Transcript of meeting in BioMOO, PPS Base 5th Jun '96 15:00 GMT: RasMol

We would like to thank Eric Martz (of the RasMol Home Page and e-mail list) for attending this session.


JohnW says, "I should begin by saying that unfortunately Roger Sayle had to pull out of todays seminar. "

PeterMR finds his way in.

PeterMR waves all

TRex waves

ClareS says, "That URL downloads a large ASCII file of coordinates in a format I don't immediately recognise"

HorstJS finds his way in.

PeterMR welcomes newcomers to BioMOO/PPS :-)

JohnW [to HenryR]: Many thanks for coming Henry...shame its slow today. Hope to see you here again soon!

JohnW says, "However, I am pleased to say that we have some other guest RasMol afficianados here today:"

(at this point JohnW intended to introduce Eric Martz of the University of Massachusetts, but the line seems to have got lost somewhere)

Giovanni finds his way in.

Giovanni waives

Luis finds his/her way in.

JohnW says, "I thouroughly recommend that you look at his RasMol pages if you have not already done so, at :"

Andrew Coulson says, "I'm sorry, folks, but the line to Edinburgh is just driving me noisily nuts -- I shall just have to leave a recorder running and come back later. Thanks anyway"

PeterMR waves andrew - nice to see you here

PeteO finds his way in.

JohnW says, "Andrew Coulson of the University of Edinburgh has written some programs to drive RasMol to display movies"

TRex says, "Eric's pages are full of excellent exa,ples of Rasmol scripts for teaching!"

Luis goes down.

ClareS says, "Andrew's pages sound very useful, do you have a URL?"

JohnW [to Andrew Coulson]: No problem, its just one of those things..thanks very much for bearing with us until now, and hope to see you here again

JohnW says, "I should add that today is the first time Eric and Andrew have been into BioMOO"

Emartz says, "Thanks, TRex. Those scripts run 1,000-2,000 lines of RasMol commands per script."

Emartz says, "I thninxxx thihx think "

Emartz gnashes his teeth

Emartz says, "I think we're all looking for an easier way to write scripts."

TRex says, "The connection seems to be infinitely slow!"

JohnW [to ClareS]: I'm not sure that Andrew has WWW pages about these programs

PeterMR waves eric and thanx

JensJL finds his way in.

TRex smiles

CrisCan finds her way in.

CrisCan waves

Emartz says, "In addition to Andrew Coulson's efforts using Visual Basic, Marco co Molinaro has plans for a movie interface built-into UCB-RasMol."

SteveTate finds his way in.

SteveTate has disconnected.

JohnW says, "Ok, well the main topic we are going to address here today is "RasMol and Movies""

ClareS agrees with Emartz

JohnW nods to TRex

SteveTate has connected.

Emartz says, "Andrew Coulson's interface is still under development, I believe, and is not yet on the web."

TRex says, "Yes, I'm intrigued by the idea of making movies. I've got a bit of an idea from the examples on Eric's pages"

TRex says, "I think it sounds like a lot of work :("

Taekwon [guest] finds its way in.

SteveTate has disconnected.

Henryb [to JohnW]: the conversation today seems rather stilted. Do you think this is a problem with the slow connection. You were talking earlier about rearranging the meeting. Do you still want to do this or should we continue?

JohnW says, "Ok, my connection has unfrozen again... before we go onto the main 'movies' part of the meeting, I would just like to respond to a few questions that Lappe posed during last weeks session:"

Emartz says, "I'd like to invite all of you to subscribe to the RasMol email list ( for info)"

TRex says, "Yes. Connection is slow - not a good experience for Andrew and Eric's first visit!"

PeterMR asks if there is an agenda?

Emartz moans

JohnW [to henryb]: I am happy to try and continue but I have a feeling that today's technical hitches will be driving everyone up the wall... perhaps we should take a vote on it?

TRex grins

JohnW [to PeterMR]: yes, the agenda is basically 'making movies with RasMol' plus any other questions left over from last session or posted since then...

TRex says, "Rescheduling will depend on our experts' timing for attendance"

ClareS wonders if anyone knows why the connection is so slow today...

Johnr says, "I think this is a vote with one's fingers issue: It's great to have people together trying. I vote 'forge on!'"

JensJL says, "I vote for going on"

The housekeeper arrives to cart SteveTate off to bed.

JohnW says, "Yes, its a great shame that things should be slow today..Eric and Andrew kindly agreed to attend at rather short notice...I was also telling them that things are usually much easier in BioMOO ;)"

Johnr says, "O yes!"

PeterMR agrees with JW

ClareS says, "I'm happy to go on, if everyone can stand it"

PeterMR wonders how many people are able to do something else at the same time so the slowness is not really critical. I am hacking C++ locally. Mind you, I am personally paying for the (local) call :-(

TRex nods agreeably

Johnr now moans

PeteO votes yes.

JohnW says, "Thats the spirit!"

PeterMR says, "of course it is a real strain on those *running* the mtg - I know!"

CrisCan says yes

ClareS has Insight running in the background

JohnW smiles

Andrew Coulson has disconnected.

JohnW says, "Ok, to address the points from last weeks meeting (there is a transcript at /PPS2/technology/RasMol/mooras.html)- Lappe asked a question about RasMol and secondary structure assignment:"

JohnW says, "i.e., if such assignment is not included in the PDB file, does RasMol calculate it. The answer is 'yes'- by the Kabsch and Sander DSSP algorithm. You can also use the command 'structure' to force RasMol to do this, even if it already has the sec struc details from the PDB file"

JohnW says, "I feel that the other questions might require Roger (unless anyone else knows)- i.e.How does RasMol calculate the flat ribbon bonds representing helices, and Is there a possibility of using an abstract representation of barrels for alpha-helices and flat ribbons for sheets ..."

Kdenton finds his/her way in.

JohnW says, "...perhaps we should leave these for next time unless anyone has any comments."

TRex nods

JohnW says, "we did not have any further questions e-mailed during the week, so we can now turn to 'movies'...but Ill just add that for any beginners, please look at the on-line RasMol reference at ../PPS2/technology/RasMol/main.html (among other places)"

Kdenton has disconnected.

ClareS nods

JohnW says, "Right- Movies. We began discussing these last time, and it was mentioned that there are several approaches. Eric, could I begin by asking you what is/are your favoured approach(es)?"

PeterMR waves bye to all

PeterMR has disconnected.

TRex waves to PeterMR

The housekeeper arrives to cart Andrew Coulson off to bed.

JohnW says, "I believe there are two main strategies... using RasMol to create a series of image files, which you then animate to produce an MPEG file or whatever..."

The housekeeper arrives to cart kdenton off to bed.

The housekeeper arrives to cart PeterMR off to bed.

TRex says, "How are the images (presumably generated with rasmol scripts) captured?"

JohnW says, "and secondly, producing scripts (lists of commands) which make RasMol produce an animated display (i.e. RasMol itself is the 'movie player')."

JohnW . o O ( I think my connection is now in intensive care )

TRex says, "I think your connection is OK John but others seem to be having troubles"

CrisCan my connection is extremely slow

JohnW [to TRex]: to create a series of images, you would indeed use scripts. You would alternate a movement command, such as 'rotate x' with the 'write "gif" <file>" command

Cathy finds his/her way in.

Johnr says, "Coming in good sequence here in USA via BBK"

Emartz says, "I'm here but it is minutes between lines from JohnW. Meanwhile I'm reading the transcript of the earlier BioMOO meeting."

Johnr Grins

Cathy says, "Hello everyone"

Johnr says, "Hullo Cathy"

TRex says, "I assume each of those 'rotate' commands would involve small movements so that the finished version was not jerky?"

TRex says, "Hi Cathy"

Lappe waves goodbye.

Lappe has disconnected.

ClareS hasn't experienced anything like it since Poznan

CrisCan says, "could be that spin command can considered as a rough animation?"

TRex smiles at ClareS

JohnW nods to TRex

JohnW adds that the 'write' command is followed by a format type then filename. The format type can be one of several image types, or indeed "script" to produce a text file with the necessary commands to produce the current image

JohnW [to CrisCan]: yes, thats right

JohnW says, "Last week Roger was explaining how RasMenu is simply a graphical front end to RasWin, and dynamically passes commands to it."

CrisCan says, "Johnw about this please i have not yet understand if using vers 2.6 I need rasmenu or no. May you tell me it?"

TRex says, "I find rasmenu doesn't interface to 2.6"

The housekeeper arrives to cart Lappe off to bed.

JohnW says, " I presume that when you type 'spin' in RasMenu, the program starts sending a series of 'rotate y' commands for example to RasWin. This principle is used in other methods to produce animations."

JohnW [to emartz]: Eric, if you can hear us ;) could you outline some of the developments in this second approach..i.e. using scripts to directly produce animations in RasMol?

CrisCan says, "I was able to install and use both, but i had problems using scripts, so I take off rasmenu, but in this case I am not more able to use spin"

JohnW says, "(which include the programs written by Andrew Coulson)"

Cathy says, "I have been using ver. 2.5. Can anyone tell me what the "stereo" in ver. 2.6 does for you?"

JohnW [to CrisCan]: No, you do not absolutely need RasMenu - RasWin should run correctly without it. In fact, RasMenu as far as I know exists only for Windows, not Macs or Unix

TRex says, "Cathy, I'm not sure about stereo - I haven't used it _ but I understand Roger has just released 2.6beta2 which has better stereo"

Emartz agrees, rasmenu works by Windows DDE under Visual Basic and there is no such in Mac or unix.

ClareS has disconnected.

CrisCan says, "yes but I have windows, in any case how can I use spin, that using rasmenu produces a small menu window?"

Emartz says, "I prefer RasMol scripts to e.g. MPEG movies of 'canned' GIF images. The latter seems to me to lose a great deal of the wonderful flexibility of RasMol scripts."

Emartz says, "One great feature of hand-created RasMol sci scripts is that they can be structured."

JohnW nods

JohnW [to emartz]: could you outline this structuring?

Emartz says, "That is, the top loe level script call calls a series of subscripts."

JohnW . o O ( beat me to it )

Emartz says, "This means you can easily omit a subscript or rearrange the sequence by hand-editing the top level script (a sim ple matter)."

Johnr jumps!

JohnW nods

TRex says, "So you can edit out a sub-routine by #?"

Johnr exclaims "well go on someone!"

JohnW says, "Presumably this means that over time we can build up a whole library of self-contained routines?"

Emartz says, "In my future dream-version of RasMol there will be a menua menu of chapters or sections of a script -- you'll be able to start the 'moveie' anywhere, and re-run sections at will."

Johnr says, "If only they were transferrable, "dumb" scripts!"

Emartz nods to JohnW

Emartz says, "Yes, you can make small scripts to spin ANY molecule, color ANY molecule in your favorite way, etc."

Emartz [to ]: Jou

JohnW says, "The possibilities are endless..."

ClareS has connected.

Emartz [to johnr]: We nee t need to distinguish between RasMol-created scripts (write script filename) and manually created scripts.

Emartz says, "Download one of my scripts to see how structured script-writing can be done."

JohnW is looking at one of Emartz's scripts

JohnW . o O ( I dont know about all of you but my connection has speeded up )

Cathy says, "Where can we get one of these scripts?"

Emartz says, "So, Johnr, by simply omitting the "load whatever.pdb" command, the script will apply to the molecule currently in the graphics window (e.g. loaded from the File, Open menu)"

Emartz says, "Scripts (and everyghing else I know about) are at"

JohnW says, "at"

Emartz thanks JohnW for pointing out the exact htm file.

Emartz says, "There are also a couple of examples of a script intnended to apply to any molecule in the RasMol email list history. Search for 'user color'."

TRex says, "Cathy, have alook at io/rasmol/"

Emartz says, "The RasMol email list hoistory i s also accessible at my web site."

Emartz says, "BTW, please don't save the address -- that is a machine-dependent address guaranteed to change."

JohnW says, "Could I just ask about the difference between manually-generated scripts and those auto-generated by RasMol:"

Emartz says, "Instead, use That address will always work."

Emartz says, "(At the moment, is what point s to, but that will change at some point in the future."

TRex says, "Oh. Thanks Eric"

Emartz says, "A manually generated script is a plain-text file of RasMol commands. It may contain 'refresh' and 'pause' commands which update the image and wait for a keystroke respectively."

Emartz says, "The 'pause' and 'refresh' commands give RasMol enormous movie-making power."

Emartz says, "A RasMol-generated script is made by issueing the command 'write script filename'."

JohnW says, "The auto-generated ones are much longer, and appear to change the structure atom-by-atom, even if the current display was generated by 'macro'-type commands such as 'select helix' etc. Why is this necessary?"

Emartz says, "RasMol-generated scripts are intended for one simple purpose: to regenerate the esxact image present t at the time the write script command was issued. "

ClareS says, "are there any quick ways of generating rasmol scripts by hand?"

Emartz says, "RasMol-generated scripts have limited uses. ONe of the best is to report (by writing it into the script) the rotation, zoom and translation commands needed to get to the current image. These can be hand-edited into a manyally-created script."

Cathy says, "Eric, could you go over the changes in the latest version of Rasmol, when you get a chance?"

Emartz says, "RasMol-generated scripts are indeed very long and in turn take a VERY long time to load and display in RasMol. Andrew Coulson's movie interface uses them a lot and hence in its present form suffers from these delays."

JohnW nods to emartz

JohnW says, "Yes, I have used the auto-scripts for that. Is that the only way of reporting the current orientation of the molecule?"

Emartz says, "It is the only way I know of to report how to get from 'reset' position to the current position. (reply to JohnW)"

JohnW thanks emartz

Emartz says, "Cathy, the main difference in 2.6-beta-2 is stereo. The enormous difference in 2.6-beta-1 was the addition of 'pause' and 'refresh', which made movie scripts possible."

JohnW says, "Surely if you start off with the 'reset' commands followed by those to turn off all renditions bar wireframe, followed by the commands you have actually typed in, will guarantee reproducing the display you currently see?"

Taekwon [guest] [to report]: (by writing it into the script) the rotation, zoom and translation

Taekwon [guest] [to report]: (by writing it into the script) the rotation, zoom and translation

Emartz says, "The complete lists of i differences between 2.5 and 2.6-beta are in .txt files provided by ""

Emartz says, "oops, provided by Roger Sayle and available on myweb site."

Emartz says, "Yes, JohnW, you're right. However, you may want to MOUSE your way to a good-looking image, and then the 'write script' method of reporting the simlplest command path to the current size and orientation is very hand.y."

Emartz says, "At present, the difficulty of writing RasMol scripts is a serious problem."

JohnW [to emartz]: Ah yes, of course... but I was thinking that the mouse movements plus any actions on the pull-down menus could be translated into a relatively concise version

Emartz says, "Several people, notably Andrew Coulson and Marco Molinaro (UCB-RasMOl) are working on easy, push-button interfaces to create and save RasMol movie scripts, but none are available yet to my knowledge."

JohnW nods

Paulyta finds his/her way in.

JohnW says, "So at the moment, its still a sort of DIY approach"

Emartz says, "I keep thinking I should write a guide to RasMol script-writing. Maybe later this summer (winter to youse guys down under)."

Emartz nods

TRex grins, and thinks it would be a good idea for Eric to spend his summer this way;)

Paulyta had network problems

Cathy says, "Eric, I am a complete novice, but I wouldn't mind assisting in such an effort."

Emartz says, "H You can see one way of structuring scripts by looking at mine, but you can't necessarily see how I got there (that's why a manual is needed)"

JohnW says, "I would recommend anyone to try writing some simple rasmol scripts- with a few basic commands its possible to get some very nice results"

Emartz makes a note of Cathy having volunteered.

TRex agrees with JohnW - practice is a good teacher

JohnW says, " Roger demonstrated here last week"

Emartz says, "Thanks, Cathy, I'll dee keep that in mind."

JohnW says, "has anyone tried any of the scripts in the current PPS material? Any comments?"

JohnW says, "(be brutally honest)"

Taekwon [guest] has disconnected.

The housekeeper arrives to remove taekwon [guest].

TRex raises his hand

ClareS has disconnected.

Paulyta raises his hand

CrisCan says, "I tried, even I need to change extension .ras to .txt"

TRex says, "A few, but some problems with hangups"

JensJL has disconnected.

JohnW says, "Personally I think some of those scripts would benefit from some pause commands, but hopefully by listing some of the commands it also acts as a sort of rasmol tutorial"

JohnW [to TRex]: go on

Emartz says, "Eric agrees with JohnW and TRex -- a script of only a few lines can do amazing things. Good to try it out!"

Cathy says, "I tried the scripts in the Assessed Assignment. They gave me some guidance as to the capabilities of rasmol. "

ClareS has connected.

JohnW [to paulyta]: lets have it!

TRex says, "One of the scipts in the helix-helix packing page, dealing with highlighting ridges, caused an 'application error' in 2.6beta1 on NT"

ClareS [to JohnW]: have what?.. just lost the connection

JohnW frowns

JohnW [to Trex..]: ok, could you let me know which one?

JohnW [to ClareS]: I asked for comments on the PPS scripts, and some hands were raised..

Emartz says, "TRex, is it reproducible?"

TRex says, "Yes John. I'll check it again and get back to you"

TRex says, "I'll keep you informed too, Eric"

JohnW thanks Trex

JohnW says, "I have noticed some apparent differences between RasMol 2.6 on different platforms. E.g. the SGI version knows what 'brown' means, but the Win one doesnt!"

Emartz says, "The only script-induced crash I've seen was the result of zooming to too large a size (Roger figured that out). reducing the zoom size avoided the crash. I believe my case concerned a very fat hydrogen bond."

Emartz says, "Correction: it wasn't zooming, it was something like 'hbonds 300'."

CrisCan waves to everyone

CrisCan has disconnected.

JohnW waves back to CrisCan

Cathy says, "I don't want to keep changing the subject, so could someone tell me whether we have an agenda for this meeting?"

HenryR has disconnected.

The housekeeper arrives to cart JensJL off to bed.

Emartz says, "In case it hasn't been mentioned, you can make any color you want. Brown would be something like [100,100,0] for the RGB (red green blue) intensities."

JohnW [to Cathy]: The agenda is "Making movies with RasMol". This includes issues concerning making scripts, as this is the principla method.

JohnW thanks emartz for the info

JohnW [to paulyta]: you raised your hand a while back... did you have a comment re the scripts in the material?

Cathy says, "Bye now"

Cathy has disconnected.

Paulyta says, ""they worked for me for the most part without any trouble"

JohnW nods

TRex says, "I have just re-run those two scripts 9_hel_1 and _2 without problems. May have been a temporary glitch before"

Henryb says, "Thanks for the info on scripts Eric. I've been quiet because I have been busy downloading your scripts and will try them out tomorrow. Must go now. Thanks for another very useful rasmol tutorial. I hope the tape recorder is still running and I can pick up on other information tomorrow. Bye everybody"

JohnW nods to Trex

Henryb has disconnected.

JohnW says, "Well, if anyone does spot any problems with the PPS scripts, please let us know.. and any comments on them are more than welcome"

JohnW says, "Yes, I am still logging this meeting even tho its not being taped by a BioMOO recorder"

JohnW says, "But I think we ought to wrap it up now."

TRex says, "Eric, do you mind me experimenting with modifications to your scripts?"

The housekeeper arrives to cart CrisCan off to bed.

ClareS [to JohnW]: Could you send me the log, please? The connection was so bad that I missed quite a lot of the session

Emartz says, "TRex, I'd love for people to modify/expand/improve my scripts. I only hope they will then send them back to me so all versions can be made available on the web."

The housekeeper arrives to cart HenryR off to bed.

TRex says, "Absoulutely - I'm not sure they will be an improvement though!"

TRex says, "Many thanks for your time and help"

Emartz says, "In case it hasn't been mentioned, Andrew Coulson has written a very useful text tutorial which walks beginners thru RasMol's capabilities using specified molecules. The tutorial and molecules are (you guessed it) on my web site, under 'classroom' stuff."

JohnW says, "I would like to thank Eric Martz for coming to todays meeting at short notice...this was his first day in the BioMOO and I think he did great, especially with the technical hitches today..."

The housekeeper arrives to cart Cathy off to bed.

ClareS says, "It was great, Eric, thanks - and it's not *always* this slow..."

JohnW says, "Eric, thanks for all the insights, this session was really useful"

JohnW agrees with ClareS

Emartz says, "It was a great pleasure to attend, JohnW, especially after the response time improved."

TRex three cheers

Johnr claps enthusiastically

HorstJS says, "thank you very much for this interesting session!! :-)"

PeteO thanks Eric and waves

Emartz waves to all

Paulyta claps

JohnW says, "Yes, it has certainly speeded up as the meeting progressed. Many thanks for bearing with us during the treacly part"

JohnW applauds

Emartz says, "It was a delight to meet some of you and I hope we can stay in touhch. And that my spelling improves."

The housekeeper arrives to cart henryb off to bed.

TRex grins

TRex says, "I'll get on to your discusion list"

Emartz wanders off to get a bite to eat.

TRex says, "Bye all"

Johnr says, "Better to have spelt and erred...""

PeteO has disconnected.

Emartz grins (hungrily)

TRex groans

Johnr has disconnected.

TRex has disconnected.

Emartz finds his way out.

JohnW [to emartz..]: AND you were using telnet...I'm impressed. On that note, Henry Rzepa had problems using the MUDDweller client, as it seemed not to support Open Transport 1.1, which he was using... if anyone has any advice, please e-mail

JohnW says, "But now, its time to go...thanks again to all of you for your patience..see you later"

JohnW switches off the virtual virtual recorder.