MUD transcript: 03-08-00
Protein Interactions; Projects
Course room(s): PPS
22:00:39 SarahL says "Hi larry how are you getting on with the course work"
22:01:30 LarryT says "absorbing sloooooooowly ,,, there is a lot here!"
22:02:34 LarryT says (to Say) "but I have access to Crystal Eyes on an SGI terminal, so it helps with 3D visualizations"
22:03:12 ClareS connects.
LarryT PPS Telnet 12m 5s 22s
SarahL PPS HTTP 4m 56s 2m 33s
ClareS PPS HTTP 0s 0s
22:03:23 ClareS says "Hi! Sorry I was late"
22:03:38 ClareS says "(a few minutes late, anyway)"
22:03:47 ClareS says "are you ready to start the meeting?"
22:05:19 ClareS says "have you chosen your projects, and are you clear about the procedure.. would you like to start by discussing those, or section 12?"
22:06:03 LarryT says (to Say) "I have chosen a topic ... I assume I put it on the web when done?"
22:06:23 SarahL says " there seems to be alot to get through , with the project to start and the exam to revise for i hope i am going to find the time, i wish that my computer was faster"
22:06:34 ClareS says "yes... you don't put it on the web, tho', we do"
22:07:14 ClareS says "all projects that pass are mounted on the Birkbeck web site"
22:07:38 LarryT says "so. I put it together ... zip the folders (anticiapte organizing structures, images and other stuff in separate folders) and send to our tutor"
22:08:01 SarahL says "yes i have chosen my topic also"
22:08:29 ClareS says "not to your tutor, to Dave Houldershaw"
22:09:00 ClareS says "and yes, you're right, you do need to zip it up so that the directory structure is maintained"
22:09:11 LarryT says "is there a limit on zize, etc."
22:10:29 ClareS says "you can see last year's list of completed projects at http://pps99.cryst.bbk.ac.uk/projects/projects.html"
22:11:01 LarryT says (to Say) "I anticiapte using Microsoft Front Page as an HTML editor ...I understand MS has it such that Web pages done by them only work on NT servers ... is that a problem, or should I use a different editor?"
22:11:04 ClareS says (to LarryT) "I presume you mean "size"???"
22:11:25 SarahL says " i haven't had much experience of zipping , i have winzip but rarely use it"
22:12:04 LarryT says (to Say) "yes I meant size ... I type 5 words a minute with 60% error (g)!"
22:12:13 ClareS says (to SarahL) "our server is not NT, but if you stick to fairly standard HTML you shouldn't have any problems"
22:12:42 ClareS says (to LarryT) "there is the 2GB file size limit that Linux insists on ;)"
22:13:06 LarryT says " yes, I meant size ... I type 5 words a minute with 80% error (g)"
22:13:23 ClareS says (to LarryT) "seriously... not that I know of. No-one's ever asked this question before tho'"
22:13:53 ClareS says (to SarahL) "winzip is pretty straightforward to use"
22:14:07 SarahL says " i also am planing on using front page express"
22:14:30 ClareS says "sticking to straightforward HTML that will work in any browser is a good tip for a beginner"
22:15:06 LarryT says "I've never done a web site before and have no sense of size for various elements ... and I anticiapte a lot of graphics/strcutures ... I want to try to render in CHIME"
22:15:58 ClareS says "some previous students have used Chime to great effect, but not remember that not everyone has / can use Chime"
22:16:48 SarahL says "do you mean that front page is a straight forward way of writing web pages."
22:17:05 LarryT says "I have always felt that CHIME rendered structures were more usefful to me as a browser ..never used as an "author""
22:17:54 ClareS says "The only problem that we have with Chime is that some of our students use unix boxes exclusively"
22:18:07 LarryT says "I have no idea what using FRONT PAGE is like .. I ASSUME its just another Office package that assembles the elements into an HTML rendered page."
22:18:52 ClareS says (to SarahL) "I mean that if you avoid using Front Page specific tricks and stick to simple elements, like text, tables, images, you won't have any problems"
22:19:04 LarryT says (to Say) "CHIME does NOT work with UNIX???? I did not realize this!"
22:19:39 ClareS says (to LarryT) "this is true, and it is a serious drawback of the software. The mac versions are there but fall over a lot"
22:21:25 LarryT says (to Say) "DAMN! I had wanted to focus on strcuture of MR receptor and ability to manipulate strcutures is soooooooooooooooo much better than a static image ...besides, I was going to use this project as an EXCUSE to force me into learning CHIME"
22:22:09 LarryT says "but if CHIME is not useable for all, I'll have to adjust and go with static stuff"
22:22:21 ClareS says "See http://www.umass.edu/microbio/rasmol/faq_em.htm#sgi for a discussion of hardware compatibility with chime"
22:22:55 ClareS says "they don't make any excuses, they just say they won't be developing it for unix!!"
22:23:25 ClareS says "there is a very old buggy version (v.0.9) that works ... sort of... on SGIs only"
22:23:47 ClareS says (to LarryT) "you could always use rasmol, that works on almost any computer anywhere in the universe"
22:24:04 LarryT says "well, I guess I'll go static image ...better than learning java scripting (g) in the time frame allowed"
22:24:54 ClareS says (to LarryT) "and what is wrong with using rasmol??"
22:25:14 SarahL says "in order for the web pages to be reproduced by all machines is it better to write in html on notepad?"
22:25:48 LarryT says "so, if I require rasmol as a helper application (and so state) I will accomplish the same thiong as CHIME, but structures will be cross platform compatible?"
22:26:17 ClareS says (to SarahL) "you'll be fine with front page as long as you only use the simple html statements discussed in section 6"
22:26:40 ClareS says (to LarryT) "yes, that's right, it just won't look as pretty"
22:27:13 LarryT says "there is nothing wrong with rasmol ..it's a great capplication .. I just thought CHIME was way to go ... my ignorance .... just cured here!"
22:27:50 ClareS says "and you'll need to put on your web pages that people will need to have rasmol installed as a helper application"
22:28:16 SarahL says "ok , then so its best not to try to be too clever ( not that I was going to of course!)"
22:28:23 ClareS says "if chime only worked on all computers it *would* be the way to go... as it is you need to choose between elegance and platform independence"
22:28:46 ClareS says (to SarahL) "yes, that's it exactly"
22:32:39 ClareS says "do you have any more comments or questions on the projects, or shall we move on to section 12?"
22:33:30 LarryT says (to Say) "thanks for clarification on the projects ....no more questions on it for now!"
22:35:04 ClareS says "how have you found section 12, then??"
22:35:29 SarahL says " i have spent quite a while going over chymotrypsin, and have just about got that sorted now."
22:36:03 ClareS says (to SarahL) "that is quite an interesting case study"
22:39:18 SarahL says " bandon and tooze is a helpful backup, i aways have to spend awhile thinking about the chemistry when it comes to it. or else i get confused"
22:39:32 ClareS says "there is, actually, quite a serious error in http://pps9900.cryst.bbk.ac.uk/ppscore/section12/serprot1.html - have either of you spotted it?"
22:40:02 ClareS says "yes, Branden & Tooze is an excellent book (which is why we recommend it in almost every section)"
22:40:34 ClareS says "we discussed the error in yesterday's MUD but you won't have been able to read the transcript yet"
22:41:51 SarahL says "was it one of the scripts or something more obvios"
22:41:55 SarahL says "was it one of the scripts or something more obvios"
22:43:22 ClareS says "it was in the text on the web page"
22:43:27 SarahL says "divergent"
22:43:31 ClareS didn't write that page
22:43:49 ClareS says (to SarahL) "I'm not quite sure what you mean?"
22:45:42 LarryT disconnects.
SarahL PPS HTTP 47m 26s 26s
ClareS PPS HTTP 42m 30s 5s
22:45:42 LarryT connects.
LarryT PPS Telnet 0s 0s
SarahL PPS HTTP 47m 26s 26s
ClareS PPS HTTP 42m 30s 5s
22:47:36 LarryT says "(to Clare) first time I have used tkmoo on my new box .. it just shut down ... not sure if it is tkmoo/win98 or a lightning strike ...got a general fault error and had to reboot"
22:47:39 ClareS says "the mistake concerns something that we were very clear about in the bioinformatics section (at least we intended to be)"
22:47:51 SarahL says "did it say divergent evolution instead of convergent evolution"
22:48:01 ClareS says (to LarryT) "you seem to be OK now, tho'??"
22:48:15 ClareS says "no, that's not the error I was thinking of"
22:48:40 ClareS says "we do mean divergent evolution here, I've just checked"
22:49:08 LarryT says "(to clare) should be OK ... telnetting is basically a no-brainer"
22:49:45 ClareS says (to LarryT) "do you find it faster from the states than the Web interface?"
22:50:08 SarahL says "oh , the homology 50% or less-- this was one of the questions in the assignment!!"
22:50:26 ClareS says (to SarahL) "yes, that's correct - well done for spotting it!!"
22:50:59 ClareS says "whoever wrote that page (and I can't remember who it was) meant 50% identity, not homology"
22:51:24 ClareS says "or possibly 50% similarity, I'd have to do the calculation myself to check"
22:51:51 LarryT says "(to Clare) before class started, the material suggested moo MUD sessions, so I went on the web and got tkMOO ..it's worked well ... since I am running a modem (now 56, before 28.8), I have always felt that telnetting was faster than browser based ..but have done no real comparisons between tkmoo and IE 5.5"
22:52:02 ClareS says "homologous" just means "evolutionarily related" so you can't use that term with percentages"
22:52:40 SarahL says " eventually, it did strike me as oddd when i read it but i hadnt marked it in my notes"
22:52:55 ClareS says "it is possible to refer to two proteins (or of course genes) as distantly homologous, tho'"
22:53:02 LarryT says "(to Clare) if I was at the U (with T3 connectivity) I'd proabably be on the browser"
22:53:14 ClareS says "that page will be re-written for next year"
22:53:32 ClareS says (to LarryT) "what time of day is it where you are?"
22:54:14 ClareS says "I'm on the Web interface from my home machine with a 28.8 modem"
22:54:30 ClareS says "it's quite fast enough but I suppose it is nearly midnight here"
22:54:54 ClareS is wondering what T3 connectivity is and how fast it is
22:55:00 LarryT says "(to Clare) with daylight savings, we are 4 hours behind GMT ...normally 5 hours"
22:55:46 ClareS says "so it is early evening east coast time - that figures"
22:56:22 SarahL says "i'm also at home on a web browser and my modemis 19.6!"
22:57:47 ClareS says (to SarahL) "is your connection fast enough?"
22:58:45 ClareS says "I guess it's almost time for bed... I'd like to wind this session up in 10 mins or so, so if you could think of your last questions..."
22:58:57 LarryT says "the only real disadvantage to tenetting is the lack of spell checking (g) and, of course, the lack of images ..but since this is text based, I did not see a reason to go with browser ..besides, it gave me a differnt application to play with and I am always looking for new toys to try! (g)"
22:59:17 ClareS says "... remembering that there won't be any more MUDs until the 2 weeks or so before the exam"
23:00:01 SarahL says " well it copes with mud sessions but it is extremely slow for down loading pdb file. the computers at work are 10x faster."
23:00:51 ClareS says "yes that can be slow from home.. and expensive. I take floppy disks to work & take the data home the old fashioned way, in my pocket"
23:01:38 SarahL says " i must be wasting alot of time downloading files"
23:02:09 ClareS says "you can always do something else while the file is downloading (like view more material)"
23:02:16 LarryT says "I do my downloading at T3 speeds at the University of MI ...try to limit downloading here ...I use a 56 K modem and an application called GOzilla that splits files into 4 packages for downloading ...speeds things up a bit"
23:02:39 LarryT says (to Say) "if you are downloading over a modem, you really need some kind of accelerator"
23:03:27 ClareS says (to LarryT) "I don't know that program"
23:03:49 SarahL says " yes i must be one of the few people that carries a spare floppy disc in my hand bag"
23:04:02 ClareS does too ;0
23:05:44 LarryT says "I visit a number of shareware/freeware sites every day ... Gozilla is an adware (bewware they ttrack aall yoour browsing habits), but the commercial version (30.00 $US) does not ... it is a TCIP manager that splits all downloads into multiple packets and reassembles ...downloads 4 tracks at once ... can also schedule downloads late at night when traggic is less"
23:06:32 ClareS grins
23:07:47 ClareS says "I have never worked out how to pay shareware fees in dollars if they can't/won't take credit cards"
23:08:01 ClareS says "without paying twice as much to convert the money"
23:08:35 SarahL says " yes Ive taken to getting up early and downloading files before the telephone rate goes up"
23:08:55 LarryT says "they take credit cards ..bTW, there are also a variety of freeware curency converters available ...some even check banks on demand to get current quotes (g)"
23:08:57 ClareS prefers going to bed late
23:09:51 LarryT says "with a download scheduler, you can go to bed and download all night (g) I just download exceed (x windows emulator) 52 meg download while I slept"
23:10:03 ClareS says "tho' it's getting rather late for me now..."
23:10:22 ClareS will have to buy a larger hard disk (or better still a new machine)
23:10:31 LarryT says "good night! Thanks gfor the project assist"
23:10:39 LarryT disconnects.
SarahL PPS HTTP 1h 12m 2m 4s
ClareS PPS HTTP 1h 7m 17s
23:10:40 ClareS says "Exceed is a brilliant X emulator, I use it all the time"
23:10:57 ClareS says "except at home for reasons you can understand"
23:11:24 ClareS yawns
23:11:36 ClareS says "Goodnight, and good luck!"