Re: [PyMOL] Error: unknown type
Re: [PyMOL] Error: unknown type From: Justin Lecher j.lec...@fz... - 2009-05-12 17:34 Attachments: signature.asc I've updated it on the Wiki. So anyone likes to try git and update the repo? -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 This actually highlights a weakness with trying to use git with the PyMOLWiki script library: updates. Until a script is written to automatically update git from the PyMOLWiki, I don't think git will help us too much--and in fact may cause confusion. The wiki already stores meta-information (comments, tags, see also's, etc) along with the code and it does have, albeit rather non-specific, versioning built in. So, summarizing: I think it's a great idea, but it will require effort on someone's part before this'll become widely used for the wiki. Thanks, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
Shiven, It appears the script was flawed: names = cmd.get_names(sel1) should be: names = cmd.get_names(selection=sel1) I've updated it on the Wiki. Cheers, Warren -Original Message- From: Shiven Shandilya [mailto:shiven.shandi...@gmail.com] Sent: Monday, May 11, 2009 4:47 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Error: unknown type Hello List, Any ideas on why this script keeps failing in the newer PyMOL builds... http://pymolwiki.org/index.php/Zero_residues I keep getting the error message: Error: unknown type: '1hpv' where 1hpv is an actual pdb file/object I am running pymol 1.2b5 rev. 3706 (compiled from svn) on Ubuntu 8.10 Anyone else face a similar issue, or is it just me Thanks! --Shiven -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
I've updated it on the Wiki. So anyone likes to try git and update the repo? -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
If people really like this git stuff, it might be interesting to move the scripts to using gist.github.com . I don't know how well that would work with the current repo that Justin created. Also, it might be useless as wikipedia already lets us track the history of the page. I could see some use in being able to see forks off from the scripts in the wiki to people's individual computers though. Somebody who actually uses has used gist extensively might know better. -David - Original Message From: Justin Lecher j.lec...@fz-juelich.de To: pymol-users@lists.sourceforge.net Sent: Tuesday, May 12, 2009 1:34:00 PM Subject: Re: [PyMOL] Error: unknown type I've updated it on the Wiki. So anyone likes to try git and update the repo? -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
gists could be useful to post short code snippets and specific usage examples of people's workflows. from what i understand, gists are originally meant as a sort of pastebin (http://en.wikipedia.org/wiki/Pastebin ). however, i don't think it is the best way to maintain a (sort-of) central repository. gist is more amenable to keep short code for the how did i do that quick pymol thing last time? rainy day... I could see some use in being able to see forks off from the scripts in the wiki to people's individual computers though. this can be readily done via the repo -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
I could see some use in being able to see forks off from the scripts in the wiki to people's individual computers though. this can be readily done via the repo Can you show how I can clone a single file out of the repository? Or how I can fork a single file from the repository? Or see what people have made forks that only modify the file I care about? -David -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
On May 12, 2009, at 8:24 PM, David Hall wrote: I could see some use in being able to see forks off from the scripts in the wiki to people's individual computers though. this can be readily done via the repo Can you show how I can clone a single file out of the repository? Or how I can fork a single file from the repository? Or see what people have made forks that only modify the file I care about? git tracks the whole dir and not the individual files. single-file tracking would have to be done on the user end by some suitable combination of blame, diff and grep commands. alternatively, the whole pymol scripts repository could be made of submodules for each script. this would allow for some users to work with just they scripts they care about without impinging on users that prefer to clone the whole repo. i'm not sure how well this would work if, say, someone were to add a new script to the repo. w -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
