Wikipedia talk:WikiProject Chemistry/Structure drawing workgroup/Archive Apr 2007

message: Just to kick things off, I'll post a few comments.
# I have tried the ChemDraw settings suggested in the style guide and found that the images are huge.  The settings can be used for drawing a single structure of a small molecule, but even there I find the font ratio poor in many cases.
# I think for general article info we may want to emulate books (such as Wade, Carey, etc) rather than journal settings.  In other words, larger images, use of colour to explain points.  For more advanced topics and structures involving more complex molecules, we should use one of the journal settings such as ACS or RSC.  For a previous discussion along these lines see this and the related article at Aldol_reaction. (This article highlights another issue, how to include pictures and drawings side by side!)
# It is regarded as good practice to create pictures larger than they are typically used in our articles.  However, this creates problems. How can we make all settings on the screen the same (say, ACS) style, if this one is scaled differently from that one?  Also, for small settings like ACS the atom labels are large in comparison to the bond length for clarity, whereas for larger book-style settings the atom labels are comparitively smaller - so how will these things scale if people use the same image at different sizes?
# Whatever settings we choose, we should make it easy for new people to put those settings into their molecule editor, whatever they use.  Many contributors don't have ChemDraw and are restricted to a variety of freeware. 
Comments, anyone? Walkerma 06:31, 9 April 2006 (UTC)
replies: text: Chemdraw and Chemsketch (and probably other programs too) allow to save drawing settings as a template. Ideally, the program used to draw structures should be irrelevant as long as we come up with a set of templates for each one and make them easily available to editors. -- Rune Welsh | ταλκ 14:10, 9 April 2006 (UTC)
thread_title:  2D drawing settings on molecule editors 

message: The ISIS version is free for private use, but I do not know if Wikipedia is included with this licence. If yes, a free program would be a good thing - then everybody can download and draw images. --Stone 10:49, 9 April 2006 (UTC)
replies: text: Another free program that anyone should be able to get access to is ChemSketch, but I'm not very familiar with its capabilities or suitablity for creating optimal images for Wikipedia. --Ed (Edgar181) 15:42, 9 April 2006 (UTC)
thread_title:  Chemdraw vs ISIS vs ChemSketch

message: After my persistent harrassing of the poor folks who so generously give their time answering dumb questions from technically challenged people like me, I got a clear answer:
:"The size (in bytes) of a thumbnail image does not depend on the size (in bytes, or in pixels) of the original full-size image.  Period.  The only exceptions are if
:#the thumbnail would be bigger (in pixels) or the same size as the original, or
:#the original image is so huge (something like over 10000 pixels across) that the MediaWiki image resizing code can't handle it."
So we can make and upload images pretty much as big as we want.  But how big do we want them to be?  Please add to the discussion above. Walkerma 05:07, 14 April 2006 (UTC)
thread_title:  Word from the Village Pump 

message: I will take silence to mean that consensus has been reached on using ACS settings for structure drawing.  I (or one of you) will update the style guide accordingly soon (I have a lab to go to now!). If you have any problems with using ACS settings, please post something on this page so we can fix it.
What should we do for the next phase?  I wonder if we should focus our attentions on laying down standards for 3D drawings.  For this we need to bring in the Jmol group.  Our focus will be on settings (colours, lengths etc.) rather than implementation.  For myself, I'd be happy to see the Jmol folks give us their suggestions, and let us discuss how this fits with other 3D formats.  But I know very little about 3D images, I rarely use them.  Thoughts, anyone? Walkerma 16:47, 27 April 2006 (UTC)
replies: text: I am not an expert on Jmol although I have put Jmol images into several web pages. I think we just have to see how it goes. Some things such as colours are fixed in the Jmol applet. If we do not like them, we discuss it on the Jmol e-mail list and get changes to the applet. That would flow through to what we do here once we install the new version of Jmol on the WP server. We need to also detemine the data file types allowed. On the Jmol wiki, only *.cml, *.pdb and *.xyz are allowed. --Bduke 21:47, 27 April 2006 (UTC)

text: Colours are not really fixed in the Jmol applet: all colours can be changed through script commands. A default script can be defined when installing the Jmol extension: it could be used to apply coherent settings (if more features like this are needed, tell me and I will add them). If you want to upload data files with the "upload file" feature of MediaWiki, you will need to decide which extensions are allowed. If you want to put data in wiki pages, deciding which extensions are allowed is not required but should still be done to ensure coherence. NicoV 16:29, 28 April 2006 (UTC)
thread_title:  Next phase 

message: Hello everyone, just dropping in as an outsider here. On Phenol red you'll see a nice chemsketch-produced diagram showing how the structure changes with increasing pH. I think the minus at the sulfate's oxygen is too small and could easily be mistaken for a dot, indicating a lone electron. (For a chemist such an unpaired electron would obviously not make any sense there, but lots of our readers are half-educated like me.) In the original-sized picture the problem is not as severe as in the scaled down version actually shown on the page. 
So I'd like to respectfully submit that the powers-that-be consider increasing the fonts of the drawing software when it comes to minus-subscripts. 
Best regards, AxelBoldt 17:17, 2 October 2006 (UTC)
replies: text: Good point.  I usually change them to Symbol font, that does the same thing.  Of course if the software producers had any sense it would be automatic...! Walkerma 19:33, 2 October 2006 (UTC)
replies: text: It is possible to set charge font style to Symbol, and this should provide an easy automatic solution. It is generally not advisable for software producers to break font standards by creating exceptions. An exception which is good for one person may easily be considered bad for others. In the interest of promoting consistency, consider choosing an appropriate font type that can be consistently applied without requiring exception rules. Michel Hachey 21:31, 11 October 2007 (UTC)
thread_title: Minus superscript is too small

message: I have successfully created SVG structures buy creating a structure in ChemDraw, saving as .wmf and then converting to .svg using SVG factory, and then making some small change to the .svg file, which I describe bellow.
Image:-7-circulene.svg|[7]circulene 
Image:-6-helicene.svg|[6]helicene
Image:B-Farnesene.svg|β-farnesene
Image:A-Farnesene.svg|α-farnesene
The svg files that SVG Factory does not have the svg name space in the file. This need to be manually inserted into your file. the top of your file should look something like the following (inserted text in bold)
 <?xml version="1.0" encoding="iso-8859-1"?>
 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20000303 Stylable//EN"
 "http://www.w3.org/TR/2000/03/WD-SVG-20000303/DTD/svg-20000303-stylable.dtd">
 
 <svg xmlns="http://www.w3.org/2000/svg"  width="3.0000in" height="2.9221in" viewBox="0 0 231 225">
I will investigate why the text problem is happening tomorrow.
Gary van der Merwe (Talk) 21:32, 9 November 2006 (UTC)
thread_title:  SVG with SVG Factory 

message: Hi,
many of you, who are using incscape to create SVGs of chemical formulas will have noticed that subscript and other baseline elements are not correctly rendered by MediaWiki software. There exists an appropriate bug report on Mediazilla, but there are still not enough votes to get any attention for this issue. As user on German Wikipedia I just wanted to ask you to vote for this bug, so that we don't need categories like this any more. Thanks. --TaxmandeTalk (de) 12:28, 26 February 2007 (UTC)
thread_title:  Mediawiki SVG Bug 

message: I have updated Wikipedia:WikiProject Chemistry/Structure drawing, please have a look at it. Cacycle 02:55, 21 March 2007 (UTC)
replies: text: Looks good!  I just need to write up the IsisDraw stuff now.... Thanks, Walkerma 04:23, 21 March 2007 (UTC)
thread_title:  [[Wikipedia:WikiProject Chemistry/Structure drawing]] overhaul 

message: I've notice that the numbering of R-groups is often given in subscript by editors e.g. .
I think it is more clear to give this numbering in superscript. e.g. 
Subscript is usually used to indicate the number of substituents (e.g. -NR2, might be misinterpreted to mean a Nitrogen attached to two R groups). By using superscript, any possible confusion is avoided (i.e. -NR2 means a -R2 group attached to Nitrogen. -- Quantockgoblin 00:46, 21 March 2007 (UTC)
replies: text: Yes, superscripts get my vote every time on this. It annoys the heck out of me when I see subscripts used in JOC! I know that in some molecule editors it tends to spit out subscripts as defaults, but is there any reason we can't state that we want superscripts for cases like this? Walkerma 03:09, 24 March 2007 (UTC)
replies: text:  We should outlaw subscripts :-) I'll add it to Wikipedia:WikiProject Chemistry/Structure drawing. Cacycle 03:14, 24 March 2007 (UTC)
thread_title: R-Groups numbering