Re: [COOT] Wincoot 0.9

[Daniel Asarnow]

I'm getting an ImportError loading the "site" module, which aborts the
program. It must be my environment, but simply clearing env variables
didn't help. Do you have a system python installed?

-da

On Fri, Apr 24, 2020 at 9:39 PM Bernhard Rupp 
wrote:

> Not sure what you are asking for – in principle it works, just unzip the
> file in a directory, and execute the batch file in the /bin directory.
>
>
>
> I was able to load local coordinates and maps.
>
>
>
> Fetch from PDB failed, but the link it has is correct
>
>
>
> DEBUG:: extracted accession code handle mode n 1
>
> BL WARNING:: retrieve of url
> https://www.ebi.ac.uk/pdbe-srv/view/files/6fak.ent failed
>
> handle_read_draw_molecule_with_recentre ("coot-download/6fak.pdb.ent", 1)
>
> WARNING:: Error reading coot-download/6fak.pdb.ent
>
>
>
> Is that your problem? I haven’t gone through the rest yet, obviously….
>
>
>
> Cheers, BR
>
> *From:* Daniel Asarnow 
> *Sent:* Friday, April 24, 2020 18:59
> *To:* b...@hofkristallamt.org
> *Cc:* COOT@jiscmail.ac.uk
> *Subject:* Re: Wincoot 0.9
>
>
>
> If you get it to run, please let us know how!
>
>
>
> Good luck,
>
> -da
>
>
>
> On Fri, Apr 24, 2020 at 5:31 PM Bernhard Rupp 
> wrote:
>
> Yes I found the beta release now thx!
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Daniel Asarnow
> *Sent:* Friday, April 24, 2020 16:57
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Re: Wincoot 0.9
>
>
>
> My apologies for the confusion!
>
>
>
> It was posted by Bernhard *Lohkamp* 12 days ago:
> https://github.com/bernhardcl/coot/releases
>
>
>
> Best,
>
> -da
>
>
>
>
>
> On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp 
> wrote:
>
> If you could reveal where you got wincoot 0.9.x from, one could perhaps
> assist…
>
> See no message to this effect maybe got lost…
>
>
>
> Cheers, BR
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Daniel Asarnow
> *Sent:* Friday, April 24, 2020 14:48
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Wincoot 0.9
>
>
>
> Hi all,
>
> Bernhard kindly posted a Wincoot build based on 0.9 recently. I was
> wondering if anyone was using it, and what is the correct way to use the
> package (with just /bin, /include, /lib provided).
>
>
>
> Thanks & best,
>
> -da
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>
>



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Re: [COOT] Wincoot 0.9

[Bernhard Rupp]

Not sure what you are asking for – in principle it works, just unzip the file 
in a directory, and execute the batch file in the /bin directory.

 

I was able to load local coordinates and maps.

 

Fetch from PDB failed, but the link it has is correct 

 

DEBUG:: extracted accession code handle mode n 1

BL WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe-srv/view/files/6fak.ent 
failed

handle_read_draw_molecule_with_recentre ("coot-download/6fak.pdb.ent", 1)

WARNING:: Error reading coot-download/6fak.pdb.ent

 

Is that your problem? I haven’t gone through the rest yet, obviously….

 

Cheers, BR

From: Daniel Asarnow  
Sent: Friday, April 24, 2020 18:59
To: b...@hofkristallamt.org
Cc: COOT@jiscmail.ac.uk
Subject: Re: Wincoot 0.9

 

If you get it to run, please let us know how!

 

Good luck,

-da

 

On Fri, Apr 24, 2020 at 5:31 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Yes I found the beta release now thx!

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 16:57
To: COOT@JISCMAIL.AC.UK  
Subject: Re: Wincoot 0.9

 

My apologies for the confusion!

 

It was posted by Bernhard Lohkamp 12 days ago: 
https://github.com/bernhardcl/coot/releases

 

Best,

-da

 

 

On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

If you could reveal where you got wincoot 0.9.x from, one could perhaps assist…

See no message to this effect maybe got lost…

 

Cheers, BR

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 14:48
To: COOT@JISCMAIL.AC.UK  
Subject: Wincoot 0.9

 

Hi all,

Bernhard kindly posted a Wincoot build based on 0.9 recently. I was wondering 
if anyone was using it, and what is the correct way to use the package (with 
just /bin, /include, /lib provided).

 

Thanks & best,

-da

 

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 =1 

 

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Re: [COOT] Coot Fink 10.15

[William G. Scott]

Hi Ed:

I invested a lot of time into fink, so I was reluctant to let it go, but it 
might be time.  When it was at its prime, it was the best-managed and and most 
science-oriented of the third-party package manager systems.  MacPorts is 
another option I want to take a look at.  To be honest, I 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 the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064  
USA
 
http://scottlab.ucsc.edu/SARS-CoV-2/

> On Apr 24, 2020, at 7:35 PM, Edward Miller  wrote:
> 
> Thanks, Bill, as always for the dedicated support.
> 
> I've been a fink user, actually due to your packages, for at least ten years.
> 
> Maybe it's time to switch to home-brew? Would they have more gtk+2 
> flexibility?
> 
> Best,
> 
> Ed Miller
> 
> On Fri, Apr 24, 2020 at 4:52 PM William G. Scott  wrote:
> Hi Ed (and COOT list):
> 
> I’ve put updated info files here:   http://scottlab.ucsc.edu/fink/finkupdate/
> 
> I’m trying to get these into fink as soon as possible, BUT there are two 
> show-stopper problems:
> 
> (1) The old refmac I have won’t compile with the newer versions of gcc, and 
> we really need a new version of this anyway for coot.  (Coot only requires 
> refmac at runtime, so it can use whatever version you might have with CCP4). 
> If anyone knows of a more recent version that is available for unrestricted 
> download and installation, please let me know.
> 
> (2) Coot itself requires a newer version of gtk+2 than what fink has, and 
> they are objecting that the newer version of gtk+2 has bugs in it that break 
> other programs, so I am stuck on a pre-release version of coot.
> 
> None of this is at all satisfactory, and I apologize.
> 
> I haven’t yet had a chance to download the most recent CCP4 package, 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
> Director, Program in Biochemistry and Molecular Biology
> 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
> 
> 
> 
> > On Apr 24, 2020, at 10:24 AM, William G. Scott  wrote:
> > 
> > Hi Ed:
> > 
> > Briefly, I need to update the package.
> > 
> > Less briefly, I need to change to gcc9, which is easy, and I need to update 
> > to the latest version of coot, 0.9, which is proving to be a nightmare.
> > 
> > I need to go teach a class and will then get back to you with something I 
> > hope will work.
> > 
> > Bill
> > 
> > PS:  If you just want the latest coot, it looks like the latest version of 
> > CCP4, just released, has it.  They are ahead of me.
> > 
> > 
> > 
> > 
> > William G. Scott
> > Director, Program in Biochemistry and Molecular Biology
> > 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
> > 
> > 
> > 
> >> On Apr 24, 2020, at 8:57 AM, Edward Miller  wrote:
> >> 
> >> Hi Professor Scott,
> >> 
> >> I'm trying to install coot via fink on OS X 10.15. This is a clean fink 
> >> install, so I completely blasted my /sw directory prior to this.
> >> 
> >> The installation is looking for a gcc5 package:
> >> 
> >> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package 
> >> "coot-0.8.9-2" (no matching packages/versions found)
> >> Exiting with failure.
> >> 
> >> Is this dependency correct?
> >> 
> >> Thanks for your help and for contributing to crystallography on os x for 
> >> all these years.
> >> 
> >> Ed Miller
> > 
> 



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Re: [COOT] Coot Fink 10.15

[Paul Emsley]

Steady on. I hope that Bill and I can finagle coot into working with 
whatever gtk+ it has been provided.


FWIW, Gtk+3 in the works and Gtk+4 is on the horizon.


Paul.


On 25/04/2020 03:35, Edward Miller wrote:

Thanks, Bill, as always for the dedicated support.

I've been a fink user, actually due to your packages, for at least ten 
years.


Maybe it's time to switch to home-brew? Would they have more gtk+2 
flexibility?


Best,

Ed Miller

On Fri, Apr 24, 2020 at 4:52 PM William G. Scott > wrote:


Hi Ed (and COOT list):

I’ve put updated info files here:
http://scottlab.ucsc.edu/fink/finkupdate/

I’m trying to get these into fink as soon as possible, BUT there
are two show-stopper problems:

(1) The old refmac I have won’t compile with the newer versions of
gcc, and we really need a new version of this anyway for coot. 
(Coot only requires refmac at runtime, so it can use whatever
version you might have with CCP4). If anyone knows of a more
recent version that is available for unrestricted download and
installation, please let me know.

(2) Coot itself requires a newer version of gtk+2 than what fink
has, and they are objecting that the newer version of gtk+2 has
bugs in it that break other programs, so I am stuck on a
pre-release version of coot.

None of this is at all satisfactory, and I apologize.

I haven’t yet had a chance to download the most recent CCP4
package, 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
Director, Program in Biochemistry and Molecular Biology
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



> On Apr 24, 2020, at 10:24 AM, William G. Scott mailto:wgsc...@ucsc.edu>> wrote:
>
> Hi Ed:
>
> Briefly, I need to update the package.
>
> Less briefly, I need to change to gcc9, which is easy, and I
need to update to the latest version of coot, 0.9, which is
proving to be a nightmare.
>
> I need to go teach a class and will then get back to you with
something I hope will work.
>
> Bill
>
> PS:  If you just want the latest coot, it looks like the latest
version of CCP4, just released, has it.  They are ahead of me.
>
>
>
>
> William G. Scott
> Director, Program in Biochemistry and Molecular Biology
> 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
>
>
>
>> On Apr 24, 2020, at 8:57 AM, Edward Miller
mailto:ebm2...@columbia.edu>> wrote:
>>
>> Hi Professor Scott,
>>
>> I'm trying to install coot via fink on OS X 10.15. This is a
clean fink install, so I completely blasted my /sw directory prior
to this.
>>
>> The installation is looking for a gcc5 package:
>>
>> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package
"coot-0.8.9-2" (no matching packages/versions found)
>> Exiting with failure.
>>
>> Is this dependency correct?
>>
>> Thanks for your help and for contributing to crystallography on
os x for all these years.
>>
>> Ed Miller
>




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Re: [COOT] Coot Fink 10.15

[Edward Miller]

Thanks, Bill, as always for the dedicated support.

I've been a fink user, actually due to your packages, for at least ten
years.

Maybe it's time to switch to home-brew? Would they have more gtk+2
flexibility?

Best,

Ed Miller

On Fri, Apr 24, 2020 at 4:52 PM William G. Scott  wrote:

> Hi Ed (and COOT list):
>
> I’ve put updated info files here:
> http://scottlab.ucsc.edu/fink/finkupdate/
>
> I’m trying to get these into fink as soon as possible, BUT there are two
> show-stopper problems:
>
> (1) The old refmac I have won’t compile with the newer versions of gcc,
> and we really need a new version of this anyway for coot.  (Coot only
> requires refmac at runtime, so it can use whatever version you might have
> with CCP4). If anyone knows of a more recent version that is available for
> unrestricted download and installation, please let me know.
>
> (2) Coot itself requires a newer version of gtk+2 than what fink has, and
> they are objecting that the newer version of gtk+2 has bugs in it that
> break other programs, so I am stuck on a pre-release version of coot.
>
> None of this is at all satisfactory, and I apologize.
>
> I haven’t yet had a chance to download the most recent CCP4 package, 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
> Director, Program in Biochemistry and Molecular Biology
> 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
>
>
>
> > On Apr 24, 2020, at 10:24 AM, William G. Scott  wrote:
> >
> > Hi Ed:
> >
> > Briefly, I need to update the package.
> >
> > Less briefly, I need to change to gcc9, which is easy, and I need to
> update to the latest version of coot, 0.9, which is proving to be a
> nightmare.
> >
> > I need to go teach a class and will then get back to you with something
> I hope will work.
> >
> > Bill
> >
> > PS:  If you just want the latest coot, it looks like the latest version
> of CCP4, just released, has it.  They are ahead of me.
> >
> >
> >
> >
> > William G. Scott
> > Director, Program in Biochemistry and Molecular Biology
> > 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
> >
> >
> >
> >> On Apr 24, 2020, at 8:57 AM, Edward Miller 
> wrote:
> >>
> >> Hi Professor Scott,
> >>
> >> I'm trying to install coot via fink on OS X 10.15. This is a clean fink
> install, so I completely blasted my /sw directory prior to this.
> >>
> >> The installation is looking for a gcc5 package:
> >>
> >> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package
> "coot-0.8.9-2" (no matching packages/versions found)
> >> Exiting with failure.
> >>
> >> Is this dependency correct?
> >>
> >> Thanks for your help and for contributing to crystallography on os x
> for all these years.
> >>
> >> Ed Miller
> >
>
>



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Re: [COOT] Wincoot 0.9

[Daniel Asarnow]

If you get it to run, please let us know how!

Good luck,
-da

On Fri, Apr 24, 2020 at 5:31 PM Bernhard Rupp 
wrote:

> Yes I found the beta release now thx!
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Daniel Asarnow
> *Sent:* Friday, April 24, 2020 16:57
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Re: Wincoot 0.9
>
>
>
> My apologies for the confusion!
>
>
>
> It was posted by Bernhard *Lohkamp* 12 days ago:
> https://github.com/bernhardcl/coot/releases
>
>
>
> Best,
>
> -da
>
>
>
>
>
> On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp 
> wrote:
>
> If you could reveal where you got wincoot 0.9.x from, one could perhaps
> assist…
>
> See no message to this effect maybe got lost…
>
>
>
> Cheers, BR
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Daniel Asarnow
> *Sent:* Friday, April 24, 2020 14:48
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Wincoot 0.9
>
>
>
> Hi all,
>
> Bernhard kindly posted a Wincoot build based on 0.9 recently. I was
> wondering if anyone was using it, and what is the correct way to use the
> package (with just /bin, /include, /lib provided).
>
>
>
> Thanks & best,
>
> -da
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>



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Re: [COOT] Wincoot 0.9

[Bernhard Rupp]

Yes I found the beta release now thx!

 

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 16:57
To: COOT@JISCMAIL.AC.UK
Subject: Re: Wincoot 0.9

 

My apologies for the confusion!

 

It was posted by Bernhard Lohkamp 12 days ago: 
https://github.com/bernhardcl/coot/releases

 

Best,

-da

 

 

On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

If you could reveal where you got wincoot 0.9.x from, one could perhaps assist…

See no message to this effect maybe got lost…

 

Cheers, BR

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 14:48
To: COOT@JISCMAIL.AC.UK  
Subject: Wincoot 0.9

 

Hi all,

Bernhard kindly posted a Wincoot build based on 0.9 recently. I was wondering 
if anyone was using it, and what is the correct way to use the package (with 
just /bin, /include, /lib provided).

 

Thanks & best,

-da

 

  _  

To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT 
 =1 

 

  _  

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 =1 




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Re: [COOT] Wincoot 0.9

[Daniel Asarnow]

My apologies for the confusion!

It was posted by Bernhard *Lohkamp* 12 days ago:
https://github.com/bernhardcl/coot/releases

Best,
-da


On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp 
wrote:

> If you could reveal where you got wincoot 0.9.x from, one could perhaps
> assist…
>
> See no message to this effect maybe got lost…
>
>
>
> Cheers, BR
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Daniel Asarnow
> *Sent:* Friday, April 24, 2020 14:48
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Wincoot 0.9
>
>
>
> Hi all,
>
> Bernhard kindly posted a Wincoot build based on 0.9 recently. I was
> wondering if anyone was using it, and what is the correct way to use the
> package (with just /bin, /include, /lib provided).
>
>
>
> Thanks & best,
>
> -da
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>



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[COOT] Wincoot 0.9

[Daniel Asarnow]

Hi all,
Bernhard kindly posted a Wincoot build based on 0.9 recently. I was
wondering if anyone was using it, and what is the correct way to use the
package (with just /bin, /include, /lib provided).

Thanks & best,
-da



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1

Re: [COOT] Coot Fink 10.15

[William G. Scott]

Hi Ed (and COOT list):

I’ve put updated info files here:   http://scottlab.ucsc.edu/fink/finkupdate/

I’m trying to get these into fink as soon as possible, BUT there are two 
show-stopper problems:

(1) The old refmac I have won’t compile with the newer versions of gcc, and we 
really need a new version of this anyway for coot.  (Coot only requires refmac 
at runtime, so it can use whatever version you might have with CCP4). If anyone 
knows of a more recent version that is available for unrestricted download and 
installation, please let me know.

(2) Coot itself requires a newer version of gtk+2 than what fink has, and they 
are objecting that the newer version of gtk+2 has bugs in it that break other 
programs, so I am stuck on a pre-release version of coot.

None of this is at all satisfactory, and I apologize.

I haven’t yet had a chance to download the most recent CCP4 package, 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
Director, Program in Biochemistry and Molecular Biology
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



> On Apr 24, 2020, at 10:24 AM, William G. Scott  wrote:
> 
> Hi Ed:
> 
> Briefly, I need to update the package.
> 
> Less briefly, I need to change to gcc9, which is easy, and I need to update 
> to the latest version of coot, 0.9, which is proving to be a nightmare.
> 
> I need to go teach a class and will then get back to you with something I 
> hope will work.
> 
> Bill
> 
> PS:  If you just want the latest coot, it looks like the latest version of 
> CCP4, just released, has it.  They are ahead of me.
> 
> 
> 
> 
> William G. Scott
> Director, Program in Biochemistry and Molecular Biology
> 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
> 
> 
> 
>> On Apr 24, 2020, at 8:57 AM, Edward Miller  wrote:
>> 
>> Hi Professor Scott,
>> 
>> I'm trying to install coot via fink on OS X 10.15. This is a clean fink 
>> install, so I completely blasted my /sw directory prior to this.
>> 
>> The installation is looking for a gcc5 package:
>> 
>> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package 
>> "coot-0.8.9-2" (no matching packages/versions found)
>> Exiting with failure.
>> 
>> Is this dependency correct?
>> 
>> Thanks for your help and for contributing to crystallography on os x for all 
>> these years.
>> 
>> Ed Miller
> 



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