Re: [COOT] coot 0.9.4.1 installation on centos 8

al other different Scientific > Linux versions of coot. However, it is still not working. I'm wondering if > it's more of a cenos8 issue in general or some other local set-up. > > Any suggestions are warmly welcomed. Thank you all again. > > best, > Ming > > O

Re: [COOT] coot 0.9.4.1 installation on centos 8

Hi Ming: I got some similar errors on my Ubuntu install. Removing some of the non-coot libraries (like libpng) that are duplicated might help. Also, make sure you have the appropriate processor architecture. Bill > On Feb 22, 2021, at 8:14 AM, Ming Sun wrote: > > Hi all > > I'm trying t

Re: [COOT] latest osx version of coot

Hi Leonard et al: I want to apologize to you and everyone for dropping the ball on this. Between a massive wildfire that almost took out our house (and destroyed those of several colleagues), the pandemic, a forced lab move on short notice, and a pile of new teaching assignments, I haven’t man

Re: [COOT] Coot Fink 10.15

kind of have burned out on this stuff in the last few years. We will figure something out. Compared to all that is going on in NYC right now, these problems will hopefully be minor. Take care. Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for

Re: [COOT] Coot Fink 10.15

, but from what I understand, it has the latest coot (and refmac), so if you need the new version, I suggest you do that. If we can’t have a more recent version of coot in fink vs. ccp4, and can’t have refmac, it kind of makes it pointless to maintain coot in fink. Bill William G. Scott

Re: [COOT] error No appropriate OpenGL-capable visual found

Try re-installing Xquartz. https://www.xquartz.org William G. Scott http://scottlab.ucsc.edu > On Apr 4, 2018, at 4:52 PM, Elena Zehr wrote: > > Hi, > > After upgrading my MacOS to High Sierra, coot stopped running giving me the > error below. Do you know what is miss

Re: [COOT] Mac Binaries (Release 0.8.9.1)

For those using fink, I’ve updated the fink package info file http://fennario.ucsc.edu/~wgscott/coot/finkinfo/coot.info I still need to figure out how to get it into fink. Meanwhile, you can put the file in /sw/fink/dists/stable/main/finkinfo/sci and build it. William G. Scott Director

[COOT] New hardware lets any computer run an interactive, 3D interface | Ars Technica

I wonder if coot might be able to take advantage of this: > https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/ > > <https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/> W

Re: [COOT] APBS binary location MacPymol

arately. You might get better responses asking about pymol on the pymol mailing list. (Asking questions about PyMOL on the coot email list is kind of like ordering flowers for your mistress on your spouse’s cell phone and credit card.) William G. Scott Director, Program in Biochemistry and Molecular

Re: [COOT] SMILES not responding

William G. Scott http://scottlab.ucsc.edu/~wgscott On Oct 8, 2014, at 5:24 AM, Paul Emsley wrote: > On 08/10/14 09:37, Lau Sze Yi wrote: >> Hi, >> >> I tried to open SMILES in COOT under Files --> SMILES but did not get any >> response. What is wrong? >>

Re: [COOT] Release 0.8

For OS X, this is now added to fink, or you can download as described here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot On Sep 23, 2014, at 6:09 AM, Paul Emsley wrote: > We are pleased to announce the release of Coot 0.8. New binaries should be > on their way shortl

Re: [COOT] Stand Alone Coot for 10.6–10.8

Sorry. I forgot to change one occurrence in the build script. Should be fixed now. William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http

[COOT] Coot on OS X 10.6.X ?

, Bill William G. Scott http://scottlab.ucsc.edu/~wgscott

Re: [COOT] extensions menu is gone

t as well. > > — Jianghai > > > From: Alexander Batyuk > Reply: Alexander Batyuk > > Date: September 3, 2014 at 2:15:56 AM > To: Jianghai Zhu > > Cc: William G. Scott >, Paul Emsley > > > Subject: Re: extensions menu is gone > >> >> Hi Jiangha

Re: [COOT] Extensions Menu disappeared

ile18-gtk_2.1-1_darwin-x86_64.deb” sudo dpkg -i *.deb This is the same package with a later epoch label so fink updates won’t touch it. On Sep 3, 2014, at 10:40 AM, William G. Scott wrote: > > On Sep 3, 2014, at 5:33 AM, Dimitry Rodionov wrote: > >> Hi Jianghai, >> Build

Re: [COOT] Extensions Menu disappeared

On Sep 3, 2014, at 5:33 AM, Dimitry Rodionov wrote: > Hi Jianghai, > Building Coot from source using fink solved this problem for me. > Regards, > Dmitry > > On Sep 3, 2014 8:22 AM, "Jianghai Zhu" wrote: > Hi all, > > I am using Coot 0.8-pre-revision-5201-1 under OS X 10.9.4. I installed it

[COOT] symmetry operator notation question

; { 1 0 1 }”. Thanks. Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott

Re: [COOT] r5166 python error on Mac

Dear Oliver et al: On Jul 20, 2014, at 8:54 AM, Oliver Clarke wrote: > WARNING:: No coot.py file found! Python scripting unavailable. It looks like this is the problem. For some reason it is no longer getting copied from the src to python directory. If I do this manually, it works. I’m work

Re: [COOT] coot crash when loading mtz file

On Jun 19, 2014, at 10:13 AM, Thomas, Leonard M. wrote: > Here is what the path currently is with out modification. Nothing about CCP4. > > DYLD_LIBRARY_PATH=/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/DTREK99/lib > >

Re: [COOT] coot crash when loading mtz file

On Jun 19, 2014, at 9:33 AM, William G. Scott wrote: > If the user has set $DYLD_LIBRARY_PATH (perhaps via ccp4), it is possible > this gets over-ridden. I can reproducibly mess coot up with this: export DYLD_LIBRARY_PATH=/Applications/ccp4-6.4.0/lib and un-mess it up wit

Re: [COOT] coot crash when loading mtz file

On Jun 19, 2014, at 9:09 AM, Paul Emsley wrote: > On 19/06/14 11:29, Paul Emsley wrote: >> On 18/06/14 19:09, Thomas, Leonard M. wrote: >>> OK this has me puzzled. Coot was working fine until I had to update >>> something in order to install the latest version of Phenix. I don't >>> remember

Re: [COOT] unable to launch coot

I am updating the “stable” coot in fink to rev. 4965 which should work fine with the latest rkdit. On Mar 14, 2014, at 11:11 AM, William G. Scott wrote: > Dear Nacho: > > The “coot-pre” package should work. In updating that, I think I probably > broke the “stable” coot packag

Re: [COOT] unable to launch coot

in/coot-real "$@" > > Can anyone tell me what I'm doing wrong? > Thank you so much in advance. > > Nacho William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/

Re: [COOT] Coot-0.8-pre???

laptop plugged into an external display, but keep my laptop as a > secondary screen. > > I've been holding off updating from 10.8 to 10.9, and wondering when or if I > should do it > > Phil > Î > On 18 Feb 2014, at 22:49, William G. Scott wrote: > >&

Re: [COOT] Coot-0.8-pre???

On Feb 11, 2014, at 7:19 PM, Joseph Noel wrote: > I've started installing the latest nightly builds of Coot that Bill Scott > maintains. They go into /usr/local/bin/coot. It will open but the screen is > white, if you move the window around on the Mac it seems to duplicate and > worse, if you

Re: [COOT] coot - save coordinates

I am clueless on this one, so I'll post it to the coot mailing list in case anyone else has seen this …. On Oct 8, 2013, at 9:53 PM, Felix Frolow wrote: > Hi Bill, I regularly update coot using FINK ( from your repository) > Since one of the recent versions of coot ( difficult to say from when,

Re: [COOT] Symbol not found: _iconv

DYLD_LIBRARY_PATH on tcsh should do it. Also, you could try installing coot from here, as a control (or an alternative): http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Good luck. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Ce

Re: [COOT] fink: coot-0.7.1.0-6 for 10.6

On Sep 5, 2013, at 3:43 AM, Steffen Schmidt wrote: >> >> coot0.7.1.0-7 Crystallographic molecular graphics >> coot-pre0.8-pre-4749Crystallographic molecular graphics >> refmac 5.7.0032-3 CCP4 refmac5 standalone update > > Great, it works for me also!

Re: [COOT] fink: coot-0.7.1.0-6 - refmac cif file not found

phics >> coot-pre0.8-pre-4749Crystallographic molecular graphics >> refmac 5.7.0032-3 CCP4 refmac5 standalone update > > Great, it works for me also! > Do you plan to have it also available for 10.6? > > Steffen Yes, I'll try to get it done (test

Re: [COOT] fink: coot-0.7.1.0-6 - refmac cif file not found

On Sep 4, 2013, at 7:42 AM, Steffen Schmidt wrote: > Hey Bill, > > I noticed that coot complains that > > WARNING: in init_refmac_mon_lib file > "/sw/share/coot/lib/data/monomers/list/mon_lib_list.cif" not found. > WARNING:: energy lib /sw/share/coot/lib/data/monomers/ener_lib.cif not found.

Re: [COOT] Downloading Coot

On Sep 3, 2013, at 1:04 PM, Dale Tronrud wrote: > I was looking for the download site for Coot but the links have > have found point to > > http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ > > but there is nothing there. Where do I go to find prebuilt coot > binaries? > > Dale Tronrud

Re: [COOT] finking the latest Coot (Nightly builds) [OS X]

Dear OS X Coot users: I've updated coot to use a stand-alone refmac, as well as the CCP4 open-source libraries, so all dependencies on proprietary parts of CCP4 should no longer be present. I've now created a second, variant fink package called "coot-pre" If you want the latest "stable" releas

Re: [COOT] Building coot with ssm-1.3

On Jul 29, 2013, at 5:05 AM, Alexander Minges wrote: > Hello, > > as a side effect in providing ArchLinux packages for internal use in our > institute I tried to compile coot against the latest versions of ssm, > clipper, > libccp4 and mmdb as provided by ftp://ftp.ccp4.ac.uk/opensource/ > >

[COOT] maintaining Coot on OS 10.6.8

On Apr 24, 2013, at 1:40 AM, Andreas Förster wrote: > Dear Özkan and all, > > this question was asked by Dave a month and a half ago > (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1303&L=coot&P=R286), but > there was no reply. > > Snow Leopard is deprecated, even though 25% of OSX users

Re: [COOT] Coot on OS 10.6 - not starting

Dear Engin: Thanks for the feedback, and glad to hear it is working. I never managed to figure out what the problem was, but for some reason there were a bunch of orphaned resource forks (hidden files that look like this: ._foo ) which I deleted. It is possible that was a source for the probl

Re: [COOT] Latest Coot from Fink crashing

Sorry. I just got my 10.6 computer back up and did another build a few hours ago. I haven't been able to reproduce the issue, but was only trying on 10.8. I'm having python mis-match problems on 10.6. On Feb 19, 2013, at 7:21 PM, Dmitry Rodionov wrote: > This seems to be a 10.6 issue si

[COOT] New pre-release for 10.8 with rdkit

8 and crashed my computer with the main website on it. Sorry. I can't drive due to a broken ankle so it might be awhile before it is up again. Good luck. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer La

Re: [COOT] coot crushes in the beginning

On Feb 8, 2013, at 3:29 PM, Arto wrote: > /Users/pulk/.coot-preferences/0-coot-history.scm Try moving or deleting that file and see if it works again.

[COOT] next version?

Which button in COOT do I press to print a PDB file represented as a ball-and-stick model to get a 3D printout from someplace like this? http://www.shapeways.com William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer

Re: [COOT] No updates

chance to unpack. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Nov 12, 2012, at 12:25 PM, Paul Emsley wrote

Re: [COOT] Release 0.7

Additional OS X builds are linked here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot On Sep 29, 2012, at 2:49 AM, Paul Emsley wrote: > Mac 10.8: > > http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip >

Re: [COOT] fink stuff (OS X)

be used for coot and the ccp4 suite, to prevent users from having to install two sets of what should be the same libraries. Peace and joy, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laborator

Re: [COOT] 0.7-pre-1-4305 crashes on OSX 10.8

Please don't ask me why, but issuing "fink remove python" solves the (run-time) problem. You won't need to recompile anything. Fink's python package, as opposed to its "python2.7" package, is just a place-holder. It shouldn't be this way, and I will have to fix the package somehow to ensure

Re: [COOT] 0.7-pre-1-4305 crashes on OSX 10.8

On Sep 4, 2012, at 2:23 AM, Martin Montgomery wrote: > The previous version (4303) was working perfectly (and still is on my laptop > with fink 0.34.2). 4303 which I have built as "stand-alone" has the same crash. I am reasonably sure it used to work...

Re: [COOT] 0.7-pre-1-4305 crashes on OSX 10.8

Sorry, my "fix" is irrelevant. This is a bigger problem. The main python thread is crashing. I will try to figure out why. Here is the crash log if anyone can make sense of it: http://psbmini.ucsc.edu/~wgscott/temp/coot_crash.log On Sep 4, 2012, at 2:23 AM, Martin Montgomery wrote: > Hell

Re: [COOT] 0.7-pre-1-4305 crashes on OSX 10.8

/python2.7/site-packages/gtk-2.0:/sw/share/coot/python and it should work. Coot is inheriting $PYTHONPATH from some other location, probably CCP4, and is getting messed up. I'm about to update the fink package, as soon as I confirm today's svn (r4386) compiles and behaves. Sorry. Bill

Re: [COOT] problem with "Auto open MTZ" in coot

ations/coot.app/Contents/coot/bin/coot-real > platform: > /usr/bin/uname > core: #f > > Best regards > > Stefano > > From: William G. Scott [wgsc...@ucsc.edu] > Sent: Friday, August 03, 2012 9:59 PM > To: Pernigo, Stefano > C

Re: [COOT] problem with "Auto open MTZ" in coot

What happens if you try to display a pdb and map downloaded from the EDS? I believe that uses the same auto-open sequence, and it would help in figuring out whether the problem is with a refmac incompatibility or something else… On Aug 2, 2012, at 8:13 AM, "Pernigo, Stefano" wrote: > Dear co

Re: [COOT] [ccp4bb] Question on stereo monitor: LG D2342P-PN

;ll bet it will work fine. If you can get it from Best Buy for under $300 and return it within 30 days for a full refund, it might be worth it. Either way, let us know. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228

Re: [COOT] CCP4 6.3.0 released

I don't, but I will try to get it done by the time 10.8 is released, if not sooner. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, Calif

Re: [COOT] CCP4 6.3.0 released

On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: > I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laborator

Re: [COOT] OSX OXT crash

Oy. I am happy to fix it, but need some guidance. I have no idea where to begin. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California

Re: [COOT] LIDIA on OS X

I've just bumped this up to 4099. Please let me know if it resolves these problems. Sorry. Bill On Apr 3, 2012, at 5:04 AM, Antony Oliver wrote: >> reworked the residue placement recently, r4072.

Re: [COOT] X11/Coot issues on OS X: kCGErrorIllegalArgument: CGSGetSurfaceBounds

I get it too. It seems worse on my faster computers with more processors, so I guess it is some multi-threading screw-up. Updating X11 shouldn't do anything because the Xquartz updates put the libraries in a different location, so coot will never know they exist. My work-around is to start up

Re: [COOT] Coot nucleic acid issue

e/coot/python export COOT_SBASE_DIR="$CCP4/share/sbase" export PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library/Coot/lib/python2.7/site-packages/gtk-2.0:/Library/Coot/share/coot/python:$PYTHONPATH /Library/Coot/bin/coot-real "$@" William G. Scott Professor Depa

Re: [COOT] Coot nucleic acid issue

/refmac/data/refmac_experimental/refmac_dictionary_v5.35.tar.gz William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459

[COOT] Coot and stereo projector

Howdie: Has anyone had success using coot with a 3D stereo projector? If so, any recommendations? Thanks. Bill William G. Scott Contact info: http://www.chem.ucsc.edu/~wgscott/

Re: [COOT] Coot Book of the Genesis

hould aim to do this for ubuntu already. Is anyone reading this a maintainer for ubuntu and/or debian? Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa C

[COOT] Coot - 3D Anaglyph

Does coot do red/greed (anaglyph) stereo? All google showed me was this: http://www.flickr.com/photos/hindt3d/2268014240/ This would be useful for classroom settings. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA

Re: [COOT] GThread-ERROR **: GThread system may only be initialized once.

On Jan 26, 2012, at 5:36 AM, Bernhard Lohkamp wrote: > Hope this resolves the problem, > > B Seems to fix it on OS X -- Bill

Re: [COOT] how to optimize this part in order to have the green blobs disappear by Coot

actor refinement. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292

Re: [COOT] coot on OS X

r help. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459

Re: [COOT] Coot 0.6.2 and X11

Well, I just build a version for 10.6, and haven't had a chance to point anyone to its web location, so I am guessing you installed the one I compiled for 10.7…. So please try this one and lemme know if it works please. Bill http://sage.ucsc.edu/~wgscott/coot/ William G. Scott Prof

Re: [COOT] Coot for OSX 10.6

Hi Phil: I haven't been able to compile coot since 11 September, due to a change in the code. I've got a 10.6.8 version of that too, but nothing newer I am afraid. Sorry. Bill On Oct 31, 2011, at 5:11 AM, Phil Evans wrote: > As I understand it, Bill Scott now only builds Coot for OSX 10.7:

Re: [COOT] key binding on OS X 10.7

On Oct 24, 2011, at 8:01 AM, Paul Emsley wrote: >> I have switched from the COOT I compiled from fink to Bill's binary COOT, >> the situation has not changed. They are both compiled with fink. The only difference is the top-level directory is /LIbrary/Coot instead of /sw

Re: [COOT] Stereo on a Mac

Hi Andrew: I don't have the hardware to test it on, but as far as I am aware, it will do active stereo. At least that is the intention. Bill PS: I'm compiling various versions of 0.6.2. Somehow I missed the fact that the stable release had come out two weeks ago. Sorry. On Jul 7, 2011, a

Re: [COOT] Python problem

I'm hosting nightly builds now, and none of the more recent versions should have this in the wrapper script. Please let me know if somehow that isn't the case. Bill On May 4, 2011, at 9:10 AM, Phil Evans wrote: > I did delete the *.pyc files in the system directories, and they have now > re

Re: [COOT] Python problem

Dear Phil, Paul, Ben, Bernhard et al: Sorry to arrive 8 hours late to the party, but first my apologies to Phil. I thought I had fixed this problem by excising from the coot wrapper script the path in /System/Library, i.e., export PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library

Re: [COOT] Mac magic mouse

I configured "Better Touch Tool" to enable a 3-fingered click to emulate the middle button. http://blog.boastr.net/ On Apr 18, 2011, at 10:48 AM, Mirek Cygler wrote: > Dear experienced Mac users, > I am trying to use coot on a Mac with the magic mouse. How can I > emulate a 3-button mous

Re: [COOT] Coot won't run OSX 10.5.8

On Apr 9, 2011, at 12:54 PM, Krystle Williams McLaughlin wrote: > I downloaded a stand-alone version and unpacked everything to /Library/Coot. As stated previously, I compiled this for 10.6 only. It will not work on 10.5. Unfortunately, I'd have to go through coot's 150+ dependencies and figure

Re: [COOT] Coot won't run OSX 10.5.8

On Apr 6, 2011, at 12:50 PM, Krystle Williams wrote: > Hi, > I had installed Coot v. 0.6-pre-1 successfully using fink a couple years ago > on an Intel iMac running OSX 10.5.8. Last week I tried to update it with > fink. When that failed, I ended up downloading a new build from > http://sage.uc

Re: [COOT] New Coot plugin for RNA building

Nice. Seems to work fine in the OS X version as well... in my 60 seconds of testing. Bill On Mar 31, 2011, at 12:58 PM, Kevin Keating wrote: >I've just released a new Coot plugin to help with building RNA structure, > so I wanted to make a quick announcement to the mailing list for any

[COOT] Stand-Alone Coot -automated builds for OS X 10.6.X 64-bit

I'm attempting to generate automated builds of coot pre-releases for OS X 10.6.X users. These are 64-bit. If all works well, there should be a new one every day (assuming a new source tarball is available). http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Please let me know

[COOT] coot on OS X 10.4

Has anyone managed to compile a recent version of coot on OS X 10.4.X via fink? Thanks. Bill Scott

Re: [COOT] Installation problems: Coot for OS X - from CCP4 / Fink

Dear Antony: First, allow me to apologize for this. I was hoping this would help make everything seamless. Mark Brooks suggested updating X11 from http://xquartz.macosforge.org/trac/wiki . Although this might help with such a problem on 10.5 with ppc., in this case I believe it shouldn't

[COOT] Stand-Alone Coot - 0.6.2 pre-release svn rev. 3072 OS X 10.6 64-bit, phenix-compliant

Sorry I haven't done this until now. Been distracted by the struggle for survival. http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3072

Re: [COOT] PyGTK in standalone OS X builds

Check /usr/local/xtal/coot64/bin/coot to see if I set $PYTHONPATH right. It should have /usr/local/xtal/coot64/lib/python2.6/site-packages/gtk-2.0 Nathaniel Echols wrote: > When I use the 0.6.1 package from Bill's web site, I get this error when I > try to start the Python scripting GUI: > > C

Re: [COOT] Problem reloading Coot.

Did you issue source /sw64/bin/init.sh (or init.csh if you are a tcsh user) first? This sets $PATH and some other needed environment variables. On May 4, 2010, at 6:01 AM, David Lisgarten wrote: > Dear Coot, > I recently installed Coot version (0.6.1 64 intel) on a > iM

Re: [COOT] MiniDisplay ports and Zalman

As a positive control, mine works with what I assume to be the same configuration: Mac Mini --> mini/DVI adapter --> Zalman-supplied DVI cable --> Zalman DVI input port. I assume you tried hitting the "detect displays" button in the "Displays" pane of System Preferences? If not, try that. BTW

Re: [COOT] Ligands

If you can define a SMILES string for your ligand, you can get coot to build the ligand with the press of a button in a fraction of a second. If the SMILES syntax is a PITA, use this: http://www.molinspiration.com/cgi-bin/properties If you need more options, phenix.elbow also permits you to use a

[COOT] coot distributed by ccp4-6.1.3 and python scripting

Hi Hari: I am about 99% sure you have to compile it with configure directives to use python. The way I compile it is to configure with both guile and python ( --with-guile --with-python=/prefix ); I don't know why they don't do it that way. HTH, Bill

Re: [COOT] cannot save my coordinates

On Feb 20, 2010, at 3:41 PM, Seth Mcdonald wrote: > Greetings coot community, > I have installed coot 0.6.1 on a mac OSX 10.6 using fink. Everything appears > to work great, except when I try to save my coordinates nothing happens. I > go File->Save Coordinates... and it tells me to select a

Re: [COOT] [ccp4bb] coot and probe clash

On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: > On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott > wrote: > >> This is available to install as a binary from here: >> >> http://molprobity.biochem.duke.edu/get_molprobity.php >> >> >> Although p

Re: [COOT] Coot 0.52 on OSX not showing molecule

> Any ideas? > > -Sam > Try something more recent.

Re: [COOT] Coot dependency problem? Power PC G4

Dear Richard: It looks like I neglected to add this as a dependency. Please try installing libcurl4-shlibs, and hopefully that will solve the problem. If not, please let me know as soon as possible. Bill On Jan 17, 2010, at 12:33 PM, Richard Kingston wrote: > > Hello Bill > > After updati

Re: [COOT] SGI dials and coot?

On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote: > Every time I'd ask a question You really ought to update. 0.1 is a bit long in the beak.

Re: [COOT] SGI dials and coot?

David Gohara wrote this. My guess is he could be talked into getting it working. He is exceptionally helpful and extremely knowledgeable, so in my humble opinion he would be a perfect contributor. On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote: > Paul, I can imagine building MacDials f

[COOT] OS X /fink coot update problems

Yo: Several people wrote to me in the last couple of days about different problems with respect to the latest coot update in fink. This all happened at the beginning of term so I haven't really had enough time to deal with this systematically. Briefly, I put coot 0.6 is in the stable and unsta

Re: [COOT] coot 0.6.1-pre update - osx 10.6 - problem with mtz and map files

Are you using the 32-bit or 64-bit coot? I have to confess only having checked the 64-bit version (which worked ok in my hands). On Jan 7, 2010, at 9:31 PM, Jan Abendroth wrote: > Hi all, > I am trying to update coot on osx 10.6 from a 0.6-pre version to the current > fink version (0.6.1-pre).

Re: [COOT] Building latest coot pre-release on OS X

I put re-1-revision-2678 info fink unstable cvs just now. (Someone has to do this; it isn't automatic). On Jan 6, 2010, at 3:38 AM, Andrew Sharff wrote: > Bill, > > How can I build the latest coot pre-release (0.6.1-pre1) on OSX with (or > without if necessary) fink > > Even if I run fink

Re: [COOT] Building latest coot pre-release on OS X

I put re-1-revision-2678 info fink unstable cvs just now. (Someone has to do this; it isn't automatic). On Jan 6, 2010, at 3:38 AM, Andrew Sharff wrote: > Bill, > > How can I build the latest coot pre-release (0.6.1-pre1) on OSX with (or > without if necessary) fink > > Even if I run fin

Re: [COOT] Scripting missing in CCP4 distribution of COOT v0.6.0 CCP4 (OS X 10.4+ universal dmg installer)

No problem. The hope is that with fink, anyone can compile and install coot without drama on OS X ppc or intel, 10.6, 10.5, 10.4 (there is no 10.6 ppc). On Jan 5, 2010, at 6:13 AM, Huw Jenkins wrote: > > On 5 Jan 2010, at 13:57, William G. Scott wrote: > >> If you use what

Re: [COOT] Scripting missing in CCP4 distribution of COOT v0.6.0 CCP4 (OS X 10.4+ universal dmg installer)

See if this works: On Jan 4, 2010, at 2:58 PM, Huw Jenkins wrote: > On 4 Jan 2010, at 22:21, Nathaniel Echols wrote: >> >> The package distributed by CCP4 was not comp

[COOT] Coot research at UC Santa Cruz

http://www.mercurynews.com/breaking-news/ci_14056830 (Sorry, off-topic, but strangely compelling.)

[COOT] Stand-Alone Coot - OS X intel 10.6

The link below is for OS X intel users. I compiled on 10.6. There is a small possibility it might work on intel 10.5, but hopefully no one would need that... http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Most_Current:

Re: [COOT] 120hz LCDs and coot stereo

Just get a $300 Zalman LCD monitor and use coot with that. No special hardware required and it is OS independent. I'm using it also as my primary monitor as I type this. Michael J Miley wrote: > I have a linux workstation with a nvidia quadro graphics card and > matching emitter/lcd glasses se

Re: [COOT] fink coot : unstable branch

On Nov 2, 2009, at 3:59 PM, Bryan W. Lepore wrote: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X "Be sure to use the so-called "unstable" branch of fink to get the latest pre-releases of coot" do i read this correctly : it means ONLY pre-releases, right? and th

Re: [COOT] A general plea

y have no cell phone, and I never use the ccp4i gui. All the best, Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott On Oct 11, 2009, at 11:59 PM, John M. Berrisford wrote: I guess sometimes its not worth instantly upgrading to the bleeding edge versions of sof

Re: [COOT] Coot 2396 troubles

This happened on a new snow leopard install. It looks like that Apple decided not to include any .la with their X11 SDK. Yes, unfortunately the only way to deal with this is to delete all the *.la files in /sw that make reference to the nonexistent libs or other *.la files. I found the

Re: [COOT] problem updating coot using fink

Dear Eleonore: As you mentioned, everyone who upgraded 32-bit fink on 10.6 runs into this. If you start fresh (either 32-bit or 64-bit), the problem doesn't arise. I hope you don't mind me cc-ing the cootbb, as this problem is a general one. The advice I was given, and with some reluct

  1   2   >