From: Jason V. <jas...@sc...> - 2010-02-22 19:47:23
|
PyMOLers, As promised: * FreeMOL is back up. * CEalign has been built into the PyMOL source code. You can check out the SourceForge code and test it out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2010-08-19 19:30:57
|
Greetings, I'd like to pass on a few notes to let you know some of what's going on in the world of PyMOL. First, the PyMOL website has been completely changed. I wanted it to be on par with the quality of images and movies one can make in PyMOL. I also wanted to make sure it didn't look too stodgy corporate-like. Anyhow, it's up and I like it alot, actually. Second, -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Sabuj P. <sa...@gm...> - 2010-08-19 19:48:44
|
> First, the PyMOL website has been completely changed. I wanted it to > be on par with the quality of images and movies one can make in PyMOL. > I also wanted to make sure it didn't look too stodgy corporate-like. > Anyhow, it's up and I like it alot, actually. I see "USER-SPONSORED" and "OPEN-SOURCE" everywhere, but I don't see a link anywhere to the USER-SPONSORED http://www.pymolwiki.org/index.php/Main_Page website, which has instructions on how to compile the OPEN-SOURCE . Sabuj |
From: Sabuj P. <sa...@gm...> - 2010-08-19 19:52:01
|
heh, nm I found it : Open-Source and Educational Users: Please consult & participate in the PyMOL Community Wiki instead, which has tons of FREE usage information. The Official PyMOL Downloads and Documentation site is for PyMOL Sponsors only. On Thu, Aug 19, 2010 at 2:48 PM, Sabuj Pattanayek <sa...@gm...> wrote: >> First, the PyMOL website has been completely changed. I wanted it to >> be on par with the quality of images and movies one can make in PyMOL. >> I also wanted to make sure it didn't look too stodgy corporate-like. >> Anyhow, it's up and I like it alot, actually. > > I see "USER-SPONSORED" and "OPEN-SOURCE" everywhere, but I don't see a > link anywhere to the USER-SPONSORED > http://www.pymolwiki.org/index.php/Main_Page website, which has > instructions on how to compile the OPEN-SOURCE . > > Sabuj > |
From: Jason V. <jas...@sc...> - 2010-08-19 20:36:45
|
Sabuj, As you noticed, things are moved around. I tried to keep the organization clean, instead of just throwing up tons of links. There are still some other links and pages I need to add back. Cheers, -- Jason On Thu, Aug 19, 2010 at 3:51 PM, Sabuj Pattanayek <sa...@gm...> wrote: > heh, nm I found it : > > Open-Source and Educational Users: Please consult & participate in the > PyMOL Community Wiki instead, which has tons of FREE usage > information. The Official PyMOL Downloads and Documentation site is > for PyMOL Sponsors only. > > On Thu, Aug 19, 2010 at 2:48 PM, Sabuj Pattanayek <sa...@gm...> wrote: >>> First, the PyMOL website has been completely changed. I wanted it to >>> be on par with the quality of images and movies one can make in PyMOL. >>> I also wanted to make sure it didn't look too stodgy corporate-like. >>> Anyhow, it's up and I like it alot, actually. >> >> I see "USER-SPONSORED" and "OPEN-SOURCE" everywhere, but I don't see a >> link anywhere to the USER-SPONSORED >> http://www.pymolwiki.org/index.php/Main_Page website, which has >> instructions on how to compile the OPEN-SOURCE . >> >> Sabuj >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Tsjerk W. <ts...@gm...> - 2010-08-19 19:59:08
|
Hi Jason, > First, the PyMOL website has been completely changed. I wanted it to > be on par with the quality of images and movies one can make in PyMOL. > I also wanted to make sure it didn't look too stodgy corporate-like. > Anyhow, it's up and I like it alot, actually. Probably the most nasty question around... where did you hide the source code? The site looks quite okay. Will have to get used to it a bit :p I was wondering though, whether the main image was photoshopped. It seems that the blue background either has a blurring gradient filter over it, or has been rendered with focal blur, either of which I don't recall having seen as Pymol feature. :D There's also a glitch: I went to the educational page and clicked to see whether my IP address was listed as an academic institution. Being at home, it's no surprise it wasn't. But the link that should bring me back gave me a 404. > Second, Yes...? Well, keep up the good work (and make it yet that bit better)! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands |
From: Jason V. <jas...@sc...> - 2010-08-19 20:45:19
|
Tsjerk, >> First, the PyMOL website has been completely changed. I wanted it to >> be on par with the quality of images and movies one can make in PyMOL. >> I also wanted to make sure it didn't look too stodgy corporate-like. >> Anyhow, it's up and I like it alot, actually. > > Probably the most nasty question around... where did you hide the source code? I do need to add the link back to the SF project. I will put that on the download page. > The site looks quite okay. Will have to get used to it a bit :p I was > wondering though, whether the main image was photoshopped. It seems > that the blue background either has a blurring gradient filter over > it, or has been rendered with focal blur, either of which I don't > recall having seen as Pymol feature. :D Thanks for the kind words. The main photo is indeed GIMP-shopped--good eye! I tried to make a tilt-shift-esque blend for the main image. There's an example of how to do this, on the PyMOLWiki in the "Gallery" (http://www.pymolwiki.org/index.php/Gallery). > There's also a glitch: I went to the educational page and clicked to > see whether my IP address was listed as an academic institution. Being > at home, it's no surprise it wasn't. But the link that should bring me > back gave me a 404. Thanks! Please feel free to use the contact form on the pymol.org page or email directly if you find other problems. I will fix this. Cheers, -- Jason > >> Second, > > Yes...? > > > Well, keep up the good work (and make it yet that bit better)! > > Cheers, > > Tsjerk > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology / > University of Groningen > The Netherlands > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Roger R. <rro...@co...> - 2010-08-19 19:59:20
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> <font face="Verdana">Could anyone comment on the demise of pymol 0.99 for download? or the education-only builds? I see if you dig enough there is an educational-only version of Pymol that requires registration. Do the downloaded educational-only executables expire, and how does it differ from the full version?</font><br> <br> Thanks.<br> <br> On 8/19/2010 3:30 PM, Jason Vertrees wrote: <blockquote cite="mid:AAN...@ma..." type="cite"> <pre wrap="">Greetings, I'd like to pass on a few notes to let you know some of what's going on in the world of PyMOL. First, the PyMOL website has been completely changed. I wanted it to be on par with the quality of images and movies one can make in PyMOL. I also wanted to make sure it didn't look too stodgy corporate-like. Anyhow, it's up and I like it alot, actually. Second, </pre> </blockquote> <div class="moz-signature">-- <br> <font face="Verdana"> <hr> Roger S. Rowlett<br> Professor<br> Department of Chemistry<br> Colgate University<br> 13 Oak Drive<br> Hamilton, NY 13346<br> <br> tel: (315)-228-7245<br> ofc: (315)-228-7395<br> fax: (315)-228-7935<br> email: <a class="moz-txt-link-abbreviated" href="mailto:rro...@co...">rro...@co...</a><br> </font> </div> </body> </html> |
From: Jason V. <jas...@sc...> - 2010-08-19 20:05:13
|
Whooops! -- Don't clean coffee off your return key when editing an email--some random combination of keys plus return, just fired off the incomplete email. Continuing... Second, JyMOL is out (http://pymol.org/jymol). JyMOL is free for non-profit research. To get JyMOL you have to fill out some information and agree to an EULA. The information is just so I can keep track of JyMOL usage and support toward the beginning of its public life. And nothing tricky in the EULA, it pretty much says you can use it freely for non-profit research applications, but you cannot redistribute JyMOL. If your friends want it, please ask them to register with us, just like you have to. Third, I'm happy to announce that we're restarting the PyMOL Open-Source Fellowship Program (PyMOL OSFP). The OSFP is us, just like DeLano Scientific in the past, directly supporting the open-source community. We offer a modest stipend to the Fellow's income for his/her time in helping PyMOL's open-source community. We will soon be calling for applications. Before applying, please check with your funding institution to ensure that additional income from an outside source is legal under your contract--sometimes your employment agreement will state that you cannot supplement your income from other sources. The scope of the first OSFP will cover continued support and enablement for the open-source community, including maintenance of the PyMOLWiki. If this goes well, we may consider starting more fellowship programs. More details on this soon. Fourth, we're working on a free AxPyMOL Reader. This free software will let you view AxPyMOL sessions in PowerPoint files generated with the full version of AxPyMOL. This could be useful for students reading others' files and also for that podium computer where we all present from. I'll announce this when it's ready. Cheers, -- Jason On Thu, Aug 19, 2010 at 3:30 PM, Jason Vertrees <jas...@sc...> wrote: > Greetings, > > I'd like to pass on a few notes to let you know some of what's going > on in the world of PyMOL. > > First, the PyMOL website has been completely changed. I wanted it to > be on par with the quality of images and movies one can make in PyMOL. > I also wanted to make sure it didn't look too stodgy corporate-like. > Anyhow, it's up and I like it alot, actually. > > > Second, > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2010-08-19 20:57:46
|
Hi Roger, I moved the 0.99 build download page because I didn't have a good place for it during the reorganization. I'll add them back when I update the Download page. Nothing has changed with the free educational builds, just the location of the link (as with 90% of the site). Don't worry, we have no plans to stop making PyMOL freely available to students, or add in time-bombs to kill PyMOL. (On the contrary, we now even offer JyMOL for free to non-profit researchers.) To be clear, the academic versions of PyMOL do not expire. Cheers, -- Jason On Thu, Aug 19, 2010 at 3:59 PM, Roger Rowlett <rro...@co...> wrote: > Could anyone comment on the demise of pymol 0.99 for download? or the > education-only builds? I see if you dig enough there is an educational-only > version of Pymol that requires registration. Do the downloaded > educational-only executables expire, and how does it differ from the full > version? > > Thanks. > > On 8/19/2010 3:30 PM, Jason Vertrees wrote: > > Greetings, > > I'd like to pass on a few notes to let you know some of what's going > on in the world of PyMOL. > > First, the PyMOL website has been completely changed. I wanted it to > be on par with the quality of images and movies one can make in PyMOL. > I also wanted to make sure it didn't look too stodgy corporate-like. > Anyhow, it's up and I like it alot, actually. > > > Second, > > > > -- > ________________________________ > Roger S. Rowlett > Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rro...@co... > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Greg L. <gre...@gm...> - 2010-12-04 05:33:05
|
Hi Jason, Coming back to an older thread: On Thu, Aug 19, 2010 at 10:57 PM, Jason Vertrees <jas...@sc...> wrote: > > I moved the 0.99 build download page because I didn't have a good > place for it during the reorganization. I'll add them back when I > update the Download page. > Since I remembered this message, I was somewhat surprised when a colleague told me that the 0.99 builds were no longer to be found. After looking around on the website a bit it seems like he's right though... Was the decision made in the end to get rid of the free builds of the old version? Thanks, -greg |
From: Jason V. <jas...@sc...> - 2010-12-06 18:41:52
|
Hi Greg, > Since I remembered this message, I was somewhat surprised when a > colleague told me that the 0.99 builds were no longer to be found. > After looking around on the website a bit it seems like he's right > though... Was the decision made in the end to get rid of the free > builds of the old version? We had planned on reinstating the PyMOL v0.99 builds after the redesign of the pymol.org website. For some time, we left these builds off the site as we considered them very old, missing many features, and difficult to support. However, given the needs of the community, we've reinstated these builds as PyMOL-legacy. PyMOL-legacy downloads are now available at PyMOL's SourceForge site (https://sourceforge.net/projects/pymol/files/Legacy/). Currently, these include all the 0.99 builds and source. Second, a new PyMOL-legacy mailing list (https://sourceforge.net/mailarchive/forum.php?forum_name=pymol-legacy) has been created for discussion; this still needs a few hours to initialize, but will be ready soon. Please note that this PyMOL-legacy mailing list is a community list and Schrodinger offers no support for these old builds. To round out the issue, we are working on a reasonable "end-of-life" policy to balance the needs of our users with ease of software maintenance. PyMOL's official end-of-life policy for builds will be posted on our website (http://pymol.org/eol) soon. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Hugo G. de T. <hug...@us...> - 2010-02-25 08:59:49
|
Hi Jason, I have compiled the last PyMOL code, and tried to used CEalign. What I wanted is to align all proteins using the first entry as reference, as it is possible with the CEalign command "alignto" (following instructions in http://pymolwiki.org/index.php/Cealign#Multiple_Structure_Alignments). But alignto command is not found .... I don't know if this is a bug. Any help to align all molecules onto the first entry is also appreciated. Cheers, Hugo Jason Vertrees wrote: > PyMOLers, > > As promised: > > * FreeMOL is back up. > > * CEalign has been built into the PyMOL source code. You can check > out the SourceForge code and test it out. > > Cheers, > > -- Jason > > -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hug...@us... http://webspersoais.usc.es/persoais/hugo.teran/ |
From: Jason V. <jas...@sc...> - 2010-02-25 14:32:24
|
Hugo, I took that out because I got very little response to the "ailgnto" command. (Do others use it?) I like it, so I might put it back in. For now, you can restore that functionality by copy/pasting this into "alignto.py": def alignto(sel1): """Just a quick & dirty multiple structure alignment""" for x in cmd.get_names(selection="*"): print "Aligning %s to %s" % (x, sel1) cmd.cealign( sel1, x ) # Let PyMOL know about the alignto command cmd.extend("alignto", alignto) Start up PyMOL and then type @/path/to/alignto.py where "path/to" is the path to where you saved the alignto.py file. 'alignto' should now be defined and working. -- Jason 2010/2/25 Hugo Gutiérrez de Teran <hug...@us...>: > Hi Jason, > > I have compiled the last PyMOL code, and tried to used CEalign. What I > wanted is to align all proteins using the first entry as reference, as > it is possible with the CEalign command "alignto" (following > instructions in > http://pymolwiki.org/index.php/Cealign#Multiple_Structure_Alignments). > > But alignto command is not found .... > > I don't know if this is a bug. > Any help to align all molecules onto the first entry is also appreciated. > > Cheers, > Hugo > Jason Vertrees wrote: >> PyMOLers, >> >> As promised: >> >> * FreeMOL is back up. >> >> * CEalign has been built into the PyMOL source code. You can check >> out the SourceForge code and test it out. >> >> Cheers, >> >> -- Jason >> >> > > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundación Pública Galega de Medicina Xenómica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 981563100 ext 13873 > e-mail:hug...@us... > http://webspersoais.usc.es/persoais/hugo.teran/ > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |