From: <ca...@mr...> - 2003-04-04 13:01:27
|
Hello fellow Pymol users! it sounds like I have the same objective as N. Sanishvili (25th Feb 2003) anyone told Nukri how you can ray-trace a stereo figure yet? I couldn't find a reply to the original question on stereo figs on the BB. I am also trying to label specific residues in my stereo figure. Older messages on the BB seem to imply this can't be done in pymol. Do you know if any progress has been made on this? Many thanks, Camille p.s. I'm running npymol on OS X. |
From: Scott C. <cl...@uc...> - 2003-04-05 00:20:52
|
If people want to see this example I can email it to you. Apparently the sourceforge list server will not accept messages longer than 40kb. Ciao, Scott > PyMOLers, > Here is a visual example of how to label a stereo figure so that the > labels appear at the proper depth when viewed in stereo. > > >> Now use a program like Illustrator or Canvas to add the stereo/depth >> cued labels. This is a little tricky to describe, but I'll give it my >> best shot. Place the two images side by side with their centers >> separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your >> labels on the LEFT figure. select all of your labels and duplicate >> them. Move the duplicated labels to the RIGHT side. For clarity sake >> let's assume we have 3 labels on the LEFT side (a,b, and c -- we will >> call then aL and aR for the left and right labels, respectively). >> Place aL near a recognizable feature of the LEFT figure that you are >> trying to label. Now horizontilly align aR with aL. Now using only >> the <-- and --> keys move the aR label until the identical portion of >> the actual label (let's say the lower right hand tip of the 'a') is >> vertically aligned with the identical portion of your model (let's >> say where the C alpha-C beta bond leaves the ribbon backbone) on both >> the LEFT and RIGHT images. Repeat these steps for each pair of >> labels. This is a nice method for adding stereo labels because it >> does not require looking at your computer screen in wall-eyed stereo >> for 2 hours in order to get proper placement of labels. >> >> By assuring that the labels are positioned in the LEFT and RIGHT >> images at positions that are identical with respect to the part of >> the model that is being labeled you automatically are also placing >> them so they are at the proper depth when the figure is finally >> viewed in stereo. ============================================== Scott Classen, Ph.D. cl...@uc... University of California, Berkeley Department of Molecular & Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ============================================== |
From: Scott C. <cl...@uc...> - 2003-04-04 18:01:18
|
Hello Camille, I will tell you how I make absolutely beautiful stereo figures in PyMOL (with Adobe illustrator too) with nicely depth cued labels. It takes a little more than clicking a single button, but it works well. create two PyMOL scripts of your view that are identical with all the beautiful ray tracing etc. then add: turn y, -3 to the first script and turn y, 3 to the second one make sure the png files exported from each script have different names (i.e. Left and Right) If you are working interactively with PyMOL then just remember to turn y, 6 and then re-ray trace and export a second PNG. Now use a program like Illustrator or Canvas to add the stereo/depth cued labels. This is a little tricky to describe, but I'll give it my best shot. Place the two images side by side with their centers separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on the LEFT figure. select all of your labels and duplicate them. Move the duplicated labels to the RIGHT side. For clarity sake let's assume we have 3 labels on the LEFT side (a,b, and c -- we will call then aL and aR for the left and right labels, respectively). Place aL near a recognizable feature of the LEFT figure that you are trying to label. Now horizontilly align aR with aL. Now using only the <-- and --> keys move the aR label until the identical portion of the actual label (let's say the lower right hand tip of the 'a') is vertically aligned with the identical portion of your model (let's say where the C alpha-C beta bond leaves the ribbon backbone) on both the LEFT and RIGHT images. Repeat these steps for each pair of labels. This is a nice method for adding stereo labels because it does not require looking at your computer screen in wall-eyed stereo for 2 hours in order to get proper placement of labels. By assuring that the labels are positioned in the LEFT and RIGHT images at positions that are identical with respect to the part of the model that is being labeled you automatically are also placing them so they are at the proper depth when the figure is finally viewed in stereo. I hope this makes sense. Just email if you want more details. Scott On Friday, April 4, 2003, at 05:56 AM, <ca...@mr...> wrote: > Hello fellow Pymol users! > > it sounds like I have the same objective as N. Sanishvili (25th Feb > 2003) anyone told Nukri how you can ray-trace a stereo figure yet? I > couldn't find a reply to the original question on stereo figs on the > BB. I am also trying to label specific residues in my stereo figure. > Older messages on the BB seem to imply this can't be done in pymol. Do > you know if any progress has been made on this? > > Many thanks, > > Camille > > p.s. I'm running npymol on OS X. ============================================== Scott Classen, Ph.D. cl...@uc... University of California, Berkeley Department of Molecular & Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ============================================== |
From: yuriwho <yu...@ma...> - 2003-06-12 08:25:58
|
This is absolutely the coolest tip for adding depth to labels in raytraced stereopairs, it works great especially when implemented with Warrens commands for creating the stereo pair ray angle=-3 png image1.png ray angle=3 png image2.png Y p.s. I am not having session save problems on 0.88 (fink version, OS X) On Friday, April 4, 2003, at 12:03 PM, Scott Classen wrote: > Hello Camille, > > I will tell you how I make absolutely beautiful stereo figures in > PyMOL (with Adobe illustrator too) with nicely depth cued labels. It > takes a little more than clicking a single button, but it works well. > > create two PyMOL scripts of your view that are identical with all the > beautiful ray tracing etc. then add: > > turn y, -3 to the first script > > and > > turn y, 3 to the second one > > make sure the png files exported from each script have different names > (i.e. Left and Right) > > If you are working interactively with PyMOL then just remember to turn > y, 6 and then re-ray trace and export a second PNG. > > Now use a program like Illustrator or Canvas to add the stereo/depth > cued labels. This is a little tricky to describe, but I'll give it my > best shot. Place the two images side by side with their centers > separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your > labels on the LEFT figure. select all of your labels and duplicate > them. Move the duplicated labels to the RIGHT side. For clarity sake > let's assume we have 3 labels on the LEFT side (a,b, and c -- we will > call then aL and aR for the left and right labels, respectively). > Place aL near a recognizable feature of the LEFT figure that you are > trying to label. Now horizontilly align aR with aL. Now using only the > <-- and --> keys move the aR label until the identical portion of the > actual label (let's say the lower right hand tip of the 'a') is > vertically aligned with the identical portion of your model (let's say > where the C alpha-C beta bond leaves the ribbon backbone) on both the > LEFT and RIGHT images. Repeat these steps for each pair of labels. > This is a nice method for adding stereo labels because it does not > require looking at your computer screen in wall-eyed stereo for 2 > hours in order to get proper placement of labels. > > By assuring that the labels are positioned in the LEFT and RIGHT > images at positions that are identical with respect to the part of the > model that is being labeled you automatically are also placing them so > they are at the proper depth when the figure is finally viewed in > stereo. > > I hope this makes sense. Just email if you want more details. > > Scott > > > On Friday, April 4, 2003, at 05:56 AM, <ca...@mr...> > wrote: > >> Hello fellow Pymol users! >> >> it sounds like I have the same objective as N. Sanishvili (25th Feb >> 2003) anyone told Nukri how you can ray-trace a stereo figure yet? I >> couldn't find a reply to the original question on stereo figs on the >> BB. I am also trying to label specific residues in my stereo figure. >> Older messages on the BB seem to imply this can't be done in pymol. >> Do you know if any progress has been made on this? >> >> Many thanks, >> >> Camille >> >> p.s. I'm running npymol on OS X. > ============================================== > Scott Classen, Ph.D. > cl...@uc... > University of California, Berkeley > Department of Molecular & Cell Biology > 237 Hildebrand Hall #3206 > Berkeley, CA 94720-3206 > LAB 510.643.9491 > FAX 510.643.9290 > ============================================== > > > > ------------------------------------------------------- > This SF.net email is sponsored by: ValueWeb: Dedicated Hosting for > just $79/mo with 500 GB of bandwidth! No other company gives more > support or power for your dedicated server > http://click.atdmt.com/AFF/go/sdnxxaff00300020aff/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Anthony D. <A....@us...> - 2003-06-12 23:32:22
|
If you don't have a program such as Illustrator or Canvas, you can do the same thing in powerpoint. However, there is a small problem with exporting pictures from powerpoint, but it can be overcome. I've pasted a description below. ____________________________________________________________________________________ PowerPoint is actually a quite effective tool in creating precise graphics, such as stereo pictures with labels, or other drawn objects, such as arrows. Unfortunately, exporting pictures from PowerPoint at reasonable resolution is non-obvious. The problem: When you copy an object from PowerPoint and paste it into a non-Microsoft Office program (eg Paint, Photoshop), the image is pasted with a resolution determined by the slide size. The solution: * In PowerPoint, go to File, Page Setup. * Increase the slide size width and height. A five-fold increase should be sufficient. eg. increase width from 24cm to 120cm, height from 18cm to 90cm. Be sure that you don't change the aspect ratio (width/height). * Select your objects (grouped or ungrouped). * Copy. * Go to Photoshop. * Create a new image (size is irrelevant). * Paste the image. * Save the image in your favourite format. ________________________________________________________________________________________ >>Now use a program like Illustrator or Canvas to add the stereo/depth cued >>labels. This is a little tricky to describe, but I'll give it my best >>shot. Place the two images side by side with their centers separated by >>6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on the >>LEFT figure. select all of your labels and duplicate them. Move the >>duplicated labels to the RIGHT side. For clarity sake let's assume we >>have 3 labels on the LEFT side (a,b, and c -- we will call then aL and aR >>for the left and right labels, respectively). Place aL near a >>recognizable feature of the LEFT figure that you are trying to label. Now >>horizontilly align aR with aL. Now using only the <-- and --> keys move >>the aR label until the identical portion of the actual label (let's say >>the lower right hand tip of the 'a') is vertically aligned with the >>identical portion of your model (let's say where the C alpha-C beta bond >>leaves the ribbon backbone) on both the LEFT and RIGHT images. Repeat >>these steps for each pair of labels. This is a nice method for adding >>stereo labels because it does not require looking at your computer screen >>in wall-eyed stereo for 2 hours in order to get proper placement of labels. >> >>By assuring that the labels are positioned in the LEFT and RIGHT images >>at positions that are identical with respect to the part of the model >>that is being labeled you automatically are also placing them so they are >>at the proper depth when the figure is finally viewed in stereo. >> >>I hope this makes sense. Just email if you want more details. >> >>Scott ---------------------------------------------------------------------- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 ---------------------------------------------------------------------- |
From: JP C. <jp...@br...> - 2003-06-13 03:43:36
|
Just to add a tip to this (should work in illustrator since it does in photoshop). You can use your mouse (instead of the arrow keys), pressing and holding down the shift key before clicking, to mouse the labels and they will be locked to the axis you start your mouse motion with. I have a photoshop action script that recreates this method and will generalize it and post it sometime soon. JP > > > >>Now use a program like Illustrator or Canvas to add the stereo/depth cued > >>labels. This is a little tricky to describe, but I'll give it my best > >>shot. Place the two images side by side with their centers separated by > >>6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on the > >>LEFT figure. select all of your labels and duplicate them. Move the > >>duplicated labels to the RIGHT side. For clarity sake let's assume we > >>have 3 labels on the LEFT side (a,b, and c -- we will call then aL and aR > >>for the left and right labels, respectively). Place aL near a > >>recognizable feature of the LEFT figure that you are trying to label. Now > >>horizontilly align aR with aL. Now using only the <-- and --> keys move > >>the aR label until the identical portion of the actual label (let's say > >>the lower right hand tip of the 'a') is vertically aligned with the > >>identical portion of your model (let's say where the C alpha-C beta bond > >>leaves the ribbon backbone) on both the LEFT and RIGHT images. Repeat > >>these steps for each pair of labels. This is a nice method for adding > >>stereo labels because it does not require looking at your computer screen > >>in wall-eyed stereo for 2 hours in order to get proper placement of labels. > >> > >>By assuring that the labels are positioned in the LEFT and RIGHT images > >>at positions that are identical with respect to the part of the model > >>that is being labeled you automatically are also placing them so they are > >>at the proper depth when the figure is finally viewed in stereo. > >> > >>I hope this makes sense. Just email if you want more details. > >> > >>Scott > > > > ---------------------------------------------------------------------- > Anthony Duff > Postdoctoral Fellow > School of Molecular and Microbial Biosciences > Biochemistry Building, G08 > University of Sydney, NSW 2006 Australia > Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 > ---------------------------------------------------------------------- > |
From: Olve P. <Olve.Peersen@ColoState.edu> - 2003-06-13 15:19:44
|
You can also hold OPTION (Mac, ALT on PCs?) to duplicate an object when you drag it. Thus, you can simply type the label once, click and drag it with OPTION & SHIFT down and the label will be duplicated and locked on axis during the move. I usually initiate the drag and then cross my eyes for stereo to set the final placement of the text - that way you can make the label pop out in the third dimension if you're wanting to highlight something coming forward in your figure (or vice versa). Olve On Thursday, June 12, 2003, at 09:42 PM, JP Cartailler wrote: > Just to add a tip to this (should work in illustrator since it does in > photoshop). You can use your mouse (instead of the arrow keys), > pressing > and holding down the shift key before clicking, to mouse the labels and > they will be locked to the axis you start your mouse motion with. > > I have a photoshop action script that recreates this method and will > generalize it and post it sometime soon. > > JP > >> >> >>>> Now use a program like Illustrator or Canvas to add the >>>> stereo/depth cued >>>> labels. This is a little tricky to describe, but I'll give it my >>>> best >>>> shot. Place the two images side by side with their centers >>>> separated by >>>> 6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on >>>> the >>>> LEFT figure. select all of your labels and duplicate them. Move the >>>> duplicated labels to the RIGHT side. For clarity sake let's assume >>>> we >>>> have 3 labels on the LEFT side (a,b, and c -- we will call then aL >>>> and aR >>>> for the left and right labels, respectively). Place aL near a >>>> recognizable feature of the LEFT figure that you are trying to >>>> label. Now >>>> horizontilly align aR with aL. Now using only the <-- and --> keys >>>> move >>>> the aR label until the identical portion of the actual label (let's >>>> say >>>> the lower right hand tip of the 'a') is vertically aligned with the >>>> identical portion of your model (let's say where the C alpha-C beta >>>> bond >>>> leaves the ribbon backbone) on both the LEFT and RIGHT images. >>>> Repeat >>>> these steps for each pair of labels. This is a nice method for >>>> adding >>>> stereo labels because it does not require looking at your computer >>>> screen >>>> in wall-eyed stereo for 2 hours in order to get proper placement of >>>> labels. >>>> >>>> By assuring that the labels are positioned in the LEFT and RIGHT >>>> images >>>> at positions that are identical with respect to the part of the >>>> model >>>> that is being labeled you automatically are also placing them so >>>> they are >>>> at the proper depth when the figure is finally viewed in stereo. >>>> >>>> I hope this makes sense. Just email if you want more details. >>>> >>>> Scott >> >> >> >> ---------------------------------------------------------------------- >> Anthony Duff >> Postdoctoral Fellow >> School of Molecular and Microbial Biosciences >> Biochemistry Building, G08 >> University of Sydney, NSW 2006 Australia >> Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 >> ---------------------------------------------------------------------- >> > > > > ------------------------------------------------------- > This SF.NET email is sponsored by: eBay > Great deals on office technology -- on eBay now! Click here: > http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ------------------------------------------------------- Olve Peersen Assistant Professor Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 ------------------------------------------------------- 970.491-0433 Office 970.491-0271 Lab 970.491-0494 Fax ------------------------------------------------------- |