This is a recording of a Biomoo session held on 11/12/96 on Section 4 of the Course Material

ClareS turns the ClareS_recorder on.

ClareS says "OK everyone - this session is now being recorded!"


ClareS says "so I would like to welcome everyone to this meeting of PPS students, tutors (welcome Jim!) and consultants"

Jim Pitts drops the T-recorder.

ClareS says "the main purpose of this meeting is to discuss Section 4 of the course material, Protein Synthesis"

Jim Pitts points the T-recorder at the TLOG1BIOMOO-PPS97.

ClareS says "and I am very grateful to Henry Brzeski for coming"

Henryb says "I'm here to try and answer the (easy) questions"

Jim_Pitts turns the T-recorder on.

ClareS says "It would help if people could open a Web browser pointing at section 4"

Henryb says "Are there specific points that anyone wants clarified or should I start with strategic questions"

ClareS says "Of course, we will be very happy to answer other questions about the course so far"

ClareS says "but I would like to try to finish by 17:30 (GMT)"

ClareS says "Are there any specific questions first, or shall I hand over to Henry?"

Lulu finds his way in.

Henryb says "I need to be gone by 1.10 GMT"

Lulu says "hello again!"

ClareS says "OK Henry - then we'll cover general questions about the course material at the end"

ClareS . o O ( I think Henry meant 1510 GMT? )

Jim_Pitts turns the T-recorder off.

Henryb says "sorry I meant 17.10 GMT"

Jim Pitts picks up the T-recorder.

ClareS [to henryb] Over to you, then

Henryb says "One question I can askk all the [aarticipants while they are assembled which has little to do with course content."

The housekeeper arrives to cart Baskin off to bed.

Henryb says "I want to put chime plugins directly in my web pages. a) how many of you have Netscape 3 and b) how many of you know what a chime plugin is?"

ClareS [to henryb] One problem with this is that chime is (I think) *still* only available for Windows

Lulu says "In my case both answers are "no""

MD says "I have Netscape 3 and know what you mean"

ClareS [to henryb] so anyone using a Mac or Unix workstation for the course won't be abnle to use chime (yet)

Cockle says "I've got Internet Explorer but I don't know chime"

Baskin finds his way in.

Henryb [to clare] It IS available for mac's but it is not as well developed. Tim Maffett of MDL promoses version 1 for both machines by mid December.

MD says "With my IRIX Netscape, I can not use plugins (I think)"

Louise finds her way in.

ClareS says "Plugins can be used with Netscape 3 for amy machine, and it's free for non-profits"

MD says "But an additional tool?"

Louise says "Hi T[Dtosay Hello to everybody"

Jim Pitts says "Hi Louise"

ClareS [to henryb] Maybe you could say a few words describing Chime, for those of us whio haven't used it yet?

Henryb says "This causes me a problem because I wanted to publish some notes I have put together for our undergraduates on DNA structure but it uses chime plugins. Obvioulsy many of you will not be able to access them. I will have to think seriously abou

t this one."

Alg says "I have and I know"

ClareS says "How many other people are using a PC with Netscape 3 and Chime plugins?"

Henryb says "Chime is like rasmol. It allows you to visualise proteins in 3 dimensions. It allows you to rotate them and change their display with a menu (eg spacefill or wireframe) but does not come with a command line (unless programmed in)."

ClareS [to henryb] One important difference between chime and rasmol is that with chime the molecular graphics is integrated within Netscape, I believe?

Henryb says "However, you can put in push buttons into the web page to pick out pre-programmed aspects of protein or DNA structure eg select one amino acid, turn it into spacefill or colour it green etc just as you can do with rasmol. In this way you can

 lead a reader through the intricacies of protein structure and interactions."

ClareS says "so it will be invaluable in a course like ours, as soon as we can be sure that everyone has access to it"

(Lulu has disconnected.)

Henryb [to ClareS] yes clare. You read a file just like a normal web page. But it can have tables or frames within it to display proteins. Go to Eric Mart's Rasmol home page to find out more. This is at http

MD goes home.

ClareS says "that URL (the Rasmol home page) is really useful, and I would recommend that everyone bookmark it, if they haven't already done so"

Henryb [to ClareS] yes thats why I asked the question. Now that Microsoft have muddied the waters with Internet explorer this gets more confusing. Especially since I don't think chime can run with IE.

ClareS doesn't know whether chime can run with IE either

Henryb says "lets talk about DNA and not computer technology. Even though it was this course that first made me aware of what computer technology can do."

ClareS says "I hope that Chime is soon released for the other platforms, so anyone with the technical requirements for the PPS course can use it"

ClareS [to henryb] Good idea!

Henryb [to ClareS] I hope so to

ClareS says "Anyone with any specific questions on Transcription or the rest of the section 4 material?"

(Lulu has connected.)

Henryb says "Does everybody feel happy with the fact that, in DNA terms, they are no different to an everyday bacterium?"

ClareS grins

Hagar says "I'm a bit bigger!"

ClareS grins again

Alg says "I do use Chime with Netscape 3; But still I think Rasmol is more powerfull"

Henryb [to Hagar] and so is your DNA but are there any more genes there (and this is not meant as a personla insult !!)

Louise says "QW[D[D[DW[Dsay"

Jim Pitts says "Are you having trouble Louise?"

Henryb [to Alg] I agree. With the command line it is very powerful in the hands of an experienced user with a pdb file in front of them. But, if you are after demonstrations, then chime with buttons in a web page is very dificult to beat.

ClareS [to henryb] do you know how many genes there are in the human genome? I can't remember

Louise says "Why are there three specific DSTOP codon and not a specific one for START codon?"

Henryb [to ClareS] I think that the original thought was 1 million but I think that now people are starting to downtrate that a little.

ClareS [to Louise] good question..

Cockle says "I think there are about 50thousends to 100 thousends genes"

MD finds his way in.

Henryb [to Louise] Don't ask me. Ask the man who made us !!! An interesting thought. Especially since E coli for isntance uses multiple stop codons fo different types as some work better than others. Pass on this one.

(MD has disconnected.)

Jim Pitts says "certainly E.coli genes often have two different stops in a row. This may mean that it is very important to the cell to stop making a protein that starting them!"

Henryb [to lousie] This is complicated still further by the fact that some organisms use slightly different genetic codes and a temination codon in one organism is an amino acid in another.

ClareS [to henryb] Do you know what the signal/s is/are for the start of a gene? (other than the initiating Methionine... but then, which Methionine??

Cockle says "to Louise I think we should in this case think a bit about the way evoultion went. there was no posssibility to start transcription with codon which means nothing and codons stop just interupt the process"

Lulu says "But by the way... Is there any relationship between stop codons and gaps (I mean deletions) among "

Lulu says "homologous proteins?"

(Baskin has disconnected.)

Alg says "to Louise The reason may be that you need a specific tRNA for initiation and need not for termination. Initiation is more complicated and more constrained."

Jim Pitts says "Some multi-domain structures show sub-units that reflect the positions of the exon/intron positions found in higher organisms. Introns are non-coding regions within a gene from a higher orgainsm which lies between the coding exon regions

and relects the codons seen in the genetic code"

Jim Pitts says "See"

The housekeeper arrives to cart MD off to bed.

(Lulu has disconnected.)

(Lulu has connected.)

ClareS says "a group of countries - like G7, but less so (& there are 24 of them)" to gustavo"

ClareS blushes

ClareS says "sorry for the interruption"

(Henryb has disconnected.)

(Hagar has disconnected.)

Alg says "Connection is really bad" to ClareS"

The housekeeper arrives to cart Baskin off to bed.

ClareS says "Is anyone else having serious problems with the connection?"

Lulu says "Yes, I've been already disconected three times during this meeting"

ClareS says "Henry has just lost his connection - he will keep trying to come back in for a bit"

ClareS says "are any of you coming in through GNA-Lab?"

Gustavo traces route to Alg's site - the problem is in Europe's network.

Gustavo wouldn't recommend using the GNA-Lab right now.

ClareS says "It seems to be OK from here"

Lulu . o O ( I hope )

ClareS says "Does anyone have any specific problems with Section 4 or any other aspect of the course so far?"

ClareS says "... or general questions?"

(Lulu has disconnected.)

Alg says "Yes. Material seems to be introductory. Are we going to have any real protein structure science?"

Alg says "And what about any assignments?"

ClareS [to Alg] the more advanced structural stuff is next term...

The housekeeper arrives to cart henryb off to bed.

The housekeeper arrives to cart Hagar off to bed.

Alg says "When does it start?"

(Lulu has connected.)

ClareS [to Alg] Last year there were two assignments, as well as the exam and the project

ClareS [to Alg] they were fairly simple...

Alg says "Will we be divided into any groups (like last year)?"

Lulu says "About the problems. I cannot get access to the archives of discussion list. I mean both lists: general and te"

Alg says "Connection improved significantly:-)"

ClareS says "the groups have already been allocated, if you don't know about this, there has been an administrative slip-up"

ClareS says "there are 3 groups allocated geographically"

Alg [to ClareS] "Generaly how do you find this year's PPS?

(Tillmann has disconnected.)

ClareS [to lulu] There is a server error with the discussion list archives (I've just checked)

Alg [to ClareS] "Don't you find it deeply sleeping?

ClareS [to lulu] I'll ask DaveH to look into this as soon as possible

Lulu [to ClareS] Thanks in advance

ClareS says "I think it would probably be appropriate to close the formal part of the meeting now and turn the recording off"

ClareS says "but do feel free to stay around and chat for as long as you like - I'll stay connected for a while"

ClareS says "... are there any other questions first?"

Alg [to ClareS] You mean the discussion on part 4 is dead?

ClareS [to Alg] only the formal discussion

ClareS [to Alg] there have been serious net problems within Europe which have rather hampered discussion

Alg [to ClareS] So what about your impressions of PPS'97

Cockle says "to ClareS could you tell me please about the test we have done some time ago in Poznan on Molecular Modeling?"

ClareS turns the ClareS_recorder off.