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MUD transcript:  06-07-00

Protein Quaternary Structure

Course room(s): PPS 

14:48:53  ClareS connects.

KevinO       PPS          HTTP    45m 30s   2m 21s
VijayK       PPS          HTTP    32m 37s   1m 44s
ClareS       PPS          HTTP         0s       0s
14:48:57  ClareS says "Hi"
14:49:35  ClareS says "good to see that you both have patience... but you are still early. We will be starting at 16:00BST (or soon after)"
14:50:11  KevinO says "hi clare, yes I'll wait!"
14:55:46  ClareS is going to get a RL cup of coffee: back soon
14:57:52  SarahL connects.
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VijayK       PPS          HTTP    41m 36s  10m 43s
ClareS       PPS          HTTP     8m 59s    2m 6s
SarahL       PPS          HTTP         0s       0s
14:59:18  SarahL says "hi everyone"
14:59:44  KevinO says "hi, sarah"
15:00:21  KevinO says "clare just popped out for a minute"
15:01:14  SarahL says "ok, has any one chosen there project title yet"
15:01:32  VijayK says "Hello sarah"
15:01:32  KevinO says "not I"
15:02:15  VijayK says "I have two options. But haven't decided"
15:02:34  ClareS is back
15:03:00  ClareS says "I think we can start now... others can join later"
15:03:17  SarahL says " I thought that I would do Beta barrels"
15:03:37  ClareS says "Would you like to start by discussing section 11, or would you like to talk about choosing projects?"
15:04:40  ClareS looks round expectantly
15:04:42  VijayK says "Clare please can you tell more about Unit cell in terms of crystallographic entity?"
15:04:45  KevinO says "I have no preference"
15:04:53  SarahL says "how many pages or words should our projects be"
15:05:20  ClareS says (to KevinO) "for which to start with... or for your project?? ;)"
15:05:38  SpyrosS connects.
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15:05:52  ClareS says (to SarahL) "the best guidance I can give you is to look through some of the projects on the web from previous years"
15:06:05  KevinO says (to ClareS) "to discuss first"
15:06:34  ClareS says "we don't set word limits as with the web (if you want to) you can produce an excellent project with (relatively) little text"
15:06:36  SpyrosS says "Hi everyone"
15:06:59  KevinO says "hi Spyros"
15:07:08  ClareS says (to SpyrosS) "Hi"
15:07:44  ClareS says "all the projects we mount on the web reached at least the standard required to pass (50%)"
15:08:32  ClareS says (to VijayK) "I haven't forgotten your question... we will come to that after any questions on the projects"
15:08:40  SarahL says "ok thanks what about reproducing diagrams from published papers do we have to get the authors permission,"
15:11:10  ClareS says "I think it should be OK -- it's more like reproducing them in an exam than like doing so in a book"
15:11:40  ClareS says "it is very important that everything is referenced and acknowledged"
15:12:26  ClareS says "so if you do reproduce a figure from a paper you should give the full ref. of the paper at least"
15:13:00  SarahL says " thats the important point then to make sure that diagrams are attributed to the author "
15:13:05  ClareS says "you will also be marked down for reproducing large chunks of material from the same source"
15:13:15  ClareS says (to SarahL) "Yes"
15:13:30  ClareS says "is that clear?"
15:14:38  SarahL says "yes"
15:15:13  SpyrosS says "Could we have some starting references for the projects? I have asked my tutor for...."
15:16:05  SpyrosS says "a list, but she told me that no-one has asked something like that before"
15:16:10  ClareS says "We don't normally give references. Literature searching is one of the important skills that we are testing here"
15:16:54  ClareS says "It will depend on your project of course, but review journals like Current Opinion in Structural Biology or (if relevant) the Trends series may be good places to start"
15:17:40  ClareS says "Are any of you members of BioMedNet? It's free for academics..."
15:18:39  SarahL says "pub med seems like a good place to start"
15:18:48  ClareS says "They are offering a database of full text of articles in many review journals"
15:19:14  ClareS says "yes, PubMed is an excellent place to start"
15:19:47  ClareS says "the great thing about BioMedNet tho' is that members get *full text access* to many of the journals."
15:20:05  ClareS says "You may not have to go to the library..."
15:23:17  SarahL says "is it ok to use a web editor such as front page or front page express to create the web page"
15:23:36  ClareS says "PubMed is a public domain search engine for MedLine, there are many others & they have different advantages"
15:23:46  ClareS says (to SarahL) "Yes, that's fine!"
15:24:16  ClareS says "we should be able to tell if you've just written your project in Word and exported as HTML"
15:25:44  SarahL says " i thought so , but your not expecting it just to be written in notepad with HTML are you."
15:26:02  ClareS says "are there any more questions on the projects?"
15:26:13  VijayK says "What is cache file"
15:26:51  SpyrosS says "Something else. The exams are on the 22/09. We have to write them also in  HTML?"
15:28:32  ClareS says (to SpyrosS) "No. The exam is a "real life" exam. It is taken in the normal way at a centre close to where you live/work"
15:28:57  ClareS says "it will be just like an ordinary exam except that many of you will be the only candidate in your centre"
15:29:17  ClareS says "you write longhand.  In the old fashioned way ;)"
15:29:47  ClareS says "Your supervisor or boss will be asked to act as invigelator or to appoint one"
15:30:10  VijayK says "Regarding preps. Can we get some model question papers from previous exams"
15:30:21  ClareS says "we will contact you some time later this summer & ask which of you are intending to take the exam"
15:30:42  ClareS says "we will then start the process of setting up the exam centres"
15:31:16  ClareS says "I will try to remember either to mount a model paper on the web or to email one to the list"
15:31:47  ClareS says "I'll not do this until later in the summer... there is still Section 12 to go"
15:32:03  ClareS says "is this clear?"
15:32:23  SpyrosS says "Yes it is"
15:33:44  ClareS says "are there any more questions on the exams or projects?"
15:34:15  ClareS says "in the mean time... would whichever of you asked a question on unit cells right at the start, repeat it please?"
15:34:22  VijayK says "My question what is a cache file?"
15:34:27  ClareS says "I've forgotten it..."
15:34:34  ClareS blushes
15:35:05  ClareS says (to VijayK) "yes, I am coming to that now"
15:35:29  VijayK says "I would like to know more about unit cell - in terms of crystalographic entity"
15:35:56  ClareS says "when you display a web page the data on that page is stored in a cache"
15:36:29  ClareS says "that cache is either in memory or on disk and they are not kept indefinitely"
15:36:48  VijayK says "Taht is after saving it or temporairly mounted while viewing"
15:36:50  ClareS says "if you ask later on for a page that is stored in cache it is the cached copy that is loaded"
15:37:07  ClareS says "no you don't need to save the file, caching happens automatically"
15:37:29  VijayK says "I think I unerstand now"
15:37:35  ClareS says "sometimes even if your server is down or you are offline you can still see a few of your frequently used pages"
15:37:50  ClareS says "that is because you are actually seeing the cached copy"
15:38:41  ClareS says "if you hit the Reload button you will get a new copy, not the cached one"
15:39:08  SarahL says "its like internet explorer 5 when you have visited a site once the computer saves this information and then you are able to access this information  offline saving your phone bill"
15:39:21  ClareS says "you will all come to use Reload a lot when you are writing your projects ;)"
15:40:13  ClareS says (to VijayK) "could you please post the URL of the page of course material with the definition of unit cell?"
15:40:42  VijayK says "is there a possibillty that a cache file gets full? I mean like the disk space etc."
15:40:57  ClareS says (to SarahL) "exactly... but (of course) the cached page is not updated. There is no point in caching Yahoo! news"
15:41:14  ClareS says "(or the PDB top page with the number of structures on ;)"
15:41:38  ClareS says (to VijayK) "yes it does and you can clear cache at any time using Netscape at least"
15:42:20  SarahL says "ok but you can synchronise the site when you next connect if you want to"
15:44:19  VijayK says "Http://pps9900.crst.bbk.ac.uk/ppscore/section11/symmetry/symmetry.htr"
15:44:55  VijayK says "See page 2 Asymmetric Unit"
15:45:02  ClareS says "I am assuming that that should end .html"
15:45:22  ClareS says "I'm looking at it now.. exactly what don't you understand?"
15:45:54  VijayK says "Sorry that,s correct. the last bit was not complete in print"
15:47:07  VijayK says "I assume that a unit cell must have some features follwoing cryst. principles to be called so is that right/"
15:47:43  ClareS says "the unit cell is the smallest unit that can be repeated to form the whole crystal"
15:48:04  ClareS says "e.g. in a cubic crystal the unit cell is a cube"
15:48:53  VijayK says "that makes it better"
15:49:18  ClareS says "the unit cell does not always contain exactly one protein molecule"
15:50:10  ClareS says "it will usually contain more than one"
15:51:05  ClareS says "the asymmetric unit is the largest unit (set of coordinates) that has no crystallographic symmetry"
15:51:49  ClareS says "applying the symmetry operations of the relevant space group to the asymmetric unit will generate a whole unit cell worth of molecules"
15:52:18  ClareS says "symmetry is a very complex subject, and quite difficult to understand"
15:52:46  ClareS says "if any of you go on to do our Protein Crystallography advanced cert. you will go into it in much more detail"
15:53:07  ClareS says "any problems?"
15:53:44  VijayK says "coming to symmetry operations - are rotation, translations symmetry ops. what is menat by translation in this context"
15:55:27  ClareS says "if you mean when I was talking about applying space group symmetry ops -- yes that's quite right!"
15:57:36  ClareS says "are there any more questions?"
15:58:09  VijayK says "about translations"
16:01:15  KevinO says "sorry, have to leave, bye all!"
16:03:03  ClareS says (to VijayK) "yes... what about translations?"
16:03:14  ClareS says (to KevinO) "bye!"
16:03:22  KevinO disconnects.
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16:04:10  VijayK says "what is menat by translation when we talk about symmetry ops."
16:04:21  SarahL says "i have to go now  I'll probably be back tomorrow"
16:04:48  ClareS says "simply moving without rotating"
16:05:32  VijayK says "I get it now. Thank you and hope to be here tomoorow as well"
16:06:07  VijayK says "bye for now"""
16:06:24  ClareS says "well if there are no more questions I'll close the meeting now.. we had a lively discussion. Thank you"
16:06:28  SpyrosS says "I have to go too, bye all"
16:06:55  SarahL disconnects.
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