[ccp4bb] Replacement for arp_waters?
I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Replacement for arp_waters?
Hi David, for example: phenix.refine does it automatically as part of usual refinement; for illustration, see the picture here: http://phenix-online.org/documentation/refinement.htm Cheers, Pavel. On 1/20/2009 10:13 AM, David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Replacement for arp_waters?
I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. At any rate, it was very handy to have this option for refmac for both Windows and Linux platforms, especially for teaching new users or undergraduates working in the CCP4i environment. I suppose I can always add ARP/WARP to CCP4i in the Linux environment, but that leave Windows users out in the cold. Just my 2 cents. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Replacement for arp_waters?
arp_waters is very useful for a variety of purposes. I would like to see it supported in future releases. Best, BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger Rowlett Sent: Tuesday, January 20, 2009 11:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Replacement for arp_waters? I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. At any rate, it was very handy to have this option for refmac for both Windows and Linux platforms, especially for teaching new users or undergraduates working in the CCP4i environment. I suppose I can always add ARP/WARP to CCP4i in the Linux environment, but that leave Windows users out in the cold. Just my 2 cents. Cheers, -- _ Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Replacement for arp_waters?
Roger Rowlett wrote: I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. May I be so bold as to point you to the documentation? http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC127 If you want to use a command line program, type findwaters on the command line and it will give a short description of the parameters it takes. (It is also documented in section 9.1 of the manual.) Paul.
Re: [ccp4bb] Replacement for arp_waters?
Part of the reasoning was that arp_waters corresponded to a very old version of arp/warp It was felt that up-to-date arp/warp and/or findwaters covered the functionality. Of course, every implementation does things in a slightly different way, and each has their fans. Which means it is hard to deprecate anything. Which means the suite bloats ... Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Roger Rowlett Sent: Tue 1/20/2009 7:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Replacement for arp_waters? I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. At any rate, it was very handy to have this option for refmac for both Windows and Linux platforms, especially for teaching new users or undergraduates working in the CCP4i environment. I suppose I can always add ARP/WARP to CCP4i in the Linux environment, but that leave Windows users out in the cold. Just my 2 cents. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Replacement for arp_waters?
Might I add yet another call for the reinstatement of arp_waters - a very useful program indeed. Steve From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: Tuesday, January 20, 2009 2:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Replacement for arp_waters? arp_waters is very useful for a variety of purposes. I would like to see it supported in future releases. Best, BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger Rowlett Sent: Tuesday, January 20, 2009 11:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Replacement for arp_waters? I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. At any rate, it was very handy to have this option for refmac for both Windows and Linux platforms, especially for teaching new users or undergraduates working in the CCP4i environment. I suppose I can always add ARP/WARP to CCP4i in the Linux environment, but that leave Windows users out in the cold. Just my 2 cents. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Replacement for arp_waters?
On 17:05 Tue 20 Jan , Paul Emsley wrote: > Roger Rowlett wrote: >> I will second noting the loss of arp_waters in CCP4 6.1. I know there >> is a "find waters" option in Coot 0.5.2 under "Calculate...Other >> modeling tools", and perhaps this is adequate, but it doesn't seem to >> have as many options for fine-tuning as arp_waters did. Coot allows >> for finding waters above a certain sigma value; arp_waters allowed >> this option plus setting minimum and maximum hydrogen bonding >> distances between heavy atoms. > > May I be so bold as to point you to the documentation? > > http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC127 > > If you want to use a command line program, type findwaters on the > command line and it will give a short description of the parameters it > takes. > (It is also documented in section 9.1 of the manual.) One of the major reasons our lab started using Coot instead of O is that you didn't have to memorize or look up a million obscure functions to do everything. It was in the Coot GUI. When we're training new people, this helps immensely for the 99% of them who have never used Linux or any type of command line before. If there isn't a GUI for it, it effectively doesn't exist for them. I would enjoy understanding what the philosophy of the Coot developers is on this matter. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpzevSbMp2N7.pgp Description: PGP signature
Re: [ccp4bb] Replacement for arp_waters?
* * * As a newbie, am I stating the obvious or missing something: What about installing ARPwARP 7.0.1 in CCP4 (really easy!)? You?ll then have in CCP4i /Model Building, the ARP/wARP Solvent Module Victor Alves Quoting "David J. Schuller" : I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] Replacement for arp_waters?
Donnie Berkholz wrote: One of the major reasons our lab started using Coot instead of O is that you didn't have to memorize or look up a million obscure functions to do everything. It was in the Coot GUI. When we're training new people, this helps immensely for the 99% of them who have never used Linux or any type of command line before. If there isn't a GUI for it, it effectively doesn't exist for them. That's right. When there are 20 programs with 20 command line switches on average in each, there is no way an average user can memorize it all and use them to their full capabilities. GUI is the only way for many programs being used efficiently by many users. Command line and scripting are great for automation and programming but that's no what an average user normally does or want to do. Dima
Re: [ccp4bb] Replacement for arp_waters?
Dear David, You can use ARP/wARP 7.0.1 (www.arp-warp.org), which should be better than old arp_waters. Either the ARP/wARP GUI module 'ARP solvent' or a command line script auto_solvent.sh Best regards, Victor David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
