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MUD transcript:  09-12-99

Revision of Sections 1-4

Course room(s): PPS 

20:58:34  ClareS says "Hi"
20:58:52  SarahL says (to Attilla) "hi ,glad to see you where are you tonight"
20:59:00  AttilaR says "Good evening"
20:59:02  ClareS says "sorry I'm a minute or so late... but it'd still be worth waiting a little longer to see if any others arrive"
20:59:25  MichaelS connects.

RamananS     PPS          HTTP    52m 39s   1m 33s
SarahL       PPS          HTTP    13m 43s      33s
AttilaR      PPS          HTTP     1m 51s      25s
ClareS       PPS          HTTP        58s      23s
MichaelS     PPS          HTTP         0s       0s
20:59:52  AttilaR says (to SarahL) "I am now in Hungary."
20:59:55  RamananS says (to good) "evening"
21:00:31  SarahL says (to c) "hi how are you"
21:00:44  PeterP connects.
RamananS     PPS          HTTP    53m 58s      49s
SarahL       PPS          HTTP     15m 2s      13s
AttilaR      PPS          HTTP     3m 10s      52s
ClareS       PPS          HTTP     2m 17s   1m 42s
MichaelS     PPS          HTTP     1m 19s      14s
PeterP       PPS          HTTP         0s       0s
21:01:25  MichaelS says " Evening all!"
21:01:26  ClareS says "Hi everyone"
21:01:36  ClareS says "welcome..."
21:01:59  PeterP says "hello - can I get this to work, or am I stuck in the mud ?"
21:02:15  ClareS says "This is an extra session which I included especially as I know that some people are having trouble making both our "usual" times..."
21:02:22  ClareS says (to PeterP) "you're doing fine"
21:02:53  ClareS says "so it's a chance for you to discuss any aspect of the first 4 sections of course material that you are having difficulty with"
21:03:03  ClareS says "(or that you're just interested in)"
21:03:47  SarahL says (to c) "I don't have to rush off this time alll my children are now in bed"
21:04:22  PeterP says (to ClareS) "thanks , I think I will get the hang of it"
21:04:47  ClareS says (to SarahL) "excellent!"
21:04:59  ClareS says "anyone like to start off with a question?"
21:05:14  PeterP says (to ClareS) "thanks, I think I will get the hang of it"
21:06:16  ClareS says "have you had a chance to look at the self-assessment exercises and quizzes yet?"
21:06:52  MichaelS says " I'm not sure if I missed something really basic, but I have been a bit confused about the angles within amino acids."
21:07:29  PeterP says "me too !"
21:07:29  AttilaR says (to ClareS) "I have problems with chi angles now. Chi 1 angle is clear for me, but it was mentioned in the lecture, that side chains, that diverse at Cbeta, for example valin or isoleucine do not like trans conformation, because either of the two metil  groups would be in gauche minus conformation. It is not clear for me, because, I think, it could be in gauche plus, I think."
21:08:13  ClareS says "OK... that's a good place to start.  What exactly is confusing you?"
21:08:35  PeterP says "does the recommended couse text, Brandon + Tooze, give good back-up ?"
21:08:49  ClareS says "(there was quite a lot of discussion of this in one of last week's MUD sessions... maybe the course material isn't very clear here?"
21:08:55  AttilaR says "I have problems with chi 2 angles mainly, but something is not clear with chi 1 , too."
21:09:03  ClareS goes to find her own copy to check...
21:10:34  ClareS says "Branden & Tooze talks a lot about the main chain torsion angles but hardly mentions the others at all"
21:12:58  ClareS says "is it the definition of the angles that is confusing you?"
21:13:24  AttilaR says "What about the chi2 and three angles, because chi 1 was clearly described, but I do not know, how to place the chi 2, because in that case I cannot use the CO and N group, just the groups and hidrogens on Cbeta."
21:14:11  ClareS says "it might be worth while your looking at one of the older references in the refs list: Schulz & Schirmer from 1979"
21:14:27  ClareS says "that goes into protein geometry in great detail"
21:14:43  ClareS says "you might have some problems finding a copy tho'"
21:15:23  PeterP says "ok - I will have a dig around !"
21:15:33  ClareS says "one useful rule to remember is that you never use hydrogens when defining these side chain torsion angles"
21:15:39  SarahL says (to c) " After the  Mud session last week i went back to check and l do think it is a bit confussing although I found the discussion on the Mud very helpful"
21:16:40  ClareS says "sorry you've found it confusing -- we'll need to make a note of this and revise it for next year"
21:17:11  ClareS says "have those of you who weren't at last week's session been able to look at the transcripts?"
21:17:59  PeterP says "I haven't seem them yet but will make sure to have a look"
21:18:51  AttilaR says "So for chi2 the best way is to view the Cgamma -Cbeta bond in a way, in which C beta is just behind Cgamma, and then to look at the angle between the substituent on C beta and on Cgamma?"
21:19:00  SarahL says (to c) "chi 1 is the torsion angle of the beta c and chi2 is the angle of the gamma atom is that right"
21:19:21  ClareS says "the session on 19 Jan was the one when we were discussing these torsion angles"
21:19:47  AttilaR says (to ClareS) "Now I understand"
21:20:10  ClareS says (to AttilaR) "yes, but to get the sign right you need to be looking down the chain from the alpha-carbon"
21:20:31  ClareS says "with the atom nearer to the main chain nearer to your eye"
21:20:44  ClareS says "(metaphorically speaking, of course ;)"
21:21:41  AttilaR says (to ClareS) "Yes, it is clear now."
21:21:41  ClareS says (to SarahL) "it depends on what you mean by "the torsion angle of the beta carbon" etc... torsion angles are defined as twist angles about bonds"
21:22:01  AttilaR says (to ClareS) "Yes, it is clear now."
21:22:31  ClareS says "chi1 is the twist angle about the CA-CB bond"
21:22:33  AttilaR says (to ClareS) "Yes, it is clear now."
21:22:49  ClareS says "is that any clearer?"
21:23:06  AttilaR says "Yes it is clear now."
21:23:52  RamananS says "Very Clear"
21:24:22  ClareS says "thanks!"
21:24:27  ClareS smiles
21:25:03  MichaelS says " I think I have a better idea, too. My question now is, once you are looking down the CA-CB, or CB-CC etc, which direction (clockwise/anticlockwise) do you go to work out if the angle is positive or negative?"
21:25:06  ClareS says "are there any other burning questions?"
21:25:16  SarahL says (to c) "would you not say "torsion angle" then? what would you say"
21:26:06  ClareS says (to SarahL) "to answer your quick question first, torsion angle is the technical term, but you might find it easier to think of them as "twist angles""
21:27:44  ClareS says "the question of the sign of angles is answered well on the page defining main chain torsion angles"
21:28:01  ClareS says "that's http://pps9900.cryst.bbk.ac.uk/ppscore/section3/jonc/peptide3.html"
21:28:23  SarahL says (to c) "thanks , that sounds better I think"
21:29:08  ClareS says "if you can move the atom closest to you onto the other atom by means of a clockwise rotation, the angle is positive"
21:29:52  ClareS says "it might help for you to get hold of some of those old-fashioned plastic models and try twisting atoms round each other"
21:30:17  ClareS says "(tho' it goes a bit against the grain to say as much, this being an on-line course"
21:30:51  MichaelS says "Thanks. I'll check it out."
21:33:19  ClareS looks round expectantly to see if anyone has a new question to raise
21:34:11  SarahL says (to c) " you can move some chi angles in the kinemage from Brandon and tooze"
21:34:43  ClareS says "the kinemages can be very useful in allowing you to manipulate as well as just visualising structures"
21:34:58  ClareS says "have you all got Mage installed, and are you finding it useful?"
21:35:17  AttilaR says "I have a rather theoretical Question. Just suppose, that all the proteins around us would be of D-amino acids. What would the Ramachandran-plot like in this case?"
21:35:49  ClareS says "that is an interesting question, and I'll have to think about it"
21:36:03  ClareS says "I think it would be a rotation of the actual one"
21:36:25  ClareS says "with the top right quadrant becoming the bottom left, and vice versa"
21:36:47  ClareS says "I couldn't swear to it, but that certainly sounds logical"
21:36:52  RamananS says "mage is wonderful except it is installed at work and I am organising it at home and hope to have more fun with it"
21:36:57  AttilaR says "Taht is what I think, but I am not extremely sure of this."
21:37:50  ClareS has just managed to crash Mage on her home machine
21:38:18  AttilaR says "Were there any measurements of this?"
21:38:46  ClareS says (to AttilaR) "measurements of what? (sorry)"
21:39:24  AttilaR says "I mean about fi and pszi angles with D- amino acids?"
21:41:19  ClareS says (to AttilaR) "I thought that was what you meant... I don't *think* it's been done in practice, tho' I may be wrong"
21:41:38  ClareS says "it's the kind of thing that it's quite easy to simulate, tho'"
21:42:14  ClareS means, in theory
21:44:26  AttilaR says "Yes, but because of L/amino acids, scientists may not be interested too much in this question, I mean it has got very little practical relevance."
21:45:12  ClareS says "there *are" D-amino acids that occur naturally (but not in proteins)"
21:45:46  AttilaR says "Yes, for example in bacterial peptides."
21:46:28  ClareS says "just as, there are very, very many types of amino acid besides the common 20, that occur naturally but not in proteins"
21:47:37  SarahL says (to c) "what about peptoglycan in bacterial cell walls"
21:49:33  ClareS is going to have to look that up, too
21:51:40  ClareS says (to SarahL) "you're right (I thought you were ;) -- there are, of course, many D-alanines in bacterial cell wall peptidoglycan"
21:52:36  ClareS says "I'd like to finish this meeting not long after 10pm.. it may be time to start thinking if there's anything else you'd like to discuss"
21:54:17  ClareS looks round expectantly
21:54:18  AttilaR says "When are we going to get teh names of our tutors, to whom we shall send the solutions for the tests?"
21:54:54  RamananS says "is it possible to know what languages/protocols will be covered in the section web authoring,to come"
21:55:25  RamananS says "I have got mail from my tutor"
21:55:43  ClareS says (to AttilaR) "I'm very sorry!! I am your tutor (there are 3 groups; the other tutors are Beatrice Gorinsky and Jim Pitts)"
21:56:23  ClareS says "I should have emailed you before now"
21:56:28  AttilaR says (to ClareS) "Thank You, I am very happy of it."
21:56:48  AttilaR says "Thank You, I am very happy of it."
21:57:08  ClareS says "The tutor groups are up on the Web: http://pps9900.cryst.bbk.ac.uk/notice/tutor-group.html"
21:57:13  SarahL says "the assesment period has been very useful so far and i am taking much more in the second time through my notes Im glad I'm not the only one that found section 3 more challenging"
21:58:01  ClareS says "I noticed that a lot of people were finding section 3 challenging -- that's why I decided to focus on protein geometry in the quiz"
21:58:30  AttilaR says "Yes, Protein Geometry is very interesting, but very difficult, too."
21:58:37  ClareS says (to RamananS) "we cover all the basic stuff -- nothing too complex, we can't teach people to write Java in 2 weeks"
21:59:00  ClareS says "we *describe* all the commonly used techniques, tho'"
21:59:58  ClareS says "and we teach stuff that is particularly important for molecular biology Web sites -- not just Rasmol/Chime, but referring directly to entries in sequence databases or Medline"
22:00:29  ClareS says "I hope that it won't be too difficult for beginners and that the others will find something new"
22:01:52  RamananS says "Thank you"
22:05:31  AttilaR says "I have to leave now, I am very sleepy, and have to get up early in the morning. Good bye for Everyone, and have a nice weekend!"
22:05:54  RamananS says "Good night everyone."
22:06:35  MichaelS says "Good night"
22:06:42  PeterP says "goodnight"
22:07:51  ClareS says "I was just about to say.. if there are no other questions, then goodnight!"
22:08:05  ClareS says "and good luck with the self-assessment exercises"
22:08:43  AttilaR says "Thank You and good luck for everyone!"
22:09:06  MichaelS disconnects.