Re: [COOT] Missing Restrains for standard amino acids

2022-08-11 Thread Ricardo Padua 
I've found a quick workaround that works for different MacOS versions
Download MacOS Coot 9.8.1 standalone from CCP-EM
https://www.ccpem.ac.uk/download.php
In Phenix point it to coot-0.9.8.1/bin/coot
Real space refinement and the connection to Phenix works

Best
Ricardo

On Wed, Aug 10, 2022 at 8:38 PM Ricardo Padua  wrote:

> I had the same issue (MacOS Catalina 10.15.7 and the same phenix version).
> The fix was:
> In PHENIX Home screen, click on Preferences, then click on the graphics
> tab, in the Coot path box point it to the coot.app as in
> (/Applications/ccp4-8.0/coot.app) instead of
> (/Applications/ccp4-8.0/bin/coot)
>
> I must point that someone else in the lab has a similar issue using MacOS
> Mojave 10.14.6 and the fix above works for the restrain problem but the
> connection to Phenix is lost
>
> Best
> Ricardo
>
> On Sun, Aug 7, 2022 at 2:09 AM Cryo EM  wrote:
>
>> Hi everyone,
>>
>> I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The
>> phenix version I am using is 1.20.1-4487.
>>
>> At the end of validation run or real space refinement for my cryo-EM map,
>> I want to fix the problems in the model interactively by the "open in coot"
>> button displayed in phenix. As soon as I click on the problems list in
>> phenix, coot takes me to that atom but I am not able to do any local real
>> space refinement in coot since it complains about the missing restrains for
>> even standard amino acids and nucleotides (screenshot attached).
>>
>> Please note that coot alone (when not connected to phenix) works for me
>> flawlessly. I guess it has something to do with missing monomer library
>> path in coot when connected to phenix but I am unable to fix this. Can
>> someone please redirect me to the solution?
>>
>> Regards and thanks!
>>
>>
>> [image: Mailtrack]
>> 
>>  Sender
>> notified by
>> Mailtrack
>> 
>>  07.08.22,
>> 07:51:32
>>
>> --
>>
>> To unsubscribe from the COOT list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>>
>
>
> --
> Ricardo A. P. de Pádua
> HHMI Research Specialist
> Kern Lab
> Brandeis University, Waltham, MA
>
>

-- 
Ricardo A. P. de Pádua
HHMI Research Specialist
Kern Lab
Brandeis University, Waltham, MA



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Re: [COOT] Missing Restrains for standard amino acids

2022-08-10 Thread Ricardo Padua 
I had the same issue (MacOS Catalina 10.15.7 and the same phenix version).
The fix was:
In PHENIX Home screen, click on Preferences, then click on the graphics
tab, in the Coot path box point it to the coot.app as in
(/Applications/ccp4-8.0/coot.app) instead of
(/Applications/ccp4-8.0/bin/coot)

I must point that someone else in the lab has a similar issue using MacOS
Mojave 10.14.6 and the fix above works for the restrain problem but the
connection to Phenix is lost

Best
Ricardo

On Sun, Aug 7, 2022 at 2:09 AM Cryo EM  wrote:

> Hi everyone,
>
> I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The
> phenix version I am using is 1.20.1-4487.
>
> At the end of validation run or real space refinement for my cryo-EM map,
> I want to fix the problems in the model interactively by the "open in coot"
> button displayed in phenix. As soon as I click on the problems list in
> phenix, coot takes me to that atom but I am not able to do any local real
> space refinement in coot since it complains about the missing restrains for
> even standard amino acids and nucleotides (screenshot attached).
>
> Please note that coot alone (when not connected to phenix) works for me
> flawlessly. I guess it has something to do with missing monomer library
> path in coot when connected to phenix but I am unable to fix this. Can
> someone please redirect me to the solution?
>
> Regards and thanks!
>
>
> [image: Mailtrack]
> 
>  Sender
> notified by
> Mailtrack
> 
>  07.08.22,
> 07:51:32
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>


-- 
Ricardo A. P. de Pádua
HHMI Research Specialist
Kern Lab
Brandeis University, Waltham, MA



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Re: [COOT] Missing Restrains for standard amino acids

2022-08-08 Thread Paul Emsley 


On 08/08/2022 16:04, Kenneth Satyshur wrote:
You can tell phenix where to find coot. Point coot to the ccp4 
version, which has the libs. The stand alone version may not have the 
link to the lib that is maintained by ccp4.




I thought that it was the other way around! :-)


Use the environment variable COOT_REFMAC_LIB_DIR to tell Coot where it 
should look for the monomer library.



Paul.




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Re: [COOT] Missing Restrains for standard amino acids

2022-08-08 Thread Kenneth Satyshur 
You can tell phenix where to find coot. Point coot to the ccp4 version, which 
has the libs. The stand alone version may not have the link to the lib that is 
maintained by ccp4.
kas



Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist, Retired From:

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Cryo EM 
Sent: Sunday, August 7, 2022 12:58 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Missing Restrains for standard amino acids

Hi everyone,

I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The phenix 
version I am using is 1.20.1-4487.

At the end of validation run or real space refinement for my cryo-EM map, I 
want to fix the problems in the model interactively by the "open in coot" 
button displayed in phenix. As soon as I click on the problems list in phenix, 
coot takes me to that atom but I am not able to do any local real space 
refinement in coot since it complains about the missing restrains for even 
standard amino acids and nucleotides (screenshot attached).

Please note that coot alone (when not connected to phenix) works for me 
flawlessly. I guess it has something to do with missing monomer library path in 
coot when connected to phenix but I am unable to fix this. Can someone please 
redirect me to the solution?

Regards and thanks!


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