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
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