[PyMOL] pymolwiki down

2016-08-05 Thread João M . Damas
Hi guys, Am I the only one experiencing problems accessing pymolwiki.org? I guess people are using google cache, but any idea of when it will be working again? Best, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613

[PyMOL] PyMOLWiki Upgraded (again)

2016-01-12 Thread Jason Vertrees
Greetings, I just discovered that the PyMOLWiki was failing due to memory limitations. I doubled the RAM on the instance and restarted it. We should be good for a while. Cheers, -- Jason -- Site24x7 APM Insight: Get Deep

Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-19 Thread H. Adam Steinberg
Thank you Jason! > On Oct 19, 2015, at 9:34 PM, Jason Vertrees wrote: > > Greetings Shane, et. al., > > The issue with the database connection should be fixed permanently now. > Search should also be consistently better. > > I've independently owned and run the wiki for almost a decade now. I

Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-19 Thread Jason Vertrees
Greetings Shane, et. al., The issue with the database connection should be fixed permanently now. Search should also be consistently better. I've independently owned and run the wiki for almost a decade now. It's heading toward 22 million page views. Anyhow, it's now on good hardware (SSD, lots o

Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-18 Thread Ramy Farid
The next time this happens, you can access a read-only mirror here: http://wiki.pymol.org Ramy > On Oct 18, 2015, at 7:57 PM, Jason Vertrees wrote: > > Shane, > > Try now. > > Cheers > > > On Sun, Oct 18, 2015, 6:35 PM Shane Caldwell

Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-18 Thread Jason Vertrees
Shane, Try now. Cheers On Sun, Oct 18, 2015, 6:35 PM Shane Caldwell wrote: > Hi Jason, pymol-users list, > > The pymolwiki seems to be down and has been for a few days now. It looks > like the server's down? > > Any page returns: > > (Can't contact the database server: Can't connect to local M

Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-18 Thread Shane Caldwell
Hi Jason, pymol-users list, The pymolwiki seems to be down and has been for a few days now. It looks like the server's down? Any page returns: (Can't contact the database server: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (111) (localhost)) Is there a mirro

Re: [PyMOL] PyMOLWiki: Quick Update

2015-09-09 Thread Matthew Baumgartner
Hi, I googled for the pymol wiki to check it out and I saw a message in the search results that says: "This site may be hacked." Do you know why that is? On 09/09/2015 07:40 AM, Osvaldo Martin wrote: Hi Jason, Thanks very much for the effort! Now the Wiki is far more useful than before! I

Re: [PyMOL] PyMOLWiki: Quick Update

2015-09-09 Thread Osvaldo Martin
Hi Jason, Thanks very much for the effort! Now the Wiki is far more useful than before! I have been trying the fixed-features and everything is working properly. I will let you now if I found a problem. Cheers, Osvaldo. On Wed, Sep 9, 2015 at 2:02 AM, Jason Vertrees wrote: > Greetings, > > It

[PyMOL] PyMOLWiki: Quick Update

2015-09-08 Thread Jason Vertrees
Greetings, It's been a while, I hope this message finds everyone well. I'm writing to briefly let you know that I recently moved, upgraded, and reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast and more useful. Feel free to report any bugs. Back to the startup-life. Cheer

Re: [PyMOL] PyMOLWiki Update

2014-10-20 Thread Sampson, Jared
Hi Justin - I see this same “weirdness" using the https protocol. If you remove the ’s’ from ‘https’ in your URL, however, it will load properly. It must be on a shared server that has something goofy happening with the handling of https traffic. I think Jason is still the admin for the wiki

Re: [PyMOL] PyMOLWiki Update

2014-10-20 Thread Justin Lecher
On 20/06/14 17:45, Jason Vertrees wrote: > Hi Suzanne, > > Everything should look and act exactly like it has in the past, including the > address. > > Cheers, > > -- Jason > Hi, I just saw some weirdness when I try to access https://www.pymolwiki.org/ That doesn't look like pymol stuff. C

Re: [PyMOL] PyMOLWiki Update

2014-06-20 Thread Jason Vertrees
wrote: > Great! Thank you Microlytic! I assume that the PyMol wiki site will > still have the same web address? > -- > *From:* Jason Vertrees [jason.vertr...@gmail.com] > > *Sent:* Friday, June 20, 2014 8:00 AM > *To:* pymol-users > *Cc:* Melanie Ad

Re: [PyMOL] PyMOLWiki Update

2014-06-20 Thread Lapolla, Suzanne M (HSC)
Great! Thank you Microlytic! I assume that the PyMol wiki site will still have the same web address? From: Jason Vertrees [jason.vertr...@gmail.com] Sent: Friday, June 20, 2014 8:00 AM To: pymol-users Cc: Melanie Adams-Cioaba Subject: [PyMOL] PyMOLWiki Update

[PyMOL] PyMOLWiki Update

2014-06-20 Thread Jason Vertrees
Greetings, It is my pleasure to let you know that Microlytic , a company that makes tools for crystallographers, has graciously offered to host the PyMOLWiki. The wiki has been successfully transferred and is serving. (The search and the port : problems have been fi

Re: [PyMOL] PyMOLWiki is Down

2012-07-05 Thread Jason Vertrees
Adam, Interesting. I haven't had any issues since the last upgrade happened. Anyhow, thanks for bringing this to our attention. We'll keep an eye on it. If it goes down again, please do let us know. Cheers, -- Jason Sent from my Android. Please excuse the concision and any typos. On Jul 5, 201

Re: [PyMOL] PyMOLWiki is Down

2012-07-05 Thread H. Adam Steinberg
I just tried it again and it does indeed work. But over the last few weeks (on first attempts) it seems to return an error. Maybe it's just my satellite ISP... Thanks On Jul 5, 2012, at 3:21 PM, Jason Vertrees wrote: > Hi Adam, > > The PyMOLWiki is working fine from here. Anyone else having pr

Re: [PyMOL] PyMOLWiki is Down

2012-07-05 Thread Jason Vertrees
Hi Adam, The PyMOLWiki is working fine from here. Anyone else having problems? Cheers, -- Jason On Thu, Jul 5, 2012 at 3:04 PM, H. Adam Steinberg wrote: > Is the wiki still in turmoil? every time I try to access a page via the > search field on the wiki, or via a Google search I get back "con

Re: [PyMOL] PyMOLWiki is Down

2012-07-05 Thread H. Adam Steinberg
Is the wiki still in turmoil? every time I try to access a page via the search field on the wiki, or via a Google search I get back "connection reset" in Firefox and "server dropped the connection" in Safari. I need the wiki! :) On Jun 12, 2012, at 8:42 AM, Jason Vertrees wrote: > Greetings,

[PyMOL] PyMOLWiki Access Restored

2012-06-12 Thread Jason Vertrees
Greetings, The PyMOLWiki is backup, safe and sound. The bug was not actually related to the well-known MySQL vulnerability, but was due to an update with php. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-712

[PyMOL] PyMOLWiki is Down

2012-06-12 Thread Jason Vertrees
Greetings, The PyMOLWiki recently went down due to a vulnerability in MySQL. If we cannot repair the system over the next day or so, we'll put up a mirror from the last backup (about 9 days ago) on a system without the vulnerability. Google has very thoroughly cached the PyMOLWiki, so in the mean

[PyMOL] PyMOLWiki Update

2009-10-09 Thread Jason Vertrees
Howdy PyMOLers, If anyone's interested here's a quick update on the PyMOLWiki and some possibly helpful links. Some useful content has been posted recently, namely: * SuperSym -- a powerful script for symmetry relations in PyMOL (http://pymolwiki.org/index.php/SuperSym) * AutoDockPlugin -- a sc

[PyMOL] PyMOLWiki MovieSchool

2009-07-12 Thread Jason Vertrees
PyMOLers, There's a new tutorial on the PyMOLWiki for making movies with the newer PyMOL versions 1.2+. It's detailed, covers concepts, and has scripts that you can directly copy/paste into PyMOL. So, if you have time and want to learn about making movies in PyMOL, check out the PyMOLWiki's

[PyMOL] PyMOLWiki RSS & Useful Performance Setting

2009-07-02 Thread Jason Vertrees
PyMOLers, (1) If you follow the PyMOLWiki closely enough, then you might be interested in knowing that you can follow all changes to the wiki via RSS. From the following link choose "RSS" or "atom" in the lower left-hand side: http://pymolwiki.org/index.php/Special:RecentChanges (2)

[PyMOL] PyMOLWiki: Survey Results & Searching

2009-04-21 Thread Jason Vertrees
PyMOLers, Thank you for taking the PyMOLWiki survey! We had a great response and now the direction of the wiki will follow the feedback. Survey results indicate that we needed better searching capabilities, so I installed a new search engine. Please hammer away at it and let me know what you th

Re: [PyMOL] PyMOLWiki Survey

2009-04-17 Thread Warren DeLano
> From: Jason Vertrees [mailto:j...@cs.dartmouth.edu] > Sent: Friday, April 10, 2009 3:24 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] PyMOLWIki Survey > > PyMOLers, > > The PyMOLWiki is thriving, we serve over 3800 pages a day, but I feel we > still need to

[PyMOL] PyMOLWIki Survey

2009-04-10 Thread Jason Vertrees
PyMOLers, The PyMOLWiki is thriving, we serve over 3800 pages a day, but I feel we still need to make more improvements. So, I'd like to hear your thoughts about the PyMOLWiki -- what you like about it, how we can improve it, and where it's lacking. Please take the short survey. You will help m

[PyMOL] PyMOLWiki Updates

2008-03-11 Thread Jason Vertrees
Fellow PyMOLers, I thought I would share a quick update of changes and relevant updates with the list about the PyMOLWiki. (1) Massive restructuring & updating -- http://www.pymolwiki.org/index.php/Main_Page We have organized the pages better. Searching should be more productive & yiel

[PyMOL] PyMolWiki Update

2007-01-18 Thread Jason Vertrees
PyMolers, In hopes to make the PyMolWiki more open to users, I've updated the software and now users can create their own accounts rather than having to go through me. You have to be logged in to edit pages, but now you can create your own account. The good news for us is that I've also insta

[PyMOL] PyMolWiki

2005-05-05 Thread tree
PyMolWiki'ers, If you're interested in the future of the PyMolWiki or would like to comment on its design, please check out the site, more directly (http://www.pymolwiki.org/index.php/Talk:Main_Page) to add your concepts of what needs to be changed or fixed or left alone. As a side note, the Py

[PyMOL] PyMolWiki Go Time

2005-02-17 Thread tree
PyMolers & PyMolWiki Editors, After reaping stacks of suggestions from users & wiki gurus I have devised the first pseudo-structure of the wiki. I say "pseudo-structure" because: MediaWiki has no built-in hierarchy; and, because as the wiki grows it'll take on its own structure regardless of what

[PyMOL] PyMolWiki is Up

2005-02-16 Thread tree
PyMolers, The new PyMol wiki is up for use! The site is still new and rough. We need volunteers to populate data and organize the site. We're using MediaWiki. I've already taken all the suggestions I've received and put them into the Initial Wiki Layout. Please make suggestions and changes to