RasMol BioMoo 12-5-97

ClareS turns the ClareS_recorder on.

ClareS says "testing recorder and tape""

ClareS turns the ClareS_recorder off.

ClareS turns the ClareS_recorder on.

ClareS says "Welcome everyone!"

Jim Pitts says "Hi"

ClareS says "This meeting is (mainly ;) to discuss RasMol - the principal molecular viewing program used in the PPS course"

ClareS says "and Eric Martz, who runs the RasMol home page & discussion list, is here to answer questions about it"

Eric.martz [guest] says "Too bad Roger Sayle couldn't come as he knows ever so much more about RasMol than I do!"

AndrewT [guest] materializes out of thin air.

ClareS . o O ( he *wrote* it )

ClareS says "the home page URL is http://www.umass.edu/microbio/rasmol/"

ClareS [to eric.martz] would you like to introduce yourself?

Eric.martz [guest] says "And the most exciting things I've been able to do with Chime are at http://www.umass.edu/microbio/chime"

ClareS says "firstly - which of you here (students, consultants, whoever?) use RasMol? and which use Chime?"

Eric.martz [guest] says "Hello, everyone. "

Eric.martz [guest] says "I'd like to know also."

Louise says "I use Rasmol, but not Chime"

ClareS says "we (in the course) assume everyone has access to Rasmol but not necessarily Chime"

ZLeifer says "I have Rasmol, not Chime, and am starting to learn it. I have been using Hyperchem for basic training."

Eric.martz [guest] says "I am very enthusiastic about Chime's ability to deliver educational tutorials via web ..."

Louise says "Ifound thr Rasmo9l tutorial by Coulson very useful"

Eric.martz [guest] says "...but I think RasMol reigns supreme for interactive exploration of a molecule"

ClareS says "We have to assume that not all students have access to the same hardware and software - Rasmol is unique in that it is free and runs on all hardware platforms we support"

ClareS says "even when the current course started, Chime hadn't been released for Unix boxes"

Eric.martz [guest] says "Chime runs on Windows 3.1, Windows 95, Macintosh, SGI Irix but not other flavors of unix."

ClareS says ".. and it has only just been released for the SGI"

Eric.martz [guest] says "And on SGI Irix, it is still in version 0.9 and has some problems."

ClareS says "we are wondering whether to move to Chime for next year's course"

Henryb [to eric.martz] How about Internet explorer on PCs?

Eric.martz [guest] says "I am missing some utterances doe to a wrapping r problem."

Eric.martz [guest] says "I missed clare's 'it has only j...'"

Eric.martz [guest] says "I missed Henry's last statement"

ClareS [to eric.martz] henry was asking about Internet Explorer for the P

ClareS . o O ( PC, of course )

ClareS says "has anyone had any particular problems with RasMol"

Eric.martz [guest] says "Anything you'd like to do with RasMol that you haven't been able to?"

The MOO Instructions for Ames Assay is put back on the bookshelf. If you are staring into space or out of the room, Marian the Librarian will make it available to others.

Louise says "sometimes while using Rasmol the program warns "cannot ope script file" I haven't understood the reason"

Eric.martz [guest] [to Louise] were you trying to run a script, 'script filename'?

Louise says "yes"

Henryb [to eric.martz] At one of the earlier rasmol meetings I asked a similar question and many people present said they accesssed the course using internet explorer so Chime has to work with this as well as Netscape. Have you any idea of what is hapening here?

Eric.martz [guest] says "You can getan image with Chime in IE"

Eric.martz [guest] says "but IE does not fully support Chime"

ClareS [to henryb] good point! - IE must be almost as widely used as Netscape by now

Eric.martz [guest] says "Therefore you can't see what IE doesn't do properly"

ClareS [to eric.martz] which versions of IE?

Henryb [to ClareS] Good old Microsoft

ClareS sighs

Eric.martz [guest] says "If you are using Chime, you MUST use Netscape 3.01 (neither earlier nor later!)"

ClareS [to eric.martz] nor later????

Eric.martz [guest] says "Netscape 4 beta last time I tried it didn't work at all with Chime"

ClareS . o O ( I wonder what will happen when all the world is using Netscape v.5 )

Eric.martz [guest] says "Presumabley eventually Netscape 4 will work properly w/ Chime."

Eric.martz [guest] [to Louise] Was the script in the local (working) directory?

Eric.martz [guest] [to Louise] Were you trying to run the script on Mac, Win, or unix?

Louise says "the script was in the Raswinus directory"

Eric.martz [guest] [to Louise] did the script filename end in .spt?

ClareS says "I have heard that because mol.biology is a relatively small discipline, we can't expect computing standards to react to us - we will have to adapt to emerging standards"

Henryb says "This variation between versions is a problem. I've been trying to write large Javascript files and these run perfectly well on a windows95 version of Netscape 3.01 but not on a Windows 3.1 version!!!"

Louise says "the script filename ended in .txt"

Eric.martz [guest] [to Louise] Try renaming the script to .spt.

Louise says "thanks"

Eric.martz [guest] [to Louise] if you still have problems, email me as we can diagnose faster that way.

Louise says "OK"

Eric.martz [guest] says "Questions can be sen to sent to me at emartz@microbio.umass.edu"

ClareS [to eric.martz] thanks!

Eric.martz [guest] [to henryb] I agree that javascript is very frustrating

Eric.martz [guest] [to henryb] however so far with persistence I've gotten it to do what I wanted

ClareS [to henryb] I only wish I had enough time to learn javascript

Eric.martz [guest] [to henryb] tho what works well in Windows (3.1 or 95) doesn't work well on Mac!

Henryb [to eric.martz] I find the lack of detailed error messages very frustrating which then involves a lot of lateral thinking.

Eric.martz [guest] [to henryb] Agreed!

ClareS is trying to download a copy of the script creation guide over a very slow transatlantic connection

Eric.martz [guest] [to ClareS] The guide to script creation is a bit obsolere obsolete, especially vis a vis Chime.

Henryb [to ClareS] I've been using Netscapes instructions. Have you got another source?

ClareS [to henryb] of what??

ClareS [to eric.martz] would you be happy for me to suggest that students email you directly with questions about rasmol?

Eric.martz [guest] [to ClareS] Yes.

Eric.martz [guest] says "Has anyone played with RasMol's 'within' command?"

Henryb [to ClareS] sorry. I thought you were talking about javaSCRIPT but you appear to be talking about chime SCRIPT. I get confused very easily !!!

ClareS says "No"

ClareS [to eric.martz] thanks a lot!

Eric.martz [guest] says "By anyone, I meant any of the students present."

(AndrewT [guest] has disconnected.)

Eric.martz [guest] says "The 'within' command allows you to find atoms closest to a moiety of interest."

Eric.martz [guest] says "For example you can find contacts between proteins or between protein and DNA."

ZLeifer says "Would it work for a small molecule ligand and DNA as well?"

ClareS would assume so

Henryb [to eric.martz] I thought you had to choose a particular group. Can you be as vague as to say protein AND dna?

ZLeifer says "Could you find a molecular mechanics minimum for ligand binding or "association" and then see which are the contacts or "nearest neighbors"?"

ClareS [to ZLeifer] Rasmol does not do molecular mechanics! If you have a structure minimised with another program you will be able to calculate the close contacts with Rasmol

Eric.martz [guest] [to ZLeifer] RasMol of course can't do any energy minimization, but the within command will indeed find nearest neighbors.

ZLeifer says "Thanks. That would be helpful."

Eric.martz [guest] [to henryb] Yes, you can 'select dna and within(3.0, protein)'

Eric.martz [guest] says "The value (e.g. 3.0) must contain a decimal point to force it to be interpreted by RasMol as Angstroms instead of a less useful unit used by RasMol."

Eric.martz [guest] says "Chime is of course free software, just like RasMol."

Eric.martz [guest] says "(But Chime's source code is not available, unlike RasMol's!)"

ClareS [to eric.martz] which do you prefer?

Eric.martz [guest] says "Who, among the students present, has viewed some Chime web pages?"

Eric.martz [guest] [to ClareS] I prefer RasMol for exploaration and Chime for delivering canned presentations.

ClareS says "... anyone? not just students?"

Eric.martz [guest] says "HenryB has authored some state of the art Chime peresentations!"

Eric.martz [guest] [to ClareS] Students in a graduate class here were assigned to do a presentation in Chime this year for the first time.

Eric.martz [guest] [to ClareS] The presentations they projected in class were excellent (accompanied by explanation).

ClareS [to eric.martz] how did they get on?

Eric.martz [guest] [to ClareS] The versions on the web are still a bit shaky.

Eric.martz [guest] [to ClareS] But for the first time around I think it went very well.

Eric.martz [guest] says "The profs of this class are Craig Martin and Lynmarie Thompson."

Henryb says "I'm trying to develop Eric's command line approach and turn Chime into a tutorial exploration package with student feedback but this is still only a vison without much work invested as yet."

Eric.martz [guest] [to henryb] Ditto -- still just a dream for me.

ClareS nods understandingly to eric & henry

ClareS says "before we finish the formal part of the meeting, are there any more questions?"

Eric.martz [guest] says "http://chemserv.chem.umass.edu/Martin/Courses/BioStruct/Proj/Proj.html"

Eric.martz [guest] says "That was the URL for the class I mentioned."

ClareS says "...and do you think we would benefit from another session on Rasmol?"

Louise says "maybe a stupid question. Is it possible to improve Rasmol in order to display the electronic density?"

Eric.martz [guest] says "What do you mean by the 'electronic density'?"

Eric.martz [guest] says "Do you mean cgarge distribution on the surface?"

Louise says "as in Frodo,for instance"

Tillmann finds his/her way in.

Eric.martz [guest] says "Sorry, I don't know anything about Frodo."

Eric.martz [guest] says "charge distribution, not cgarge"

Louise says "I mean the electronic density collected by X-ray"

Eric.martz [guest] says "Roger Sayle has recently been joined by Mike Hartshorn and they are working on improved versions of RasMol."

ClareS [to Tillmann] Hi

Eric.martz [guest] [to Louise] I don't think RasMol can display electron density, but you should ask Roger by email directly.

Eric.martz [guest] says "Anyone is welcome to subscribe to the RasMol email list."

ClareS says "could you remind us of Roger's email address? (Would he mind?)"

ClareS says "... and the address for the listserv"

Eric.martz [guest] says "It has light traffic, average 1.3 messaes per day."

Henryb [to Ertic.martz] does this mean that rasmol and chime will go separate ways? Are Tim and Roger collaborating with one another on program development?

Eric.martz [guest] says "Roger reads the list and often responds to good questions like Louise's -- that way all interested parties can see the discussion."

Eric.martz [guest] says "Tim Maffett and Roger Sayle are in constant communication and are developing RasMol and Chime in parallel to the extent that is possible."

Eric.martz [guest] says "(Tim Maffett is the author of Chime.)"

Eric.martz [guest] says "To subscribe to the RasMol email list, or view the history, go to the RasMol Home Page (URL given earlier today)."

Eric.martz [guest] says "www.umass.edu/microbio/chime"

Eric.martz [guest] says "www.umass.edu/microbio/rasmol"

ClareS [to eric.martz] thanks - not everyone was here when that URL was given first time

Henryb [to eric.martz] that's good. That makes our life easier as well as we don't have to develop two sets of scripts.

(Tillmann has disconnected.)

Eric.martz [guest] says "Roger's direct email is ras32425@ggr.co.uk"

Eric.martz [guest] says "But it wouild be more fun for everyone if you subscribe to the list and ask there."

Eric.martz [guest] says "For 'movie' scripts, Chime is so much more powerful than RasMol that I don't plan to develop any more RasMol scripts for distribution as such."

Eric.martz [guest] says "RasMol is still very useful for developing sequences of script commands which are then published as a Chime presentation."

Eric.martz [guest] says "I wrote five 'major' (1,000-2,000 lines of script commands) RasMol scripts in early 1996."

Eric.martz [guest] says "They are available at my web site given above."

Eric.martz [guest] says "Henry Brzeski has also written large RasMol scripts."

Henryb says "sorry folks - I must be off. Thanks for the exciting and interesting discussion. See ya!!!"

ClareS [to henryb] thanks for coming and for your valuable contributions

Henryb [to eric.martz] bye eric. See you again soon.

ClareS says "shall we draw the formal part of the meeting to a close now?"

Eric.martz [guest] says "Since nobody said they've looked at a Chime page, I urge you all to do so."

(Henryb has disconnected.)

ClareS turns the ClareS_recorder off.