the definition of torsion angles?"
16:07:36  RobertO says "yes good place to start"
16:07:46  SpyrosS says "yes"
16:09:02  ClareS says "I have just re-read the course material and I don't think it is as clear as it could be"
16:10:15  ClareS says "chi1 is the torsion angle of the beta-carbon, chi2 the angle of the gamma-atom and so on"
16:10:17  CharafB says "the most helpfull tool was the kinemage"
16:10:32  ClareS says "is that clear or shall I explain a bit more?"
16:10:56  CharafB says "ok to me."
16:11:02  ClareS agrees with charafb, the kinemages are very useful abd clear
16:11:16  SarahL says "kinemage was very good for showing this visually"
16:12:20  ClareS says "best to look at it as... chi1 is the angle of twist about the CA-CB bond"
16:12:49  ClareS says "chi2 is the angle of twist about the CB-CG bond (or CB-OG or whatever, of course)"
16:14:05  AttilaR connects.
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16:14:21  ClareS says "the convention of calling clockwise torsion angles positive only applies if the protein is viewed with the N terminal or CA of the side chain closest to you"
16:14:37  ClareS says (to attilar) "welcome!"
16:15:09  ClareS says "if you look along the chain in the other direction the reverse convention applies"
16:15:12  AttilaR says "Hello, I am very happy to be here again"
16:15:23  RobertO says "I am not sure what you mean the chain closest to you"
16:15:35  ClareS says (to attilar) "Happy New Year (rather late)"
16:16:03  RobertO says "do you mean looking from the n terminus is one convention and toward it is another?"
16:16:51  ClareS says "you should imagine yourself looking at a full scale model of the protein"
16:18:18  ClareS says "By convention torsion angles are described imagining you are looking "down" the N-CA bond, for instance..."
16:18:32  ClareS says "...rather than with the molecule the other way up"
16:19:16  RobertO says "ok that was what I needed to be positioned in my visualization, thanks"
16:20:51  ClareS says "so a positive value of psi seems clockwise if the molecule is viewed "down" the chain in the direction N1-C-CO-N2"
16:21:11  ClareS says "if the convention had happened to be the other way round, positive would be anticlockwise"
16:21:27  ClareS says "is that OK now?"
16:22:27  ClareS says "in a few years I expect we'll have these meetings in a VR environment and be able to manipulate model molecules ;)"
16:22:42  RobertO says "yes I think so, so we would never have -90 but would see that as a +270...meaning the angles are always positive no matter how large"
16:22:52  CharafB says "yes, if I got it well, for chi1 the direction is N-CA-CB-CG"
16:23:21  ClareS says (to charafb) "yes, that's right"
16:23:54  ClareS says "and that's why chi1 and chi2 seem wrong in the side chain diagrams..."
16:24:14  RobertO says "yes a vr with ability to see would help here, I am very visual"
16:24:24  ClareS says "these figures have been drawn "upside down" with the CG atom closest to the eye"
16:24:40  ClareS says "so the angles are the opposite way round from the conventional way"
16:24:59  ClareS says "I don't know why Jon who wrote this material drew the figure like that"
16:25:31  ClareS says (to roberto) "-90 is of course exactly the same as +270"
16:26:31  ClareS says "that nicely answers Charaf's third question (I hope ;)"
16:26:34  RobertO says (to clares) "yes, that is what I meant..the convention is always positive even though the angle would be larger"
16:26:39  CharafB says (to clare) "I suppose we have to stick to the + and - if we don't want to get mixed up with the Ramachandran plot"
16:27:23  CharafB says (to clar) "yes ;)"
16:27:29  ClareS says "the Ramachandran plot would not work with a 0 to 360 convention as 180 would be in the middle rather than at the edges"
16:27:34  RobertO says "good point, I must still be sleeping over here"
16:27:52  ClareS says (to roberto) "what time is it with you?"
16:29:09  RobertO says (to clares) "it is 8:30am but got to bed at 3am, trying to do some refinements and couldnt sleep...oh I see we DO need + and -...now I am confused"
16:29:48  ClareS says (to roberto) "what is confusing you.. we'll try to help"
16:30:29  RobertO says (to clares) "what is the largest angle we can have...the comment on ramachandran plot just confused me"
16:30:53  ClareS says "the largest angle is the same as the smallest... using the convention I have been describing"
16:31:24  ClareS says "i.e. a torsion angle of 180 deg is exactly the same (physically) as one of -180 deg"
16:31:24  RobertO says (to clares) "do we ever have negative numbers them when we measure or do they stay positive"
16:32:07  ClareS says "the usual convention is -180 to 180 so we have negative numbers about half the time"
16:32:47  ClareS says "but that's just convention, we could just as easily refer to the geometric position we call -90 as +270"
16:32:50  RobertO says (to clares) "example if I had an angle that was greater than +180, say 270 would I call it -90 or +270 by convention"
16:33:08  ClareS says "... we just don't (often ;)"
16:33:27  ClareS says "if you wanted to be conventional you'd call it -90"
16:33:40  KevinO connects.
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16:34:09  RobertO says (to clares) "oh so the +- is ok but I guess we must use it for the plots"
16:34:11  ClareS says "of course, you might not want to... but it would be inconvenient as some people wouldn't understand you and the Ramachandran plot wouldn't look right"
16:34:33  ClareS says (to kevino) "welcome, we're discussing torsion angles & the Ramachandran plot (from section 3)"
16:34:50  RobertO says (to clares) "sorry to be so dense today"
16:35:12  KevinO says (to clares) "hi"
16:35:27  ClareS says "don't worry, I'm never properly awake until 09:30GMT"
16:35:49  ClareS says (to roberto) "does that now make sense?"
16:36:05  RobertO laughs in understanding
16:36:56  RobertO says (to clares) "yes now it makes sense, it has been some time since I read that module and obviously need to go back and refresh."
16:37:32  ClareS says "we should really have had a MUD session on that earlier, but Christmas & the Millennium got in the way ;)"
16:38:08  SarahL says "I had trouble with Procheck I didnt manage to Un tar it so didn't actually look at this"
16:38:27  RobertO says "yes I do feel a little disconnected by the break"
16:39:14  ClareS says "the UK almost shut down for 2 weeks... not the Bug, parties"
16:39:26  ClareS says "and now we have a flu almost-epidemic"
16:39:56  ClareS says (to sarah) "back to Procheck.. you would only have been able to untar the file if you were using a Unix machine"
16:40:11  RobertO says (to clares) "bummer..we all had y2k paranoia here and our parties were a bust, not like london and paris"
16:41:14  ClareS says "the file is both tarred and compressed (.tar.Z extension) and you have to run 2 unix programs on it"
16:41:25  ClareS says "uncompress first, then tar"
16:41:35  SarahL says "oh well that figures then! I don't know what I did wrong but I didn't succeed"
16:41:58  RobertO says (to clares) "I assume it is an x86 binary or does it need compiling"
16:42:05  ClareS says "you can try out Procheck without installing it locally using the Protein Validation Suite at the EBI"
16:42:25  KevinO says (to clares) "doesn't winzip handle tar and .Z files?"
16:43:17  ClareS says "have any of you got that to work?"
16:43:21  SarahL I have to go now
16:43:37  ClareS can never remember exactly which formats winzip can & can't handle
16:43:49  RobertO says "bye sarah"
16:44:17  CharafB says (to sar) "bye!"
16:44:42  SpyrosS says (to SarahL) "Bye!"
16:44:47  AttilaR says (to SarahL) "Bye!"
16:45:20  SpyrosS says (to ClareS) "What is the assessment that will start on the 24th?"
16:45:22  CharafB says (to clar) "I think I had it working ok, if i remember well..."
16:45:28  ClareS says (to sarahl) "bye -- look out for the transcript soon"
16:45:48  ClareS has just checked the doc, winzip will work on these file types
16:45:55  RobertO says (to clares) "I think you missed my question on if it was an x86 binary that is tarred or is it source code to be compiled"
16:45:59  SarahL says "bye every one see you soon"
16:46:06  ClareS says "(at least if you use an up to date version of winzip)"
16:46:47  ClareS says "this is the source code, there is no certainty that it will compile on any given platform"
16:46:54  RobertO says (to clares) "unfortunately most unix boxes are not intel processors"
16:47:02  ClareS says "except the most common types of unix box"
16:47:16  ClareS says (to roberto) "apart from some running Linux"
16:48:08  RobertO says "yes I am the king of unix here but we mostly have sgi and sun...I am the one trying to push the linux systems"
16:48:27  SarahL disconnects.
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16:49:07  RobertO says "and unfortunately I usually get the task of compiling everything for the linux boxes since most things dont cpme as binaries yet"
16:49:36  ClareS sympathises with Robert
16:49:51  ClareS says (to spyross) "now, about that assessment..."
16:50:27  ClareS says "it's fairly low-key -- just to give you an idea of how you are doing"
16:50:48  ClareS says "there are two components, multiple choice quizzes and short answer questions"
16:51:36  ClareS says "we will provide links to multiple choice quizzes on web forms, you will get instant feedback from these"
16:52:01  ClareS says "we don't even get to find out which of you access these, let alone how you do"
16:52:30  ClareS says "the short answer questions will also be released on the web"
16:53:12  ClareS says "before then you will get an email message assigning you to a tutor group"
16:53:13  RobertO says "do we have to complete one in one sitting or can we do part then do the rest later...this is how my day usually is, broken up and interrupted"
16:53:56  ClareS says "we would like you to send your (short) answers to your tutor by email"
16:54:13  ClareS says "during the 2 weeks of the self-assessment period"
16:54:36  ClareS says (to roberto) "do you mean the multi-choice or the short answer questions"
16:54:54  RobertO says "tutor may have a different menaing here than there, can you explain what tutors do in the english system"
16:56:09  ClareS says "tutors will mark your short answer questions (3 sets, each covering 4 course sections)"
16:56:36  ClareS says "you are also encouraged to email any serious scientific problems you're having with the course material to your tutor"
16:57:15  ClareS says "but of course you can also email the list -- anyone, including another student, may be able to answer your question"
16:57:31  ClareS says "and of course tutors also get the messages on the list"
16:58:45  ClareS says "is that clear?"
17:00:00  SpyrosS says (to ClareS) "yes"
17:00:44  ClareS says "good... are there any more questions or issues for discussion?"
17:01:34  RobertO says (to yes) "with the exception of if we can interrupt the multiple choice questions and start in the middle or do we have to go all the way through in one sitting"
17:02:15  ClareS says "you will be able to interrupt the multi-choice questions as long as you keep the web form open"
17:02:30  RobertO says "oops forgot the quote mark, did you get that last question Clare"
17:02:41  ClareS says "there are only about a dozen questions in each quiz, tho', so the problem may well not apply"
17:03:06  RobertO says "ok so there is no resume at a specific place"
17:03:24  CharafB says "I found section 4 like an oasis after desert crossing of section 3 which was completely new to me"
17:03:29  RobertO says "yes I agree since they are so short"
17:03:51  AttilaR says "Shall we be able to use the Lecture Material during the the next two weeks?"
17:04:28  ClareS says (to attilar) "yes, of course! the material will be freely available to you when you attempt the questions"
17:06:37  RobertO says (to clares) "I will probably be moving right before the final assesment since my wife will be taking an assoc professor position at either Dartmouth or University of michigan. how much time do I need to allow to set up the testing"
17:08:08  AttilaR says "I have questions about the gamma turns and the disulfide bonds. How common is the gamma turn in proteins, because I never heard about them before, just about beta/turns. My next question is, which is the more common type of disulfide bonds?"
17:09:07  ClareS says (to roberto) "as much time as possible, but it can be done quickly if necessary"
17:09:37  ClareS says (to roberto) "it would help if you could contact your new employers before you move"
17:10:03  RobertO says (to clares) "I will try to let you know as soon as she decides then and try to make arrangements before we move"
17:10:30  ClareS says (to attilar) "I'm not sure what you mean - I don't know of different types of disulphide bonds"
17:11:40  ClareS says "as for gamma turns, they are a type of reverse turn which involves 3 residues"
17:11:55  ClareS says "they are rarer than the beta turns which involve 4 residues"
17:12:09  SpyrosS says "bye everyone"
17:12:37  ClareS says "but very confusingly many people use the term "beta turn" to refer to all types of reverse turn"
17:12:47  KevinO disconnects.
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17:13:05  ClareS says (to spyross) "bye!"
17:13:25  AttilaR says "Yes, I understand, so the same disulfide bond can move between two states, which were described in Lecture 3?"
17:13:34  CharafB says (to spy) "bye"
17:13:56  AttilaR says (to SpyrosS) "Bye!"
17:14:02  KevinO connects.
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17:14:20  RobertO says (to clares) "I have to go soon I have a 1 1/2 hour commute and need to get to work if I am to make it today at all..will we be much longer"
17:14:26  ClareS says (to kevino) "are you having problems with your connection?"
17:15:09  ClareS says (to roberto) "not much longer... you're free to go whenever you like... and there's always to-morrow's session which may be at a more convenient time of day for you?"
17:15:10  KevinO says (to clares) "sorry, i am trying to use a different mud reader"
17:15:14  SpyrosS disconnects.
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17:15:39  ClareS says (to kevino) "are you referring to left- and right-handed disulphides?"
17:16:21  KevinO says (to clares) "?? wasn't me that referred to them!"
17:16:26  ClareS says (to attilar) "very sorry, I meant to have addressed that question to you!"
17:16:35  AttilaR says "Yes, but I am Attila, not Kevin."
17:16:40  ClareS blushes and apologises to Kevin as well
17:17:09  ClareS sometimes has problems maintaining more than one conversation at once in the MUD
17:17:21  KevinO says (to clares) "no need to apologize"
17:17:31  ClareS says (to attila) "*was* that what you meant??"
17:18:48  AttilaR says "I don't understand the question."
17:19:16  ClareS says "when you refer to two types of disulphide bond, what are the two types you mean?"
17:19:49  KevinO disconnects.
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17:20:09  RobertO grumble to himself about his long commute and waves goodbye to all
17:20:29  RobertO says "bye all wish I could stay longer"
17:21:15  ClareS says "disulphides *can* be categorised into right- and left-handed spirals depending on their geometry..."
17:21:27  CharafB says (to rob) "Bye Robert, I trust you'll make it, ;)"
17:21:43  ClareS says "... but in practice this distinction isn't often made in describing protein structures"
17:21:53  ClareS waves goodbye to Robert
17:22:52  ClareS would like to end the meeting soon
17:23:13  ClareS looks round to see if there are any last minute questions
17:23:23  AttilaR says "Yes, thank You, now I understand."
17:24:41  AttilaR says "Good bye everybody, I have to go too. Thank You for helping me."
17:24:53  ClareS says "thank you all for making it such a lively discussion"
17:24:55  KevinO connects.
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17:25:22  CharafB says (to clar) "Thanks a lot for your help, it's been a great session!"
17:25:49  ClareS says (to charafb) "I'm glad you found it helpful"
17:26:11  CharafB waves goodbye
17:26:12  KevinO says "sorry to keep dropping out like that! I think I'm fine now :-)"
17:26:23  KevinO says "sorry to keep dropping out like that! I think I'm fine now :-)"
17:27:09  KevinO says "bye, see you next time!"
17:27:25  CharafB disconnects.
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17:27:33  AttilaR says "Bye!"
17:28:57  KevinO disconnects.