Unfortunately MoleculeSketch has no feature to automatically add numbering labels to atoms yet. If you want to label the atoms in a molecule with numbers you have to do it manually.
Hi – how do I add deuterium? I want to create CD3 groups and also does the software calculate the correct molecular mass when H are substituted for D? Thanks!
Thank you for your question.
To add deuterium atoms just draw the molecule with hydrogen atoms. Then double-click on the hydrogen atoms. In the text box change H to D.
Unfortunately the automatic mass calculation does not work with isotopes. Nevertheless, I have put your suggestion on the list for future updates.
Hi! I’ve been loving the app but is there any way I can save my files as .cdx, .sdf, or .mol file formats? If not, I’ll look forward to new file formats in the next upgrade 🙂
It seems that you have a corrupt file. Try to copy everything (command-a), open a new file and paste it there. Save the new file with a different name. Close/delete the old file.
I hope this works.
Hello,
With the macOS version of MoleculeSketch you can export your drawings as pdf-file. You can then import the pdf-File into a vector drawing app if you wish. When you copy-paste a MolekuleSketch drawing into Word or other apps that are able to handle pdf-data, the drawings will be resizable without loosing quality. Unfortunately this is not possible with the iPad version.
Hi,
I was loving the program until now I find it says it can’t open saved files in MSF format, but that is the format it saved them in!!
Am I doing something wrong?
Thanks
James
Horizontal and vertical mirrors do nothing on my Mac. I can’t find the “flip” button and Help doesn’t help
While I am here, how do I draw NH4+ with brackets. Brackets don’t work but suddenly they do… what did I do? How do I add the 4th H without the + sign coming between the N and H?
It has taken me several hours to get to the point where I can use the app for simple molecules but I am doing it in a way which does not appear to be described in your explanations. I could give you more details if you wish.
Is there a helpline online?
You find the two flip buttons in the toolbar right next to the selection tool (two triangles with a dashed line in-between).
In order to see an effect when mirroring something horizontally or vertically you first need to select a (asymmetrical) molecule or more than one object.
You can add brackets with the bracket tool from the menu bar. Just choose the type of bracket you need by clicking on the button (more options show up when clicking on the blue arrow beneath the bracket button or just by clicking several times on the bracket button). To draw the bracket click and drag on the drawing canvas. You can adjust the bracket shape with control points with the selection tool by clicking once on the bracket.
NH4+ can be drawn by adding a single nitrogen-atom and right-clicking on it. In the attributes panel increase the charge and check „show H atoms“ (if you do it the other way around the hydrogen atoms disappear when increasing the charge. In this case just uncheck and check to „show H atoms“ again. That is obviously a bug! *damn*)
MoleculeSketch does not automatically support the placement of a charge between the atom symbol and displayed H atoms.
Nevertheless you can accomplish this by transforming the N atom into a functional group. You can do this as follows:
add a N atom and then double click on it. In the textfield add following text „N+H4“. Format the + as superscript and 4 as subscript. Unfortunately the charge will not be recognised in this situation.
When developing MoleculeSketch I tried to implement drawing routines which are also found in other common molecule drawing apps and following my own intuition how I would want to use my app, which by the way I regularly do!
If MoleculeSketch is you first molecule drawing app you may not be familiar with those workflows. But hopefully you will find out how to do it by trying out.
As this app is a personal project I do not have the resources to produce more help topics, video tutorials or manage an online helpline, sorry. But as you did, just post your questions or send them by email. I will try to answer you as quick as possible.
Stefan
Thank you for using MoleculeSketch. I am sorry, that you have encountered some difficulties using the app.
If you are using MoleculeSketch on your mac please have a look at the help that can be accessed from the menu bar. Allmost all features are explained there.
If you are working on the iPad you will find a help button either in the file browser view (with the i-Icon) or in the preference panel (three dots on the top right corner) when in drawing mode. A few short videos will explain you the most basic functions there.
You can also access help from the MoleculeSketch homepage: https://moleculesketch.stefandolder.ch/mac-version-2-1-en/help-documentation/ (although not the most updated version of it)
Unfortunately I have no time to produce video tutorials at the moment as I am developing the app in my spare time, which is really spare at the moment…
I am sorry, that you cannot open MoleculeSketch on macOS Sierra anymore. The current version should work with macOS Sierra. Do you have crash-logs? Did you reinstall it from the AppStore?
Moleculesketch would be the best app for drawing structures using IPAD. I have used all chemistry drawing apps (iOS) available but I keep only this one. However, I do not know how to add subscripts when adding chemicals as formula such as KMnO4. Thank you.
Hello,
Thank you for your feedback. I am glad to here that you like to work with MoleculeSketch.
Concerning your question: if you add a formula as text (“abc” button in menu bar), just double-tap on the text. You will then be presented with a textfield, the text will be highlighted and a context menu appears. Adjust the selection (this may be a bit fiddly. On iPadOS 14: tap into the blue region and drag) and change the format to subscript (x2 button in context menu). If the context menu disappears tap again on the selection. More formatting options are available when tapping on the button “Format” from the context menu. I hope this helps.
If you have more questions or suggestions, just write again.
Hello Stefan,
I’m happy about my purchase, because your software is pretty cheap, BUT I really can’t understand why you didn’t put any shortcut to switch between elements, and to switch between selection tool and bond tool, or arrow tool. I really can’t get to a decent workflow because I have to click here and there every second. I really think you should add this feature, and this should not be hard to do. I also find frustrating that panning with two fingers can’t go outside the border, the only way I can move to the right empty space of the molecule is to zoom out and them zoom in to the right.
I also found a bug, that close the software when pressing CMD+Z to delete the last action. This happens one time per file, the first time I use the CMD+Z function.
Dear Diego,
Thank you for your comments and suggestions. I am always happy to hear about ideas for improvements. I am aware that my app may not be yet improved for a flawless workflow. As self-taught indie developer some features are sometimes much harder or time consuming to implement then I thought. Nevertheless I will surely consider your feedback for future updates.
Concerning the bug, I will definitely have to look into it!
Thank you for the positive feedback.
The problem that you have when exporting, seems to be a bug. I tried to reproduce the bug, but was not able to do so.
Do you have more information when or how exactly this is happening? To which file format are you exporting? Do you use the latest app version (on macOS 2.0 and on iOS 1.0.1)? Do you use the mac or iPad version of the moleculeSketch?
Hopefully I will be able to solve this export bug soon.
Hi, I’m having big problems with the new version on my mac. When I paste from one file to another the pasted items only partially appear and then when I try to save I get amessage that the model configuration used to open the store is incompatible with the one used to create the store. I cannot then save the documents.
Stephen
I am sorry to read, that you have some problems with the new version of MoleculeSketch.
I tried to repeat the copy/paste problems that you described in your message. Unfortunately I was not able to reproduce the same errors you found.
From what you wrote, it seems that there is some mismatch with the new and old program version. When you open a file that has been saved with MoleculeSketch prior to version 2.0 you should get a message, that the file has been converted. If not please check, if the file has really been opened in the new program version. You can check this by clicking on MoleculeSketch in the menu bar next to the Apple Logo and then choosing „About MoleculeSketch“. In the appearing Window the current version number 2.0 (43) should be displayed. If not, it seems as if the program has not been updated or as if the old version of MoleculeSketch is still present. In this case try to locate and delete the program in your Applications folder or redownload it from the AppStore.
If this does not help, could you please send me more information about how the error occurs or even a file that produces these problems.
Hi Stefan,
I think this is a great app but I still have some problems trying to figure out some minor details.
In the pictures you see in the App Store, there apear equations with subscripts and superscripts.
How do I insert them in the textbars?
Also, it would be nice to have a little more liberty with changing colors.
Apart from that, I think it’s all good.
To insert sub- or superscripts in textboxes, just choose the text button (“abc”) in the menubar and click in a textbox or double click in a textbox with the selection tool (crossed arrows), then select the text you want to format and right-click on the selection to reveal the context menu. From there you can choose different format styles or change the font of the selected text.
Element labels can also be formatted. Just double click on an atom label and type into the appearing textbox. There are special markup commands that can be used to format the label. You can find more information about this in the Help section “Editing atoms, adding functional groups”. I hope to find some time soon to develop a more intuitive UI implementation for the label formatting.
Hi Stefan I downloaded your programme and it is really quite useful, but is there a possibility to convert the msf file into another one for example xcd?
Thanks
Sincerely Emilia
Unfortunately it is not possible to convert the msf files into other formats. But I will put it onto the to-do list!
Sorry for the inconvenience.
Sincerely, Stefan
Hi Stefan, I too find this to be an excellent program. I have a collaborator who uses Chemdraw. Is there anyway to read these files with Chemdraw and vice versa.
Thanks, Stephen
Thank you for your positive feedback. Import and export capabilities of MoleculeSketch are unfortunately a bit restricted. You can import files in the MDL mol format (V2000). Chemdraw may be able to export to this file format. MoleculeSketch on the other hand has no export function (yet).
Hi Stefan,
I’m having a very, very hard time figuring out how to use this program unfortunately! Like, if I want to create N2, how do I do that? Is there a shortcut way to add elements other than selecting them with the mouse up in the toolbar? Do you have videos explaining how to use molecule sketch? I have been through the support documentation, and haven’t had much luck learning how to use the program :/ It looks like the functionality is great though and I really want to learn to use it!
Hi Matt,
I am sorry, that the use of MoleculeSketch is not as intuitive as it should be. I am developing this app on my own and do not have a lot of time in my spare time to work on tutorials and how-tos. At the moment all my effort is focused on developing an iPad version of MoleculeSketch, which will hopefully be finished soon…
To answer your troubles:
– to draw a N2 just choose the nitrogen atom in the toolbar and click in the drawing area. Then double click on the atom symbol. You can edit the symbol now. Just click after the “N” and type a “2”. When you click somewhere else in the drawing area you should get N2 (with correct subscript).
– any atom in your structures can be edited by double clicking. You can even type complex functional groups using special formating commands, that are described in the second chapter of help under “editing atoms, adding functional groups”. If you want to add greek letters, just type the characters in latin letters, mark them and right click over the selected text. You will find an option “convert to greek characters” in context menu.
I hope this will help you. If you have more questions, just ask.
Sincerely
Stefan
Hi Stefan, just bought your program and I really like it.
My needs are simple – get structures, formulas and reactions into an article, and your app delivers.
I have one wish though, the ability to export the selection to png, jpg.
Thank you for the positiv feedback! I will take the possibility to directly export to png/jpg on the wish list for future improvements. In the mean time it is not too complicated to get a png or jpg of a MoleculeSketch structure. Just copy the structure and paste it in the standard macOS Preview App (in Preview App choose Edit in the menu bar an copy from pasteboard). You can then do whatever you like.
Structure can also be pasted in any other (office) programs that support pdfs. This has the advantage, that you can scale the structure without loosing quality.
Thanks for making this app! Any chance that the ability to generate the name of a molecule could be added in the future? I’m a high school teacher and am using this to help make worksheets and practice problems in organic chemistry.
Hi,
Thanks for your great feedback. I am a chemistry teacher too and it’s good to hear that my program seems to be useful. I have already thought about a name generator, but it’s not on top of my list of new features for MoleculeSketch. Mostly because I think, that it’s not an easy task to program. Anyway, I will keep it on the wish list. Just let me know, if you have other suggestions.
Stefan
41 Responses
Tommy
Hi,
I’m not sure if the app allows us to do atom numbering (for carbon and hydrogen)
Stefan
Unfortunately MoleculeSketch has no feature to automatically add numbering labels to atoms yet. If you want to label the atoms in a molecule with numbers you have to do it manually.
Stefan
Hi – how do I add deuterium? I want to create CD3 groups and also does the software calculate the correct molecular mass when H are substituted for D? Thanks!
Stefan
Thank you for your question.
To add deuterium atoms just draw the molecule with hydrogen atoms. Then double-click on the hydrogen atoms. In the text box change H to D.
Unfortunately the automatic mass calculation does not work with isotopes. Nevertheless, I have put your suggestion on the list for future updates.
Shaira
Hi! I’ve been loving the app but is there any way I can save my files as .cdx, .sdf, or .mol file formats? If not, I’ll look forward to new file formats in the next upgrade 🙂
Stefan
Unfortunately it is not possible to save the files in other file formats yet. Sorry!
Muse
When I try to save the file it says “The document could not be autosaved, could not merge changes”. What can I do to save my file?
Stefan
It seems that you have a corrupt file. Try to copy everything (command-a), open a new file and paste it there. Save the new file with a different name. Close/delete the old file.
I hope this works.
jf
I looking how to save or export in any vectoriel format , is absolutly necessay to have this option to print in good quality
Stefan
Hello,
With the macOS version of MoleculeSketch you can export your drawings as pdf-file. You can then import the pdf-File into a vector drawing app if you wish. When you copy-paste a MolekuleSketch drawing into Word or other apps that are able to handle pdf-data, the drawings will be resizable without loosing quality. Unfortunately this is not possible with the iPad version.
James
Hi,
I was loving the program until now I find it says it can’t open saved files in MSF format, but that is the format it saved them in!!
Am I doing something wrong?
Thanks
James
Anna
Hello, how to draw loads or partial loads please?
Geoff Weston
Horizontal and vertical mirrors do nothing on my Mac. I can’t find the “flip” button and Help doesn’t help
While I am here, how do I draw NH4+ with brackets. Brackets don’t work but suddenly they do… what did I do? How do I add the 4th H without the + sign coming between the N and H?
It has taken me several hours to get to the point where I can use the app for simple molecules but I am doing it in a way which does not appear to be described in your explanations. I could give you more details if you wish.
Is there a helpline online?
Stefan
You find the two flip buttons in the toolbar right next to the selection tool (two triangles with a dashed line in-between).
In order to see an effect when mirroring something horizontally or vertically you first need to select a (asymmetrical) molecule or more than one object.
You can add brackets with the bracket tool from the menu bar. Just choose the type of bracket you need by clicking on the button (more options show up when clicking on the blue arrow beneath the bracket button or just by clicking several times on the bracket button). To draw the bracket click and drag on the drawing canvas. You can adjust the bracket shape with control points with the selection tool by clicking once on the bracket.
NH4+ can be drawn by adding a single nitrogen-atom and right-clicking on it. In the attributes panel increase the charge and check „show H atoms“ (if you do it the other way around the hydrogen atoms disappear when increasing the charge. In this case just uncheck and check to „show H atoms“ again. That is obviously a bug! *damn*)
MoleculeSketch does not automatically support the placement of a charge between the atom symbol and displayed H atoms.
Nevertheless you can accomplish this by transforming the N atom into a functional group. You can do this as follows:
add a N atom and then double click on it. In the textfield add following text „N+H4“. Format the + as superscript and 4 as subscript. Unfortunately the charge will not be recognised in this situation.
When developing MoleculeSketch I tried to implement drawing routines which are also found in other common molecule drawing apps and following my own intuition how I would want to use my app, which by the way I regularly do!
If MoleculeSketch is you first molecule drawing app you may not be familiar with those workflows. But hopefully you will find out how to do it by trying out.
As this app is a personal project I do not have the resources to produce more help topics, video tutorials or manage an online helpline, sorry. But as you did, just post your questions or send them by email. I will try to answer you as quick as possible.
Stefan
Geoffrey Weston
Is there a video showing how to use Molecule Sketch? Try as I might I am getting nowhere.
Stefan
Thank you for using MoleculeSketch. I am sorry, that you have encountered some difficulties using the app.
If you are using MoleculeSketch on your mac please have a look at the help that can be accessed from the menu bar. Allmost all features are explained there.
If you are working on the iPad you will find a help button either in the file browser view (with the i-Icon) or in the preference panel (three dots on the top right corner) when in drawing mode. A few short videos will explain you the most basic functions there.
You can also access help from the MoleculeSketch homepage: https://moleculesketch.stefandolder.ch/mac-version-2-1-en/help-documentation/ (although not the most updated version of it)
Unfortunately I have no time to produce video tutorials at the moment as I am developing the app in my spare time, which is really spare at the moment…
Anuar Gómez Tagle González
I’ve been using this app for year but with macOS Sierra I can’t open it… I use it almost everyday.
I’ve tried to reinstall it but nothing works. 🙁
Stefan
I am sorry, that you cannot open MoleculeSketch on macOS Sierra anymore. The current version should work with macOS Sierra. Do you have crash-logs? Did you reinstall it from the AppStore?
Organic Chemist
Moleculesketch would be the best app for drawing structures using IPAD. I have used all chemistry drawing apps (iOS) available but I keep only this one. However, I do not know how to add subscripts when adding chemicals as formula such as KMnO4. Thank you.
Stefan
Hello,
Thank you for your feedback. I am glad to here that you like to work with MoleculeSketch.
Concerning your question: if you add a formula as text (“abc” button in menu bar), just double-tap on the text. You will then be presented with a textfield, the text will be highlighted and a context menu appears. Adjust the selection (this may be a bit fiddly. On iPadOS 14: tap into the blue region and drag) and change the format to subscript (x2 button in context menu). If the context menu disappears tap again on the selection. More formatting options are available when tapping on the button “Format” from the context menu. I hope this helps.
If you have more questions or suggestions, just write again.
Diego
Hello Stefan,
I’m happy about my purchase, because your software is pretty cheap, BUT I really can’t understand why you didn’t put any shortcut to switch between elements, and to switch between selection tool and bond tool, or arrow tool. I really can’t get to a decent workflow because I have to click here and there every second. I really think you should add this feature, and this should not be hard to do. I also find frustrating that panning with two fingers can’t go outside the border, the only way I can move to the right empty space of the molecule is to zoom out and them zoom in to the right.
I also found a bug, that close the software when pressing CMD+Z to delete the last action. This happens one time per file, the first time I use the CMD+Z function.
Stefan
Dear Diego,
Thank you for your comments and suggestions. I am always happy to hear about ideas for improvements. I am aware that my app may not be yet improved for a flawless workflow. As self-taught indie developer some features are sometimes much harder or time consuming to implement then I thought. Nevertheless I will surely consider your feedback for future updates.
Concerning the bug, I will definitely have to look into it!
Stefan
Simon Dobbs
I love this program. However, the latest version crashes on opening. Please fix it, I need it.
Kadeshia
This is a wonderful app! I am only having one problem: When I go to export the backbone of my molecule disappears. Are there ways to circumvent this?
Stefan
Thank you for the positive feedback.
The problem that you have when exporting, seems to be a bug. I tried to reproduce the bug, but was not able to do so.
Do you have more information when or how exactly this is happening? To which file format are you exporting? Do you use the latest app version (on macOS 2.0 and on iOS 1.0.1)? Do you use the mac or iPad version of the moleculeSketch?
Hopefully I will be able to solve this export bug soon.
Stefan
Stephen
Hi, I’m having big problems with the new version on my mac. When I paste from one file to another the pasted items only partially appear and then when I try to save I get amessage that the model configuration used to open the store is incompatible with the one used to create the store. I cannot then save the documents.
Stephen
Stefan
Dear Stephan,
I am sorry to read, that you have some problems with the new version of MoleculeSketch.
I tried to repeat the copy/paste problems that you described in your message. Unfortunately I was not able to reproduce the same errors you found.
From what you wrote, it seems that there is some mismatch with the new and old program version. When you open a file that has been saved with MoleculeSketch prior to version 2.0 you should get a message, that the file has been converted. If not please check, if the file has really been opened in the new program version. You can check this by clicking on MoleculeSketch in the menu bar next to the Apple Logo and then choosing „About MoleculeSketch“. In the appearing Window the current version number 2.0 (43) should be displayed. If not, it seems as if the program has not been updated or as if the old version of MoleculeSketch is still present. In this case try to locate and delete the program in your Applications folder or redownload it from the AppStore.
If this does not help, could you please send me more information about how the error occurs or even a file that produces these problems.
Stefan
Karl
Hi Stefan,
I think this is a great app but I still have some problems trying to figure out some minor details.
In the pictures you see in the App Store, there apear equations with subscripts and superscripts.
How do I insert them in the textbars?
Also, it would be nice to have a little more liberty with changing colors.
Apart from that, I think it’s all good.
Thank you for your time,
Karl
Stefan
Hi Karl,
To insert sub- or superscripts in textboxes, just choose the text button (“abc”) in the menubar and click in a textbox or double click in a textbox with the selection tool (crossed arrows), then select the text you want to format and right-click on the selection to reveal the context menu. From there you can choose different format styles or change the font of the selected text.
Element labels can also be formatted. Just double click on an atom label and type into the appearing textbox. There are special markup commands that can be used to format the label. You can find more information about this in the Help section “Editing atoms, adding functional groups”. I hope to find some time soon to develop a more intuitive UI implementation for the label formatting.
Sincerely
Stefan
Emilia
Hi Stefan I downloaded your programme and it is really quite useful, but is there a possibility to convert the msf file into another one for example xcd?
Thanks
Sincerely Emilia
Stefan
Hi Emilia,
Unfortunately it is not possible to convert the msf files into other formats. But I will put it onto the to-do list!
Sorry for the inconvenience.
Sincerely, Stefan
Stephen
Hi Stefan, I too find this to be an excellent program. I have a collaborator who uses Chemdraw. Is there anyway to read these files with Chemdraw and vice versa.
Thanks, Stephen
Stefan
Hi Stephen,
Thank you for your positive feedback. Import and export capabilities of MoleculeSketch are unfortunately a bit restricted. You can import files in the MDL mol format (V2000). Chemdraw may be able to export to this file format. MoleculeSketch on the other hand has no export function (yet).
Sincerly
Stefan
Matt
Hi Stefan,
I’m having a very, very hard time figuring out how to use this program unfortunately! Like, if I want to create N2, how do I do that? Is there a shortcut way to add elements other than selecting them with the mouse up in the toolbar? Do you have videos explaining how to use molecule sketch? I have been through the support documentation, and haven’t had much luck learning how to use the program :/ It looks like the functionality is great though and I really want to learn to use it!
Stefan
Hi Matt,
I am sorry, that the use of MoleculeSketch is not as intuitive as it should be. I am developing this app on my own and do not have a lot of time in my spare time to work on tutorials and how-tos. At the moment all my effort is focused on developing an iPad version of MoleculeSketch, which will hopefully be finished soon…
To answer your troubles:
– to draw a N2 just choose the nitrogen atom in the toolbar and click in the drawing area. Then double click on the atom symbol. You can edit the symbol now. Just click after the “N” and type a “2”. When you click somewhere else in the drawing area you should get N2 (with correct subscript).
– any atom in your structures can be edited by double clicking. You can even type complex functional groups using special formating commands, that are described in the second chapter of help under “editing atoms, adding functional groups”. If you want to add greek letters, just type the characters in latin letters, mark them and right click over the selected text. You will find an option “convert to greek characters” in context menu.
I hope this will help you. If you have more questions, just ask.
Sincerely
Stefan
Tor
Hi Stefan, just bought your program and I really like it.
My needs are simple – get structures, formulas and reactions into an article, and your app delivers.
I have one wish though, the ability to export the selection to png, jpg.
Keep up the good work!
Tor
Stefan
Hi Tor,
Thank you for the positiv feedback! I will take the possibility to directly export to png/jpg on the wish list for future improvements. In the mean time it is not too complicated to get a png or jpg of a MoleculeSketch structure. Just copy the structure and paste it in the standard macOS Preview App (in Preview App choose Edit in the menu bar an copy from pasteboard). You can then do whatever you like.
Structure can also be pasted in any other (office) programs that support pdfs. This has the advantage, that you can scale the structure without loosing quality.
Sincerely
Stefan
Tor
Thank you Stefan, good tips there.
Cheers, Tor
Ryan
Thanks for making this app! Any chance that the ability to generate the name of a molecule could be added in the future? I’m a high school teacher and am using this to help make worksheets and practice problems in organic chemistry.
Thanks again!
Ryan
Not that I can’t generate the names myself, it just saves time.
Stefan
Hi,
Thanks for your great feedback. I am a chemistry teacher too and it’s good to hear that my program seems to be useful. I have already thought about a name generator, but it’s not on top of my list of new features for MoleculeSketch. Mostly because I think, that it’s not an easy task to program. Anyway, I will keep it on the wish list. Just let me know, if you have other suggestions.
Stefan