Re: [COOT] use of RPATH in coot libraries

2009-06-02 Thread Clemens Vonrhein
http://linuxreviews.org/man/ld.so/ http://blogs.sun.com/dipol/entry/dynamic_libraries_rpath_and_mac http://www.codeshorts.ca/tag/osx/ It works great for us. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing

Re: [COOT] use of RPATH in coot libraries

2009-06-02 Thread Clemens Vonrhein
that just gets unpacked it is a solution. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK

Re: [COOT] Automatic column asignment for refmac

2009-11-30 Thread Clemens Vonrhein
Dear Alexander, FCTR looks like it is coming from a BUSTER refinement: http://www.globalphasing.com/buster/manual/buster/manual/chapter5.html#mlphas This column is obviously only intended for looking at maps (however: usually one looks at the 2FOFCWT/PH2FOFCWT and FOFCWT/PHFOFCWT maps). So

Re: [COOT] Automatic column asignment for refmac

2009-11-30 Thread Clemens Vonrhein
as expected, yes. Running % coot --pdb refine.pdb --auto refine.mtz after BUSTER works perfectly for me every time ;-) Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd

Re: [COOT] Problem with Coot Density Fit Analysis with PHENIX map coefficients

2013-01-21 Thread Clemens Vonrhein
greenery? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK

[COOT] real-space refinement with hydrogens

2020-03-29 Thread Clemens Vonrhein
s for adding, editing and deleting 3D annotations? And how do I automatically save/load those upong startup/exiting? Sorry if these questions are already answered somewhere else ... any pointer/hint would be very much apreciated! Cheers Clemens -- *----

Re: [COOT] Coot scheme woes

2020-07-13 Thread Clemens Vonrhein
Dear all, On Fri, Jul 10, 2020 at 03:56:28PM +0100, Andrew Sharff wrote: > I would love to try today's revision - where can I download a MacOS binary > from? You only have linux binaries on your website - we only see the > problems on MacOS. Following on from Andrew's question: I must confess

Re: [COOT] Coot scheme woes

2020-07-15 Thread Clemens Vonrhein
Hi Paul, On Fri, Jul 10, 2020 at 11:16:55AM +0100, Paul Emsley wrote: > Maybe you could give today's reversion a bash > (efde451d59318f6f58c7f8295c93c86f764126e5) What does that mean? I guess it is meant as a git commit ID, right? Is that a commit relative to https://github.com/pemsley/coot?

Re: [COOT] Coot scheme woes

2020-07-15 Thread Clemens Vonrhein
Hi Paul, On Wed, Jul 15, 2020 at 08:28:36AM +0100, Paul Emsley wrote: > > So you are saying that one should use the "refinement" branch in order > > to get the latest "Coot"? > > > The build-it script builds a tar file that is generated from the refinement > branch. Aaah - that was the bit of

Re: [COOT] DGL (D-glutamic acid) adds a L-glutamic acid

2020-06-03 Thread Clemens Vonrhein
lemens [1] http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/chem_comp_chir.html [2] http://www.ccp4.ac.uk/html/mon_lib.html -- *------ * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sher

Re: [COOT] Coot scheme woes

2020-07-16 Thread Clemens Vonrhein
Hi Erwin, On Thu, Jul 16, 2020 at 09:43:26AM +0200, Erwin Pannecoucke wrote: > Just popping in here to confirm that the workflow suggested by Clemens > below, is indeed the way to go. > This night, I was able to compile coot on WSL1/Ubuntu 18.04 LTS. Oddly enough, I failed on Ubuntu 18.04 LTS

Re: [COOT] Coot scheme woes

2020-07-16 Thread Clemens Vonrhein
Hi Guillaume, On Thu, Jul 16, 2020 at 01:40:32PM +0200, Guillaume Gaullier wrote: > Would you mind explaining what you changed in the build-it script to make it > work? This is the patch: --- build-it~2020-07-15 10:34:50.037806692 +0200 +++ build-it 2020-07-15 14:56:31.593086262

Re: [COOT] Mac OS and Coot Update from CCP4

2021-09-21 Thread Clemens Vonrhein
Hi Paul, On Sat, Sep 18, 2021 at 11:56:33AM +0100, Paul Emsley wrote: > Your message will make Clemens laugh - shadenfreude - or some such :-) Not at all: it's much better when software works exactly as intended - as Coot nearly always does! Cheers Clemens

Re: [COOT] Disulphide sphere refinement fails in COOT when PDB file comes from BUSTER?

2023-03-24 Thread Clemens Vonrhein
Dear all, just to avoid confusion: BUSTER version numbering is maybe a bit unusual and differs between academic and commercial users (for various historic reasons). The most relevant version information is the release data, ie 20230217 currently [1]. Another short note: we also don't see that

Re: [COOT] Disulphide sphere refinement fails in COOT when PDB file comes from BUSTER?

2023-03-24 Thread Clemens Vonrhein
868 43 | +46 73 322 93 27 > martin.mo...@ki.se | ki.se > __ > Karolinska Institutet – a medical university > > -Original Message- > From: Clemens Vonrhein > Sent: den 24 mars 2023 10:26 > To: Martin Moche > Cc: COOT@jiscmail.ac