Re: [COOT] WinCoot 0.9 beta2 waters

2020-06-26 Thread Paul Emsley 


On 26/06/2020 21:01, Haji-Ghassemi, Omid wrote:


Dear fellow WinCoot users,

I recently updated my Wincoot to the latest 0.9 beta and changed the 
start-up script to load all of the library and dictionary files 
required for refinement (as Bernhard suggested).


Everything seem to work fine, but my waters appear as a small red dots 
instead of the more visually pleasing red cross. I know this is a 
minor issue and I could just move on, but I would like to change it 
back if possible. Any ideas? Have anyone else experienced this?




It isn't possible in 0.9. Using tiny atoms for waters was a backwards 
step it now seems. I have improved the atom radius for waters in 0.9.1.



Paul.





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[COOT] WinCoot 0.9 beta2 waters

2020-06-26 Thread Haji-Ghassemi, Omid 
Dear fellow WinCoot users,

I recently updated my Wincoot to the latest 0.9 beta and changed the start-up 
script to load all of the library and dictionary files required for refinement 
(as Bernhard suggested).
Everything seem to work fine, but my waters appear as a small red dots instead 
of the more visually pleasing red cross. I know this is a minor issue and I 
could just move on, but I would like to change it back if possible. Any ideas? 
Have anyone else experienced this?

Best,
Omid
---
---
Omid Haji-Ghassemi, Ph.D.
Postdoctoral Fellow
University of British Columbia
Faculty of Medicine
Department of Biochemistry & Molecular Biology
2350 Health Sciences Mall
Vancouver, BC, V6T 1Z3
Canada






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Re: [COOT] WinCoot 0.9 beta2 - refinement setup failure

2020-06-26 Thread Aleksandr Sverzhinsky 
For what it's worth, I found the monomer library in the older coot installation 
(share>coot>lib) and copied it to the same place in coot 0.9. Refinement works 
now, but I may run into more problems as I go.



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Re: [COOT] WinCoot 0.9 beta2 - refinement setup failure

2020-06-26 Thread Daniel Asarnow 
I think the simplest way is to install the last available WinCoot 0.8x
installer, then unpack 0.9 in that directory.

Best,
-da

On Fri, Jun 26, 2020 at 10:59 AM Aleksandr Sverzhinsky <
aleksandr.sverzhin...@umontreal.ca> wrote:

> Thank you, that confirms that I'm using it as intended. Pardon the naive
> question, but how do I get the dictionary from the old coot or from phenix?
>
> Aleksandr
>
> On Thu, 25 Jun 2020 20:51:21 +0200, Bernhard Lohkamp <
> bernhard.lohk...@ki.se> wrote:
>
> >Hello,
> >
> >On 25/06/2020 18:05, Aleksandr Sverzhinsky wrote:
> >> Hello,
> >>
> >> I downloaded the WinCoot 0.9 beta2 folder to my C:\ directory as was
> done using the WinCoot 0.8.9.3 installer. Since there isn't an installer
> for this version, I don't have the shortcuts automatically created, but I
> found the wincoot64.bat file. Is this the correct way to install WinCoot
> 0.9?
> >
> >Yes and no. WinCoot 0.9 beta (2) is not an installer but just a zip
> >archive, so it will just unpack all (WinCoot) files. You run it by
> >running the wincoot64.bat file (or a link to it - or edit the old links
> >to point to this new bat file).
> >
> >> Now when I try real space refinement I get the error "Warning:
> Refinement setup failure. Failed to find restraints for: ALA"; this happens
> for all residues. Any help is appreciated.
> >
> >This can be expected especially if you dont have CCP4 installed. The
> >current archive (!) ships without the dictionary so you will need to get
> >this form elsewhere (old Coot, Phenix, CCP4). Maybe I should add some
> >more instructions on this and/or add the dictionary... Maybe for 0.9
> >(still likely to be without an installer though). Too many covid-19
> >issues to deal with first though...
> >
> >HTH!?
> >
> >Stay safe,
> >
> >B
> >
> >--
> >***
> >
> >Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
> >
> >Div. Molecular Structural Biology/Biomedicum D9
> >Dept. of Medical Biochemistry and Biophysics (MBB) |
> >Karolinska Institutet
> >SE-171 77 Stockholm
> >Sweden
> >+46 8 52487055
> >bernhard.lohk...@ki.se | ki.se
> >
> >
> >När du skickar e-post till Karolinska Institutet (KI) innebär detta att
> KI kommer att behandla dina personuppgifter. Här finns information om hur
> KI behandlar personuppgifter<
> https://ki.se/medarbetare/integritetsskyddspolicy>.
> >
> >
> >Sending email to Karolinska Institutet (KI) will result in KI processing
> your personal data. You can read more about KI’s processing of personal
> data here.
> >
> >
> >
> >To unsubscribe from the COOT list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing
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Re: [COOT] WinCoot 0.9 beta2 - refinement setup failure

2020-06-26 Thread Aleksandr Sverzhinsky 
Thank you, that confirms that I'm using it as intended. Pardon the naive 
question, but how do I get the dictionary from the old coot or from phenix? 

Aleksandr

On Thu, 25 Jun 2020 20:51:21 +0200, Bernhard Lohkamp  
wrote:

>Hello,
>
>On 25/06/2020 18:05, Aleksandr Sverzhinsky wrote:
>> Hello,
>>
>> I downloaded the WinCoot 0.9 beta2 folder to my C:\ directory as was done 
>> using the WinCoot 0.8.9.3 installer. Since there isn't an installer for this 
>> version, I don't have the shortcuts automatically created, but I found the 
>> wincoot64.bat file. Is this the correct way to install WinCoot 0.9?
>
>Yes and no. WinCoot 0.9 beta (2) is not an installer but just a zip
>archive, so it will just unpack all (WinCoot) files. You run it by
>running the wincoot64.bat file (or a link to it - or edit the old links
>to point to this new bat file).
>
>> Now when I try real space refinement I get the error "Warning: Refinement 
>> setup failure. Failed to find restraints for: ALA"; this happens for all 
>> residues. Any help is appreciated.
>
>This can be expected especially if you dont have CCP4 installed. The
>current archive (!) ships without the dictionary so you will need to get
>this form elsewhere (old Coot, Phenix, CCP4). Maybe I should add some
>more instructions on this and/or add the dictionary... Maybe for 0.9
>(still likely to be without an installer though). Too many covid-19
>issues to deal with first though...
>
>HTH!?
>
>Stay safe,
>
>B
>
>--
>***
>
>Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
>
>Div. Molecular Structural Biology/Biomedicum D9
>Dept. of Medical Biochemistry and Biophysics (MBB) |
>Karolinska Institutet
>SE-171 77 Stockholm
>Sweden
>+46 8 52487055
>bernhard.lohk...@ki.se | ki.se
>
>
>När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI 
>kommer att behandla dina personuppgifter. Här finns information om hur KI 
>behandlar personuppgifter.
>
>
>Sending email to Karolinska Institutet (KI) will result in KI processing your 
>personal data. You can read more about KI’s processing of personal data 
>here.
>
>
>
>To unsubscribe from the COOT list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
>This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
>hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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