Re: [ccp4bb] Which is the better way to combine the dataset from different crystals?
I would normally do the second, unless they are pretty clearly nonisomorphous. If you combine them in Pointless, this will reset the batch numbers automatically. Phil On 2 Jul 2010, at 05:35, Fengyun Ni wrote: > Hi all, > > I have a question on how to combine two dataset from different crystal of > the same > protein. > > The first way I could think of is that, > 1) Merge two dataset seperately; > 2) Scale them to see whether they are consistent with each other enough as > indicated by > the R-factor; > 3) If the R is low enough, say below 10 or 15%, then take the average for > both the F and > SIGF. > > The other way is that, > 1) Take the unmerged file from MOSFLM, and reset their batch number; > 2) Run SCALA to scale these two unmerged dataset at the same time. > > Could anyone tell which way is the better or the correct way? > Thank you in advance! > > -- > alphar
Re: [ccp4bb] ccp4MG quits - mac
I dearly love ccp4mg and use it a lot, but it has to be said that it is still a bit crashy. I know Stuart & Liz are continuously trying to make it less so. Two pieces of advice: File -> Save as default status ... when you have set up a complicated scene Keep up to date (Tools -> Check for updates) - version 2.4.1 is definitely better (though alas still not immune to crashing) and (to Liz & Stuart) I do think it's great Phil On 1 Jul 2010, at 17:13, Regina Kettering wrote: > Greetings. I have been using CCP4MG to create images on my Mac OS 10.6.4 and > have been having problems with it unexpectedly quitting. It appears to be > linked to either large changes (such as having a surface displayed and then > changing the properties of that surface) or displaying things like disulfide > bridges. I do not have a video card with extra processing power, but my > computer is less than a year old, so the problems are unexpected. Is this a > known bug, or is there a way to avoid this problem (other than using, say, > Pymol)? > > Thanks, > Regina Kettering > > >
[ccp4bb] attachments
Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
[ccp4bb] BIOCRYS 2010 - Registration Reminder
Dear colleagues, On behalf of the organizers, Maria Armenia Carrondo and Thomas R. Schneider *COURSE ANNOUNCEMENT - BIOCRYS 2010* Fundamentals of Modern Methods in Biocrystallography - 'What you always wanted to know about crystallography but never dared to ask' http://biocrys2010.itqb.unl.pt/ 9th - 16th October 2010 at the Instituto de Tecnologia Química e Biológica, Oeiras, Portugal. The topics of the fifth edition of this course will run from fundamentals such as symmetry, point groups and crystal systems, basic diffraction physics, reciprocal space and the Ewalds sphere, radiation damage, data processing, structure factors, Patterson function to modern methodologies including molecular replacement, SAD, MAD, MIR and maximum likelihood phasing, density modification, refinement, model building, twinning and structure validation. The course will be organized with lectures in the mornings and interactive practicals and tutorials in the afternoons. Evening lectures on current topics will be presented by the invited speakers. A poster presentation will be held in the afternoon of the first two days of the course. speakers and tutors: M. Archer, I. Bento, G. Bunkoczi, K. Cowtan, Z. Dauter, C. Frazão,, E. Garman, C. Hermes,E. Hough, G. Leonard, A. Leslie, A. Liljas, B. Lohkamp, P. Matias, C. McVey, A. Perrakis, T. Schneider, C. Vonrhein. 36 participants will be selected with preference to scientists at the beginning of their crystallographic career. A registration fee of 600 Euros for academic and 1000 Euros for non-academic applicants is requested for full board and accommodation. Selected applicants will have to pay the registration fee by bank transfer before arrival. A limited number of grants is available for PhD and postdoctoral fellows within five years of obtaining PhD from the FEBS Youth Travel Fund (YTF). Applicants from Africa, Asia, North and South America may benefit from a Transcontinental YTF grant. The YTF (and TransYTF) grants support for travel, registration, as well as accommodation and food. Applicants to these grants must provide additional information and fulfill those conditions as specified in the FEBS website, in particular be a member of a national FEBS Constituent Society or IUBMB-related national or international. For an application, please fill the form on the web page by the 31th of July. For more information visit the course web page http://biocrys2010.itqb.unl.pt/ -- *Colin E. McVey, DPhil* Auxilliary Researcher Structural Genomics Lab Macromolecular Crystallography Unit Instituto de Tecnologia Química e Biológica Av. da Republica, EAN | Phone:(351)214469663 Apartado 127 | Fax :(351)214433644 2781-901 Oeiras | email:mc...@itqb.unl.pt PORTUGAL
Re: [ccp4bb] attachments
Maybe this netiquette is a little outdated. Sending a few MB to thousands of people is probably not much more than noise compared to current net traffic. There is the IMAP protocol which overcomes the problem of modem connections, which anyhow probably only affects a very, very small amount of people nowadays, and there are plenty of mail user agents which do not have a paperclip button, e.g. mutt, pine, etc, which address the very same problem. It's is a lot easier to show a jpg-image a few kB in size than to attempt to describe what you see with words. Anyhow, the FAQ (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to explicitly allows MIME attachments, even though I also conside MIME outdated and am extremely glad I do not need to fiddle with uu-en/de-code anymore. Again: maybe it's time to update the CCP4 netiquette. Tim P.S.: I wonder how much traffic this email will induce ;-) On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: > Several recent posts with decently sized attachments (now in cross eyed > stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky > for me, I can just recycle the old messages: > > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html > > Cheers from the self-appointed thought police, > > Ed. > > -- > "I'd jump in myself, if I weren't so good at whistling." >Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] attachments
Why not put images, maps, or data files on your own web page and then send out a link to that material? Then the e-mails are small and anyone that wants to see the files has easy access. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 2 Jul 2010, Tim Gruene wrote: Maybe this netiquette is a little outdated. Sending a few MB to thousands of people is probably not much more than noise compared to current net traffic. There is the IMAP protocol which overcomes the problem of modem connections, which anyhow probably only affects a very, very small amount of people nowadays, and there are plenty of mail user agents which do not have a paperclip button, e.g. mutt, pine, etc, which address the very same problem. It's is a lot easier to show a jpg-image a few kB in size than to attempt to describe what you see with words. Anyhow, the FAQ (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to explicitly allows MIME attachments, even though I also conside MIME outdated and am extremely glad I do not need to fiddle with uu-en/de-code anymore. Again: maybe it's time to update the CCP4 netiquette. Tim P.S.: I wonder how much traffic this email will induce ;-) On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Odd loop stabilised by an cation
You can look for similar loops in other structures in the PDB using the Protein Geometry Database (http://pgd.science.oregonstate.edu/). The search page allows you to specify phi/psi ranges for loops up to ten amino acids long and the "Browse Results" page will list out the ID codes and residues of any matches found. If you need any detailed assistance using this server, I'd be happy to help. Dale Tronrud On 07/02/10 05:44, Domen Zafred wrote: > Dear all, > > There is an odd loop on the surface of my structure. Three back-bone > oxygen atoms are turned in the same direction the structure is > stabilized by an cation and water molecules. > Also, the ion is probably partly occupied (as discussed in the recent > post of Ivan Xaravich). The pictures in crossed-eye stereo are in the > attachment. Electron densities are at 1.8 and 3.5 sigma. > I have two problems regarding this loop: > > Is such a loop something known or common, or is it unique? How could I > find structure with a similar feature? > > Is there a smart guess for finding out the right ion? Mg is the smallest > of all and there is still some red density. Ca on the other hand is more > common in cells and the puzzle is whether it is a small ion or is it > bigger, but with lover occupancy. > > Any suggestions, comments or answers will be greatly appreciated. > > Regards, > > Domen Zafred
Re: [ccp4bb] attachments
On Fri, Jul 2, 2010 at 3:48 PM, Tim Gruene wrote: > allows MIME attachments, even though I also conside MIME outdated and am > extremely glad I do not need to fiddle with uu-en/de-code anymore. As you no doubt know, MIME is a collection of Internet standards which allow binary content such as images, movies, program executables, MTZ files etc (and viruses of course!) to be encoded as an e-mail attachment using 'base64' encoding. It also provides an e-mail standard which among other things allow multiple versions of a message to be sent so that the e-mail client is free to decide which version it's best able to display, and to encode characters absent from the 7-bit ASCII set, such as those used in languages other than English. Without MIME you wouldn't have any of this, so if it's outdated then I'm not clear what you are proposing to replace it with? - unless of course you're referring to 'yEnc' (the Usenet binary encoding standard that replaced uuencode - but even this would probably be best incorporated into MIME rather than replacing it). I'm happy to accept that none of the additional features that MIME provides is strictly necessary for the BB, but I think you would have a hard time persuading users to switch to another method (assuming there is one!) for sending their attachments, non-English text etc. Uuencode/uudecode was the pre-MIME (and pre-yEnc) method of binary encoding and has nothing to do with MIME. Cheers -- Ian
Re: [ccp4bb] attachments
Dear Ian, I did not know correctly and confused it with the pre-MIME era you mention at the very end of your email when we actually had to use uuencode in order to send non-7-bit data by email. Thanks for the clarification, I'll do my homework. Cheers, Tim On Fri, Jul 02, 2010 at 04:54:28PM +0100, Ian Tickle wrote: > On Fri, Jul 2, 2010 at 3:48 PM, Tim Gruene wrote: > > allows MIME attachments, even though I also conside MIME outdated and am > > extremely glad I do not need to fiddle with uu-en/de-code anymore. > > As you no doubt know, MIME is a collection of Internet standards which > allow binary content such as images, movies, program executables, MTZ > files etc (and viruses of course!) to be encoded as an e-mail > attachment using 'base64' encoding. It also provides an e-mail > standard which among other things allow multiple versions of a message > to be sent so that the e-mail client is free to decide which version > it's best able to display, and to encode characters absent from the > 7-bit ASCII set, such as those used in languages other than English. > > Without MIME you wouldn't have any of this, so if it's outdated then > I'm not clear what you are proposing to replace it with? - unless of > course you're referring to 'yEnc' (the Usenet binary encoding standard > that replaced uuencode - but even this would probably be best > incorporated into MIME rather than replacing it). I'm happy to accept > that none of the additional features that MIME provides is strictly > necessary for the BB, but I think you would have a hard time > persuading users to switch to another method (assuming there is one!) > for sending their attachments, non-English text etc. > > Uuencode/uudecode was the pre-MIME (and pre-yEnc) method of binary > encoding and has nothing to do with MIME. > > Cheers > > -- Ian -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] attachments
Which "own web page"??? I don't have an "own" web page from my internet provider, there is one at work (not everyone at work has a such web page, in my case dedicated to PX), in order to get something added to that web page I have to provide the material to the person in charge of the web pages for the lab, then it requires approvals (with signatures), and once every 6 months the web page can be updated. So I don't think this will do! Fred. > Message du 02/07/10 17:05 > De : "Frances C. Bernstein" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : Re: [ccp4bb] attachments > > > Why not put images, maps, or data files on your own web page > and then send out a link to that material? Then the e-mails > are small and anyone that wants to see the files has easy > access. > > Frances Bernstein > > = > Bernstein + Sons > * * Information Systems Consultants > 5 Brewster Lane, Bellport, NY 11713-2803 > * * *** > * Frances C. Bernstein > * *** f...@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 > =
Re: [ccp4bb] attachments
On Friday 02 July 2010 09:54:13 am Frederic VELLIEUX wrote: > Which "own web page"??? I don't have an "own" web page from my internet > provider, there is one at work (not everyone > at work has a such web page, in my case dedicated to PX), in order to get > something added to that web page I have to > provide the material to the person in charge of the web pages for the lab, > then it requires approvals (with > signatures), and once every 6 months the web page can be updated. How about a policy that requests people to upload their density photos, etc, to the CCP4 wiki? There could be a wiki page dedicated to ccp4bb attachments. If disk use becomes excessive (although I think that's a danger yet) there could be a 2 month expiration policy or something of the sort. Ethan > > So I don't think this will do! > > Fred. > > > Message du 02/07/10 17:05 > > De : "Frances C. Bernstein" > > A : CCP4BB@JISCMAIL.AC.UK > > Copie à : > > Objet : Re: [ccp4bb] attachments > > > > > > Why not put images, maps, or data files on your own web page > > and then send out a link to that material? Then the e-mails > > are small and anyone that wants to see the files has easy > > access. > > > > Frances Bernstein > > > > = > > Bernstein + Sons > > * * Information Systems Consultants > > 5 Brewster Lane, Bellport, NY 11713-2803 > > * * *** > > * Frances C. Bernstein > > * *** f...@bernstein-plus-sons.com > > *** * > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > = > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] attachments
On Friday 02 July 2010 10:01:15 am Ethan Merritt wrote: > On Friday 02 July 2010 09:54:13 am Frederic VELLIEUX wrote: > > Which "own web page"??? I don't have an "own" web page from my internet > > provider, there is one at work (not everyone > > at work has a such web page, in my case dedicated to PX), in order to get > > something added to that web page I have to > > provide the material to the person in charge of the web pages for the lab, > > then it requires approvals (with > > signatures), and once every 6 months the web page can be updated. > > How about a policy that requests people to upload their density photos, > etc, to the CCP4 wiki? There could be a wiki page dedicated to ccp4bb > attachments. > If disk use becomes excessive (although Ithink that's a danger yet) there ^ don't > could be a 2 month expiration policy or something of the sort. > > Ethan > > > > > > So I don't think this will do! > > > > Fred. > > > > > Message du 02/07/10 17:05 > > > De : "Frances C. Bernstein" > > > A : CCP4BB@JISCMAIL.AC.UK > > > Copie à : > > > Objet : Re: [ccp4bb] attachments > > > > > > > > > Why not put images, maps, or data files on your own web page > > > and then send out a link to that material? Then the e-mails > > > are small and anyone that wants to see the files has easy > > > access. > > > > > > Frances Bernstein > > > > > > = > > > Bernstein + Sons > > > * * Information Systems Consultants > > > 5 Brewster Lane, Bellport, NY 11713-2803 > > > * * *** > > > * Frances C. Bernstein > > > * *** f...@bernstein-plus-sons.com > > > *** * > > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > > = > > > > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] attachments
How about having people just link to uploaded photos on flickr (http://www.flickr.com/) or similar free service? If you upload the photos and select 'all images' a link is produced that can be easily shared (http://farm5.static.flickr.com/4134/4755503052_bc6835dcdc.jpg). CCP4 doesn't have worry about maintaining the pictures and people don't need their own web-pages. How that helps, Sean
Re: [ccp4bb] attachments
My opinion is that attached images in bb posts should be allowed: 1) Storage & network bandwidth is cheap 2) Attached (even inline) images are convenient to understanding the question/issue at hand 3) Emails are very easily deleted 4) If images are to be "attached" via web-links, then it may not be possible to refer to them appropriately in the archives if the images are ever removed from the hosting server. - it seems to me that the archive of the bb is an excellent resource, but is diminished if the content can not be maintained centrally. -Doug On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: Why not put images, maps, or data files on your own web page and then send out a link to that material? Then the e-mails are small and anyone that wants to see the files has easy access. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 2 Jul 2010, Tim Gruene wrote: Maybe this netiquette is a little outdated. Sending a few MB to thousands of people is probably not much more than noise compared to current net traffic. There is the IMAP protocol which overcomes the problem of modem connections, which anyhow probably only affects a very, very small amount of people nowadays, and there are plenty of mail user agents which do not have a paperclip button, e.g. mutt, pine, etc, which address the very same problem. It's is a lot easier to show a jpg-image a few kB in size than to attempt to describe what you see with words. Anyhow, the FAQ (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to explicitly allows MIME attachments, even though I also conside MIME outdated and am extremely glad I do not need to fiddle with uu-en/de-code anymore. Again: maybe it's time to update the CCP4 netiquette. Tim P.S.: I wonder how much traffic this email will induce ;-) On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] attachments
I agree to this. What are the actual reasons against attachments? If one really has a slow network connection and cannot use IMAP instead of POP3 (if I understand correctly, with IMAP one does not need to download the emails until one actually wants to read them, but I may be wrong here, too), would it be a compromise to restrict image sizes to e.g. 500kB? On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: > My opinion is that attached images in bb posts should be allowed: > 1) Storage & network bandwidth is cheap > 2) Attached (even inline) images are convenient to understanding the > question/issue at hand > 3) Emails are very easily deleted > 4) If images are to be "attached" via web-links, then it may not be > possible to refer to them appropriately in the archives if the images > are ever removed from the hosting server. - it seems to me that the > archive of the bb is an excellent resource, but is diminished if the > content can not be maintained centrally. > > -Doug > > On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: >> Why not put images, maps, or data files on your own web page >> and then send out a link to that material? Then the e-mails >> are small and anyone that wants to see the files has easy >> access. >> >> Frances Bernstein >> >> = >> Bernstein + Sons >> * * Information Systems Consultants >> 5 Brewster Lane, Bellport, NY 11713-2803 >> * * *** >> *Frances C. Bernstein >> * *** f...@bernstein-plus-sons.com >> *** * >> * *** 1-631-286-1339FAX: 1-631-286-1999 >> = >> >> On Fri, 2 Jul 2010, Tim Gruene wrote: >> >>> Maybe this netiquette is a little outdated. Sending a few MB to >>> thousands of >>> people is probably not much more than noise compared to current net >>> traffic. >>> >>> There is the IMAP protocol which overcomes the problem of modem >>> connections, >>> which anyhow probably only affects a very, very small amount of >>> people nowadays, >>> and there are plenty of mail user agents which do not have a >>> paperclip button, >>> e.g. mutt, pine, etc, which address the very same problem. >>> >>> It's is a lot easier to show a jpg-image a few kB in size than to >>> attempt to >>> describe what you see with words. >>> >>> Anyhow, the FAQ >>> (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the >>> CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to >>> explicitly >>> allows MIME attachments, even though I also conside MIME outdated and am >>> extremely glad I do not need to fiddle with uu-en/de-code anymore. >>> >>> Again: maybe it's time to update the CCP4 netiquette. >>> >>> Tim >>> >>> P.S.: I wonder how much traffic this email will induce ;-) >>> >>> On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs >>> >>> -- >>> -- >>> Tim Gruene >>> Institut fuer anorganische Chemie >>> Tammannstr. 4 >>> D-37077 Goettingen >>> >>> GPG Key ID = A46BEE1A >>> >>> >> >> -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] attachments
Anyone still on PINE should consider a new email application :) Flip On 7/2/2010 20:29, Tim Gruene wrote: I agree to this. What are the actual reasons against attachments? If one really has a slow network connection and cannot use IMAP instead of POP3 (if I understand correctly, with IMAP one does not need to download the emails until one actually wants to read them, but I may be wrong here, too), would it be a compromise to restrict image sizes to e.g. 500kB? On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: My opinion is that attached images in bb posts should be allowed: 1) Storage& network bandwidth is cheap 2) Attached (even inline) images are convenient to understanding the question/issue at hand 3) Emails are very easily deleted 4) If images are to be "attached" via web-links, then it may not be possible to refer to them appropriately in the archives if the images are ever removed from the hosting server. - it seems to me that the archive of the bb is an excellent resource, but is diminished if the content can not be maintained centrally. -Doug On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: Why not put images, maps, or data files on your own web page and then send out a link to that material? Then the e-mails are small and anyone that wants to see the files has easy access. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 2 Jul 2010, Tim Gruene wrote: Maybe this netiquette is a little outdated. Sending a few MB to thousands of people is probably not much more than noise compared to current net traffic. There is the IMAP protocol which overcomes the problem of modem connections, which anyhow probably only affects a very, very small amount of people nowadays, and there are plenty of mail user agents which do not have a paperclip button, e.g. mutt, pine, etc, which address the very same problem. It's is a lot easier to show a jpg-image a few kB in size than to attempt to describe what you see with words. Anyhow, the FAQ (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to explicitly allows MIME attachments, even though I also conside MIME outdated and am extremely glad I do not need to fiddle with uu-en/de-code anymore. Again: maybe it's time to update the CCP4 netiquette. Tim P.S.: I wonder how much traffic this email will induce ;-) On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] attachments
On Jul 2, 2010, at 9:54 AM, Frederic VELLIEUX wrote: Which "own web page"??? A facebook account A blogger account A flickr account A photobucket account etc. For any of these options, anonymity can be ensured by your not sharing your personal information. If complete anonymity is desired, do everything behind tor. This is recommended for our North Korean colleagues, for example. There is really no reason not to put pictures on a web page that would otherwise be included as an attachment to a bb list. Attachments still clog email boxes because of any of a number of causes (1) clueless email users (2) aversion to gmail (3) clueless system administrators (4) clueless institutional administrators (5) very very large attachments (6) outdated infrastructure, etc. James
Re: [ccp4bb] attachments
On Fri, Jul 2, 2010 at 11:29 AM, Tim Gruene wrote: > I agree to this. > What are the actual reasons against attachments? > If one really has a slow network connection and cannot use IMAP instead of > POP3 > (if I understand correctly, with IMAP one does not need to download the > emails > until one actually wants to read them, but I may be wrong here, too), would > it > be a compromise to restrict image sizes to e.g. 500kB? Another reason is that some institutions still inflict email quotas on their users. I manage the phenixbb list (which is certainly smaller than ccp4bb) and I get occasional notifications from other servers that an account has been disabled because it exceeded the local quota. If some unfortunate university professor leaves for vacation for two weeks and doesn't check email the entire time, it won't take long to fill the inbox. I suspect whoever manages ccp4bb gets these notifications too. Personally, I keep this GMail account just for subscribing to lists - currently at 5% of quota. At least Coot outputs PNGs now - that cuts down the mean attachment size by, what, 90%? -Nat
Re: [ccp4bb] attachments
On 07/02/10 14:40, Flip Hoedemaeker wrote: Anyone still on PINE should consider a new email application :) Flip Alpine, for example. It even comes in a .rpm for easy installation with Fedora or Redhat. http://www.washington.edu/alpine/ It may not be as fancy as some of the other mail clients, but I can run it in a shell window. Cheers, -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] attachments
pine is quite handy if you can ssh to your email server (Brandeis allows that, for instance). Uses very little resources, fast, and poses zero danger of ever executing a malicious code. There is very little functionality added in other email clients. I don't use pine anymore, but there is no need to give it bad name. And you can use colors a-la-matrix :) On Fri, 2010-07-02 at 20:40 +0200, Flip Hoedemaeker wrote: > Anyone still on PINE should consider a new email application :) > > Flip > > On 7/2/2010 20:29, Tim Gruene wrote: > > I agree to this. > > What are the actual reasons against attachments? > > If one really has a slow network connection and cannot use IMAP instead of > > POP3 > > (if I understand correctly, with IMAP one does not need to download the > > emails > > until one actually wants to read them, but I may be wrong here, too), would > > it > > be a compromise to restrict image sizes to e.g. 500kB? > > > > > > On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: > >> My opinion is that attached images in bb posts should be allowed: > >> 1) Storage& network bandwidth is cheap > >> 2) Attached (even inline) images are convenient to understanding the > >> question/issue at hand > >> 3) Emails are very easily deleted > >> 4) If images are to be "attached" via web-links, then it may not be > >> possible to refer to them appropriately in the archives if the images > >> are ever removed from the hosting server. - it seems to me that the > >> archive of the bb is an excellent resource, but is diminished if the > >> content can not be maintained centrally. > >> > >> -Doug > >> > >> On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: > >>> Why not put images, maps, or data files on your own web page > >>> and then send out a link to that material? Then the e-mails > >>> are small and anyone that wants to see the files has easy > >>> access. > >>> > >>> Frances Bernstein > >>> > >>> = > >>> Bernstein + Sons > >>> * * Information Systems Consultants > >>> 5 Brewster Lane, Bellport, NY 11713-2803 > >>> * * *** > >>> *Frances C. Bernstein > >>>* *** f...@bernstein-plus-sons.com > >>> *** * > >>>* *** 1-631-286-1339FAX: 1-631-286-1999 > >>> = > >>> > >>> On Fri, 2 Jul 2010, Tim Gruene wrote: > >>> > Maybe this netiquette is a little outdated. Sending a few MB to > thousands of > people is probably not much more than noise compared to current net > traffic. > > There is the IMAP protocol which overcomes the problem of modem > connections, > which anyhow probably only affects a very, very small amount of > people nowadays, > and there are plenty of mail user agents which do not have a > paperclip button, > e.g. mutt, pine, etc, which address the very same problem. > > It's is a lot easier to show a jpg-image a few kB in size than to > attempt to > describe what you see with words. > > Anyhow, the FAQ > (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the > CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to > explicitly > allows MIME attachments, even though I also conside MIME outdated and am > extremely glad I do not need to fiddle with uu-en/de-code anymore. > > Again: maybe it's time to update the CCP4 netiquette. > > Tim > > P.S.: I wonder how much traffic this email will induce ;-) > > On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: > > Several recent posts with decently sized attachments (now in cross eyed > > stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky > > for me, I can just recycle the old messages: > > > > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html > > > > Cheers from the self-appointed thought police, > > > > Ed. > > > > -- > > "I'd jump in myself, if I weren't so good at whistling." > > Julian, King of Lemurs > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > >>> > >>> > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] attachments
ssh may not be necessary, (al)pine can be configured to connect to a POP3 or IMAP server, one of which a reasonable mail server would probably offer. Tim On Fri, Jul 02, 2010 at 05:27:24PM -0400, Ed Pozharski wrote: > pine is quite handy if you can ssh to your email server (Brandeis allows > that, for instance). Uses very little resources, fast, and poses zero > danger of ever executing a malicious code. There is very little > functionality added in other email clients. I don't use pine anymore, > but there is no need to give it bad name. And you can use colors > a-la-matrix :) > > On Fri, 2010-07-02 at 20:40 +0200, Flip Hoedemaeker wrote: > > Anyone still on PINE should consider a new email application :) > > > > Flip > > > > On 7/2/2010 20:29, Tim Gruene wrote: > > > I agree to this. > > > What are the actual reasons against attachments? > > > If one really has a slow network connection and cannot use IMAP instead > > > of POP3 > > > (if I understand correctly, with IMAP one does not need to download the > > > emails > > > until one actually wants to read them, but I may be wrong here, too), > > > would it > > > be a compromise to restrict image sizes to e.g. 500kB? > > > > > > > > > On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: > > >> My opinion is that attached images in bb posts should be allowed: > > >> 1) Storage& network bandwidth is cheap > > >> 2) Attached (even inline) images are convenient to understanding the > > >> question/issue at hand > > >> 3) Emails are very easily deleted > > >> 4) If images are to be "attached" via web-links, then it may not be > > >> possible to refer to them appropriately in the archives if the images > > >> are ever removed from the hosting server. - it seems to me that the > > >> archive of the bb is an excellent resource, but is diminished if the > > >> content can not be maintained centrally. > > >> > > >> -Doug > > >> > > >> On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: > > >>> Why not put images, maps, or data files on your own web page > > >>> and then send out a link to that material? Then the e-mails > > >>> are small and anyone that wants to see the files has easy > > >>> access. > > >>> > > >>> Frances Bernstein > > >>> > > >>> = > > >>> Bernstein + Sons > > >>> * * Information Systems Consultants > > >>> 5 Brewster Lane, Bellport, NY 11713-2803 > > >>> * * *** > > >>> *Frances C. Bernstein > > >>>* *** f...@bernstein-plus-sons.com > > >>> *** * > > >>>* *** 1-631-286-1339FAX: 1-631-286-1999 > > >>> = > > >>> > > >>> On Fri, 2 Jul 2010, Tim Gruene wrote: > > >>> > > Maybe this netiquette is a little outdated. Sending a few MB to > > thousands of > > people is probably not much more than noise compared to current net > > traffic. > > > > There is the IMAP protocol which overcomes the problem of modem > > connections, > > which anyhow probably only affects a very, very small amount of > > people nowadays, > > and there are plenty of mail user agents which do not have a > > paperclip button, > > e.g. mutt, pine, etc, which address the very same problem. > > > > It's is a lot easier to show a jpg-image a few kB in size than to > > attempt to > > describe what you see with words. > > > > Anyhow, the FAQ > > (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the > > CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to > > explicitly > > allows MIME attachments, even though I also conside MIME outdated and > > am > > extremely glad I do not need to fiddle with uu-en/de-code anymore. > > > > Again: maybe it's time to update the CCP4 netiquette. > > > > Tim > > > > P.S.: I wonder how much traffic this email will induce ;-) > > > > On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: > > > Several recent posts with decently sized attachments (now in cross > > > eyed > > > stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky > > > for me, I can just recycle the old messages: > > > > > > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html > > > > > > Cheers from the self-appointed thought police, > > > > > > Ed. > > > > > > -- > > > "I'd jump in myself, if I weren't so good at whistling." > > > Julian, King of Lemurs > > > > -- > > -- > > Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > > > > > >>> > > >>> > > > > > -- > Edwin Pozharski, PhD, Assistant Professor > Univ
Re: [ccp4bb] attachments
On Fri, 2010-07-02 at 13:35 -0400, Douglas Jacobsen wrote: > My opinion is that attached images in bb posts should be allowed: > 1) Storage & network bandwidth is cheap Glad to hear that University of Michigan administrators agree with you. However, you should not forget that cheap is a complicated concept, and some poor grad student in Uzbekistan may not have access to ultrafast internet. > 2) Attached (even inline) images are convenient to understanding > the question/issue at hand Of course. And so are images you can open in your web browser. > 3) Emails are very easily deleted Another excellent point. But the goal of posting a question is to elicit an answer. Even if there are very few people who automatically delete ccp4bb posts with attachments, your audience is reduced. > 4) If images are to be "attached" via web-links, then it may not > be > possible to refer to them appropriately in the archives if the images > are ever removed from the hosting server. - it seems to me that the > archive of the bb is an excellent resource, but is diminished if the > content can not be maintained centrally. Good point. One more reason to have a collection of "what-is-this-density?" images on ccp4wiki. Such gallery would be much more accessible than images attached to an obscure post deep in ccp4bb archives. One of the recent posts with images was "Odd loop stabilised by an cation" - why would I search with this combination of words? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
Re: [ccp4bb] attachments
I like pine. It is especially useful if I am travelling and have a bad connection, or (as at the moment) I am at home and one or more of our children (three of whom are computer experts) are hogging our modest internet connection! And using it on the computer at the lab via ssh I dont get troubled by viruses or large attachments. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 2 Jul 2010, Ed Pozharski wrote: > pine is quite handy if you can ssh to your email server (Brandeis allows > that, for instance). Uses very little resources, fast, and poses zero > danger of ever executing a malicious code. There is very little > functionality added in other email clients. I don't use pine anymore, > but there is no need to give it bad name. And you can use colors > a-la-matrix :) > > On Fri, 2010-07-02 at 20:40 +0200, Flip Hoedemaeker wrote: > > Anyone still on PINE should consider a new email application :) > > > > Flip > > > > On 7/2/2010 20:29, Tim Gruene wrote: > > > I agree to this. > > > What are the actual reasons against attachments? > > > If one really has a slow network connection and cannot use IMAP instead > > > of POP3 > > > (if I understand correctly, with IMAP one does not need to download the > > > emails > > > until one actually wants to read them, but I may be wrong here, too), > > > would it > > > be a compromise to restrict image sizes to e.g. 500kB? > > > > > > > > > On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: > > >> My opinion is that attached images in bb posts should be allowed: > > >> 1) Storage& network bandwidth is cheap > > >> 2) Attached (even inline) images are convenient to understanding the > > >> question/issue at hand > > >> 3) Emails are very easily deleted > > >> 4) If images are to be "attached" via web-links, then it may not be > > >> possible to refer to them appropriately in the archives if the images > > >> are ever removed from the hosting server. - it seems to me that the > > >> archive of the bb is an excellent resource, but is diminished if the > > >> content can not be maintained centrally. > > >> > > >> -Doug > > >> > > >> On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: > > >>> Why not put images, maps, or data files on your own web page > > >>> and then send out a link to that material? Then the e-mails > > >>> are small and anyone that wants to see the files has easy > > >>> access. > > >>> > > >>> Frances Bernstein > > >>> > > >>> = > > >>> Bernstein + Sons > > >>> * * Information Systems Consultants > > >>> 5 Brewster Lane, Bellport, NY 11713-2803 > > >>> * * *** > > >>> *Frances C. Bernstein > > >>>* *** f...@bernstein-plus-sons.com > > >>> *** * > > >>>* *** 1-631-286-1339FAX: 1-631-286-1999 > > >>> = > > >>> > > >>> On Fri, 2 Jul 2010, Tim Gruene wrote: > > >>> > > Maybe this netiquette is a little outdated. Sending a few MB to > > thousands of > > people is probably not much more than noise compared to current net > > traffic. > > > > There is the IMAP protocol which overcomes the problem of modem > > connections, > > which anyhow probably only affects a very, very small amount of > > people nowadays, > > and there are plenty of mail user agents which do not have a > > paperclip button, > > e.g. mutt, pine, etc, which address the very same problem. > > > > It's is a lot easier to show a jpg-image a few kB in size than to > > attempt to > > describe what you see with words. > > > > Anyhow, the FAQ > > (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the > > CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to > > explicitly > > allows MIME attachments, even though I also conside MIME outdated and > > am > > extremely glad I do not need to fiddle with uu-en/de-code anymore. > > > > Again: maybe it's time to update the CCP4 netiquette. > > > > Tim > > > > P.S.: I wonder how much traffic this email will induce ;-) > > > > On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: > > > Several recent posts with decently sized attachments (now in cross > > > eyed > > > stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky > > > for me, I can just recycle the old messages: > > > > > > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html > > > > > > Cheers from the self-appointed thought police, > > > > > > Ed. > > > > > > -- > > > "I'd jump in myself, if I weren't so good at whistling." > >
Re: [ccp4bb] attachments
I wouldn't mind sticking to the current ccp4 netiquette and adding links to the images in question instead of attaching the images themselves. However, I would prefer a server dedicated to this BB rather than something like twitter, flickr, second life, google maps or ... - there is 'free' and there is 'free', and I prefer to separate at least my work related communication from these aforementioned servers/ services... (that's also why I usually start a net search with ixquick.com instead of google.com) So maybe someone from the people in charge of ccp4.ac.uk or one of the ccp4-Wikis could comment on how much space they have available on their machines and whether it would be a concern for them if there were such an upload area. Tim On Fri, Jul 02, 2010 at 06:30:25PM +0100, Sean Seaver wrote: > How about having people just link to uploaded photos on flickr > (http://www.flickr.com/) or similar free service? If you upload the photos > and select 'all images' a link is produced that can be easily shared > (http://farm5.static.flickr.com/4134/4755503052_bc6835dcdc.jpg). CCP4 > doesn't have worry about maintaining the pictures and people don't need their > own web-pages. > > How that helps, > > Sean -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
