[COOT] what python command to mutate with stub ?

Hello Cootaholics I'd like to add a custom button (or key binding, or both) that will do a simple mutate, keep the residue type the same, and trim it back to the beta carbon. This would be the same as the stub function in the Simple Mutate dialogue box. I am finding that I repeat this action

Re: [COOT] key binding for waters added to mol 0

Hi Seth, I think if you place your first water using the place atom at this position button on the right side, then select your PDB file - all subsequent invocations of the w key will add waters to your PDB of interest instead of putting them in a separate PDB. Sincerely, Scott On Jan 9,

[COOT] two amino acids at the same position

% that are not identical and that are sufficiently well ordered to see differences) have mixtures of two different amino acids at the same position. How should he deal with this in coot? Thanks, Scott ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced

[COOT] pointer distances not visible

Hello When I turn on Pointer Distances or Environment Distances or manually measure a distance or angle I am not seeing any distance labels only the dotted lines between atoms. I'm running 0.7 build 4459 on OS X 10.8.2 and XQuartz 2.7.4 (xorg-server 1.13.0) help ….please Thanks, Scott

Re: [COOT] turn on core dumps [was Re: 0.7-pre-1-revision-4322 crashing on CentOS 6]

Hi Paul, I received this message after the crash: [New Thread 13701] [Thread debugging using libthread_db enabled] Core was generated by `/programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real'. Program terminated with signal 6, Aborted. #0 0x2b54f07c98a5 in raise () from

Re: [COOT] distances not being displayed in 0.7-pre-1

: ++972-3640-9407Cellular: 0547 459 608On Oct 18, 2011, at 12:22 , Paul Emsley wrote:On 14/10/11 17:15, Scott Classen wrote:Hello,I've installed Coot 0.7-pre-1 (revision 3632) via fink on my Mac running OS X 10.7.2Atom labels are working correctly, but the distances are not being displayed

[COOT] distances not being displayed in 0.7-pre-1

, Scott Classen ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~

Re: [COOT] mon_lib_list.cif?

. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: COOT@JISCMAIL.AC.UK Subject: mon_lib_list.cif? Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my

Re: [COOT] mon_lib_list.cif?

the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott

[COOT] can't edit DNA chi angles

Hello, I'm using coot 0.6-pre release 2172 via fink after selecting a DNA base to edit and selecting the chi angle that I would like to move I get the following errors when I drag the mouse: Click on an atom in the residue that you want to edit (setup-edit-chi-angles1) (0) C2

Re: [COOT] problems with ssDNA chi angles

Thank you! That's exactly what I needed. I guess the randomness I was experiencing previously was just me randomly clicking on different atoms in the residue. Scott On Mar 5, 2009, at 10:45 AM, Paul Emsley wrote: Scott Classen wrote: Hi All, I am trying to manually fit ssDNA. Sometime

[COOT] OS X coot-0.6-pre-1-revision-1876 - minor bug

I just upgraded via fink and now in the Display Manager I am unable to chose which map to bind to the scroll wheel. I can properly bind using the HID--ScrollWheel--Attach scroll wheel to which map? pulldown, but not from the radio button in the Display Manager window. Thanks, Scott

[COOT] DNA restraints not working

23.404 35.176 25.100 1.00 44.90 DO Thanks, Scott ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O

Re: [COOT] Fedora 8 binary core dumps - please help

- Original Message - From: Scott Classen [EMAIL PROTECTED] Date: Friday, October 17, 2008 4:24 pm Subject: Fedora 8 binary core dumps - please help To: COOT@JISCMAIL.AC.UK Hi all I've attempting to install COOT 0.5 I downloaded the stable tarball coot-0.5-binary-Linux-i386-fedora-8

Re: [COOT] Fedora 8 binary core dumps - please help

Scott Classen wrote: - Original Message - From: Scott Classen [EMAIL PROTECTED] Date: Friday, October 17, 2008 4:24 pm Subject: Fedora 8 binary core dumps - please help To: COOT@JISCMAIL.AC.UK Hi all I've attempting to install COOT 0.5 I downloaded the stable tarball