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Re: [ccp4bb] Web site GOOD, Attachment BAD (was: salt sensitive complex) |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 31 January 2008Subject: Re: Web site GOOD, Attachment BAD (was: salt sensitive complex) From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL Date: 2008-01-31 bit color but 2-bit color (b/w) will do. I know how to do that in PhotoShop but not in Image Magick, although I am sure its trivial to do. And here some more preaching: Screen (eg Power Point): Do 400x400 pixels, 800x800 at most if full screen Submit paper: 1200x1200 is far enough to print fairly well in full page - most journals these days truncate to less to send to referees anyway. Dont use 32-bit color for line graphs, best is to submit these as eps! Accepted paper: use the formula (dpi journal recommends) x (final intended size in inches) to decide the size in pixels. ... sorry for the trivialties. Tassos On Jan 31, 2008, at 10:40, Clemens Vonrhein wrote: > To not only say what not to do, maybe also some tips on how to > convert/resize/scale images - for Linux with Imagemagick tools. > > * converting between formats (PNG seems something everyone is happy > with these days): > > % convert Image.jpg Image.png > > % ps2epsi Image.ps # gets rid of all the white border > # fluff > % convert Image.epsi Image.png > > * resizing (no need for a 3000x2000 image - 400x400 to 800x800 is > usually big enough I guess): > > % convert -resize 400x400 Image.jpg Image.png > > * cutting a bit out of an image (makes it easier to concentrate on > the important bit): > > % display Image.jpg > > -> left mouse click in image > -> Transform > -> Crop > -> left mouse and pan (is that the right word?) to mark > the rectangular region > -> Crop > -> File > -> Save (as Image.png) > > * screen shot of some picture/window/plot (to show error messages, > CCP4i input window etc etc) > > a) get e.g. your CCP4i loggraph window on screen > > b) open another terminal (make sure this terminal doesn't overlap > with the CCP4i loggraph window) and run > > % import test.png > > c) the mouse cursor should change to a "+" sign (kind of): just > click into the window you want to get a picture off - it will > be saved as test.png (control with "display test.png") > > Lots of other tools I guess. For more info on ImageMagick see e.g. > > http://www.imagemagick.org/script/index.php > http://www.imagemagick.org/Usage/ > > or > > % convert -help > > Clemens > > On Thu, Jan 31, 2008 at 08:58:04AM +0000, Frank von Delft wrote: >> Actually, it's not book keeping, it's simple courtesy -- and not >> only on >> a BB: an attachment is lazy, and a large attachment is downright >> rude. >> >> I am routinely stuck with a slow connection (travelling), and >> others are >> *permanently* stuck with one. So please be nice... ;) >> >> phx. >> >> >> >> Anastassis Perrakis wrote: >>> Dear all - >>> >>> Sorry to intervene on a 'book keeping' issue, but indeed over the >>> last >>> few months an increasing number of people (Jerry is not the >>> first, so >>> Jerry please do not take it personally) attach pictures etc. I think >>> in a bb standard practice dictates to only use text - if >>> illustrations >>> are needed to explain the problem, you can put them in eg a web >>> site. >>> >>> Some text like that was in the 'code of conduct' off ccp4bb in the >>> past, but I could no longer find it. >>> >>> Thus apologies if I am wrong and policies have changed, but maybe >>> the >>> ccp4 crowd could tell us what is the suggested policy. >>> >>> And, if you really want to send an image please do bother to make it >>> small. The initial posting had a 630k image, which it took me 1 >>> min to >>> make 20k and it still makes the point (attached so I can also >>> violate >>> the rules i am suggesting - I love inconsistency). >>> >>> Thanks, Tassos >>> >>> >>> >>> >>> On Jan 30, 2008, at 20:11, Jerry McCully wrote: >>> >>>> >>>> Dear All: >>>> >>>> Thanks a lot for the prompt reply on this topic of salt >>>> sensitive complex. >>>> >>>> Attached please find one ITC final figure done under 25mM >>>> Tris(pH8.0), 60mM NaCl. >>>> >>>> As mentioned before, the ionization of Tris will interfere >>>> with >>>> the ITC experiments. >>>> >>>> Therefore I am sure of my binding results. >>>> >>>> Can anyone give me some comments on this ITC experiment? >>>> Basically do these two proteins bind to each other? If so, how >>>> should >>>> I improve the ITC experiments to get a similar affinity shown by >>>> BIAcore(about 0.5uM)? >>>> >>>> Thanks again. >>>> >>>> Jerry >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ----- >>>> >>>> Hi Jerry, >>>> >>>> Tris can cause problems, you are better off using something like >>>> HEPES, and HEPES should be ok at pH 8. (Buffers with an >>>> ethane-sulphonic acid group tend to be the best - those >>>> ending in >>>> 'ES', so MES, TES and HEPES) >>>> >>>> FYI, the error on your K is bigger than the actual measurement - >>>> 1.49x10^5 ± 1.5x10^5. >>>> Signal to noise to is probably your enemy, which is making >>>> the curve >>>> fitting difficult. Changing buffer may help this - there may >>>> be some >>>> non-specific component to what you're seeing - increasing >>>> salt a bit >>>> or dropping in something like 5% glycerol may help with this. >>>> >>>> Would you be able to post a jpeg/pdf of the curve? >>>> >>>> Regards, >>>> >>>> David >>>> >>>> >>>> On 25/01/2008, Jerry McCully wrote: >>>>> >>>>> Dear All: >>>>> >>>>> Firstly I would like to thank many folks here for >>>>> giving me >>>> great >>>>> ideas several days ago. >>>>> >>>>> The following are some updates for this question. >>>>> >>>>> I did ITC experiments again using 25mMTris(pH8), 60mM NaCl >>>>> (low >>>> salt >>>>> condition). >>>>> >>>>> But things still turn out to be a little weird. >>>>> >>>>> I increased the concentration of both proteins(60uM in the >>>>> cell >>>> and >>>>> 1200uM in the syringe). At the end of the ITC, I saw a little of >>>>> precipitation of both the proteins. >>>>> >>>>> Fortunately I can roughly fit the curve this time. However, >>>>> the >>>> heat was >>>>> still low, around 1Kcal/mole of per injectant. I am not sure >>>>> about >>>> the >>>>> fitting statistics. >>>>> >>>>> >>>>> >>>>> N 1.10 ±0.17 >>>>> >>>>> K 1.49E5 ±1.5E5 >>>>> >>>>> DH -893.5 ±213 >>>>> >>>>> DS 20.7 >>>>> >>>>> Was the enthalpy was offset by the ionization of Tris buffer? >>>>> >>>>> Can I use Hepes buffer around pH8 to do ITC? >>>>> >>>>> >>>>> Welcome any comments about the statistics and suggestions on how >>>> to >>>>> improve the ITC experiments.have a nice weekend. >>>>> >>>>> Jerry >>>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ----- >>>> Helping your favorite cause is as easy as instant messaging. You >>>> IM, we give. Learn more. >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ----- >>>> Shed those extra pounds with MSN and The Biggest Loser! Learn more. >>>> >>>> >>> >> > > -- > > *************************************************************** > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * > * Global Phasing Ltd. > * Sheraton House, Castle Park > * Cambridge CB3 0AX, UK > *-------------------------------------------------------------- > * BUSTER Development Group (http://www.globalphasing.com) > *************************************************************** CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 31 January 2008 |
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