Re: [ccp4bb] COOT problem

[Rajesh Kumar]

Dear Paul,

It seems that XQuartz 2.7.7 is working in my macbook and I can run COOT a
bit faster.

Thank you for the help.

-Rajesh



On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley 
wrote:

> On 27/02/2018 21:11, Rajesh Kumar wrote:
>
>>
>> I just had installed new SSD and latest macOS High Sierra 10.13.3 into my
>> macbook pro.
>>
>> It seems my macbook is much faster but running COOT is a bit problem.
>>
>> When I open COOT, screen becomes gray for a second and then it opens.
>> When I try to move from one residue to next, it does not move faster.
>>
>
> Just to be clear what you mean, did you expect Coot to move between one
> residue and another because you installed and SSD and updated the operating
> system?
>
>
> Did anyone of you have had same experience with macOS High Sierra 10.13.3?
>>
>>
>>
>>
>> Before I had HDD and macOS Sierra 10.12 and everything worked well.
>>
>>
> Do you mean that everything does not work well now?
>
> Here's a thought: it seems to me that the behaviour of Coot depends more
> on the version of XQuartz than the version of the OS, I use 2.7.8.
>
> Paul.
>

Re: [ccp4bb] COOT problem

[Rajesh Kumar]

Dear Paul,

Thank you very much. Only COOT is giving problem. Other programs work very
well.

I will change XQuartz to 2.7.8 and see if COOT works.

regards,
Rajesh



On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley 
wrote:

> On 27/02/2018 21:11, Rajesh Kumar wrote:
>
>>
>> I just had installed new SSD and latest macOS High Sierra 10.13.3 into my
>> macbook pro.
>>
>> It seems my macbook is much faster but running COOT is a bit problem.
>>
>> When I open COOT, screen becomes gray for a second and then it opens.
>> When I try to move from one residue to next, it does not move faster.
>>
>
> Just to be clear what you mean, did you expect Coot to move between one
> residue and another because you installed and SSD and updated the operating
> system?
>
>
> Did anyone of you have had same experience with macOS High Sierra 10.13.3?
>>
>>
>>
>>
>> Before I had HDD and macOS Sierra 10.12 and everything worked well.
>>
>>
> Do you mean that everything does not work well now?
>
> Here's a thought: it seems to me that the behaviour of Coot depends more
> on the version of XQuartz than the version of the OS, I use 2.7.8.
>
> Paul.
>

Re: [ccp4bb] COOT problem

[Paul Emsley]

On 27/02/2018 21:11, Rajesh Kumar wrote:


I just had installed new SSD and latest macOS High Sierra 10.13.3 into my 
macbook pro.

It seems my macbook is much faster but running COOT is a bit problem.

When I open COOT, screen becomes gray for a second and then it opens. When I try to move from one residue to 
next, it does not move faster. 


Just to be clear what you mean, did you expect Coot to move between one residue and another because you 
installed and SSD and updated the operating system?




Did anyone of you have had same experience with macOS High Sierra 10.13.3?




Before I had HDD and macOS Sierra 10.12 and everything worked well.



Do you mean that everything does not work well now?

Here's a thought: it seems to me that the behaviour of Coot depends more on the version of XQuartz than the 
version of the OS, I use 2.7.8.


Paul.

[ccp4bb] COOT problem

[Rajesh Kumar]

Dear All,

I just had installed new SSD and latest macOS High Sierra 10.13.3 into my
macbook pro.

It seems my macbook is much faster but running COOT is a bit problem.

When I open COOT, screen becomes gray for a second and then it opens. When
I try to move from one residue to next, it does not move faster. Did anyone
of you have had same experience with macOS High Sierra 10.13.3?


The configuration of my current macbook is attached.


Before I had HDD and macOS Sierra 10.12 and everything worked well.

Suggestions will be really appreciated.

Thank you
Rajesh

---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777  |  Fax: 718.430.8565

[ccp4bb] Coot problem

[Md Shaik]

Dear all, 

I am using coot 0.6.2 on MacBook. It was working nicely when I was using 
previous version. With this new coot I am problem as I can not do anything 
except visualisation. If I try to build or refine always show the message 
refinement setup failure, Failed to find restraints or missing dictionary. 
I reinstall the coot but still have the same problem. I was not able to locate 
the dictionary. Can please anybody suggest me something, how to solve the 
problem.  


Thanks in advance

Md. Munan Shaik

Department of Biological Chemistry
School of Bioscience and Biotechnology
via G. Colombo 03
University of Padova
Padova 35131, Italy
Mobile: 00393275671896
E-mail: munanbt2...@yahoo.com
 munan.sh...@unipd.it

Re: [ccp4bb] Coot problem

[Paul Emsley]

Dear all,

I am using coot 0.6.2 on MacBook. It was working nicely when I was 
using previous version. With this new coot I am problem as I can not 
do anything except visualisation. If I try to build or refine always 
show the message refinement setup failure, Failed to find 
restraints or missing dictionary. I reinstall the coot but still 
have the same problem. I was not able to locate the dictionary. Can 
please anybody suggest me something, how to solve the problem.




It is not clear if you are using a Bill Scott binary or not (I believe 
those binaries run the test suite before distribution).


Coot 0.6.2 is synched to CCP4 6.2 for the dictionary.  If you are 
experiencing problems, that may be due to a version mis-match.


You should read the console - it might provide some insight.

You may wish to contact me (off-list) to pursue this.

Paul.

Re: [ccp4bb] Coot Problem! adding r-nucleotide in DNA

[Christian Biertuempfel]

Hi Yusuf,
I had a similar problem once when my pdb file did not have the right
format. Check your input coordinate file if your DNA nomenclature is
correct for coot. Maybe, the program does not recognize your molecule as
DNA.

Good luck,
christian



Yusuf Akhter wrote:
 Hi everybody!
 I am using coot version 0.5.
 I am trying to build a DNA sequence in my model.
 
 At certain positions when i add residues and then used simple mutate
 to make it according to real sequence, it always add ribonucleotide
 (guanine ribonucleotide, Gr) in place of deoxyribonucleotide (guanine
 deoxynucleotide Gd). When i say add residue it adds adenine
 deoxynucleotide but on using simple mutate function this problem occurs.
 
 In rest of the positions in sequence everything works fine except at
 this particular position.
 
 have anybody faced similar problem??
 
 Any suggestion will be appreciated.
 
 
 Thanks in advance.
 
 
 Yusuf
 
 
 
 
 
 
 
 
 

-- 
___

Dr. Christian Biertümpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health  phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03  fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA
___

Re: [ccp4bb] Coot Problem! adding r-nucleotide in DNA

[Yusuf Akhter]

Thanks to Paul and Christian..for responding very quickly to my query.

I tried all versions of coot and it worked in only ver 0.4. Now everything
is fine.

Cheers!
Yusuf



On Thu, Feb 26, 2009 at 7:04 PM, Yusuf Akhter yusuf.akh...@gmail.comwrote:

 Hi everybody!
 I am using coot version 0.5.
 I am trying to build a DNA sequence in my model.

 At certain positions when i add residues and then used simple mutate to
 make it according to real sequence, it always add ribonucleotide (guanine
 ribonucleotide, Gr) in place of deoxyribonucleotide (guanine deoxynucleotide
 Gd). When i say add residue it adds adenine deoxynucleotide but on using
 simple mutate function this problem occurs.

 In rest of the positions in sequence everything works fine except at this
 particular position.

 have anybody faced similar problem??

 Any suggestion will be appreciated.


 Thanks in advance.


 Yusuf

Re: [ccp4bb] COOT Problem

[Tim Fenn]

On Sat, 13 Dec 2008 09:33:11 + Paul Emsley
paul.ems...@bioch.ox.ac.uk wrote:

 Ethan Lai wrote:
  Dear all,
  
  I have recently installed Coot version 0.5 on Fedora 9. However,
  when I tried to open a mtz file, the following error occurs.
  
  CCP4 library signal library_file:Bad mode (Error)
   raised in ccp4_file_readchar 
  
  Any advices? Thanks! 
 
 
 Something of a shot in the dark, but we have recently seen problems 
 (crashes) when using F8 binaries on a F9 machine.  On switching to
 the Ubuntu build things worked OK (this is IIUC).
 
 Ideally there should be a native F9 build of Coot.
 

Once coot gets through the review process:

https://bugzilla.redhat.com/show_bug.cgi?id=472150

it will be available via yum for all supported fedora releases (F9
and F10 atm).

-tim

Re: [ccp4bb] COOT Problem

[Jayashankar]

Yes CCP4I, works better,


S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.


On Sat, Dec 13, 2008 at 6:43 AM, William Scott
wgsc...@chemistry.ucsc.eduwrote:

 Does ccp4i work?



 On Thu, December 11, 2008 8:06 pm, Jayashankar wrote:
  since its a same coot problem,
  i have one more,
 
  i am using mac 10.5 leopord osx  the thing is, i dont get any pop upped
   table even after i do a translate and do a real space refinement .
  is it a bug  or is it a problem in setups of other supportive
  libraries
 
 
  S.Jayashankar
  Research Student
  Institute for Biophysical Chemistry
  Hannover Medical School
  Germany.
 
 
  On Fri, Dec 12, 2008 at 2:22 AM, Ethan Lai tf...@imcb.a-star.edu.sg
  wrote:
 
  Dear all,
 
  I have recently installed Coot version 0.5 on Fedora 9. However, when I
  tried to open a mtz file, the following error occurs.
 
   CCP4 library signal library_file:Bad mode (Error)
  raised in ccp4_file_readchar 
 
  Any advices? Thanks!
 
 



 William G. Scott

 Contact info:
 http://chemistry.ucsc.edu/~wgscott/http://chemistry.ucsc.edu/%7Ewgscott/

Re: [ccp4bb] COOT Problem

[Paul Emsley]

Ethan Lai wrote:

Dear all,

I have recently installed Coot version 0.5 on Fedora 9. However, when I
tried to open a mtz file, the following error occurs.


CCP4 library signal library_file:Bad mode (Error)

 raised in ccp4_file_readchar 

Any advices? Thanks! 



Something of a shot in the dark, but we have recently seen problems 
(crashes) when using F8 binaries on a F9 machine.  On switching to the 
Ubuntu build things worked OK (this is IIUC).


Ideally there should be a native F9 build of Coot.

Paul.

Re: [ccp4bb] COOT Problem

[Jayashankar]

Paul and William,

since we are end users,

we have to depend on big heads like you.
and i believe that things will be bug free and efficient soon.

If it is a trivial problem, then please do update the FAQs so as to make our
ccp4bb not just to bug with these type of questions .

should i uninstall coot from fink list and download from official site and
install it again.




S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.


On Sat, Dec 13, 2008 at 10:33 AM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:

 Ethan Lai wrote:

 Dear all,

 I have recently installed Coot version 0.5 on Fedora 9. However, when I
 tried to open a mtz file, the following error occurs.

  CCP4 library signal library_file:Bad mode (Error)

 raised in ccp4_file_readchar 

 Any advices? Thanks!



 Something of a shot in the dark, but we have recently seen problems
 (crashes) when using F8 binaries on a F9 machine.  On switching to the
 Ubuntu build things worked OK (this is IIUC).

 Ideally there should be a native F9 build of Coot.

 Paul.

Re: [ccp4bb] COOT Problem

[William G. Scott]

On Dec 13, 2008, at 7:38 AM, Jayashankar wrote:



since we are end users,


As am I.


we have to depend on big heads like you.


Is this an oblique Santa Cruz reference?



and i believe that things will be bug free and efficient soon.


Some people believe Obama will soon repeal the Patriot Act, restore  
Habeas Corpus and Posse Comitatus, and not send 20,000 additional  
troops into Afghanistan and the NIH will soon begin to fund again  
beyond the 15th %-ile too.




If it is a trivial problem, then please do update the FAQs so as to  
make our

ccp4bb not just to bug with these type of questions .


An additional option is to use the COOT bulletin board mailing list:
http://www.jiscmail.ac.uk/lists/coot.html




should i uninstall coot from fink list and download from official  
site and

install it again.


No.

Re: [ccp4bb] COOT Problem

[William Scott]

Does ccp4i work?



On Thu, December 11, 2008 8:06 pm, Jayashankar wrote:
 since its a same coot problem,
 i have one more,

 i am using mac 10.5 leopord osx  the thing is, i dont get any pop upped
  table even after i do a translate and do a real space refinement .
 is it a bug  or is it a problem in setups of other supportive
 libraries


 S.Jayashankar
 Research Student
 Institute for Biophysical Chemistry
 Hannover Medical School
 Germany.


 On Fri, Dec 12, 2008 at 2:22 AM, Ethan Lai tf...@imcb.a-star.edu.sg
 wrote:

 Dear all,

 I have recently installed Coot version 0.5 on Fedora 9. However, when I
 tried to open a mtz file, the following error occurs.

  CCP4 library signal library_file:Bad mode (Error)
 raised in ccp4_file_readchar 

 Any advices? Thanks!





William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

[ccp4bb] COOT Problem

[Ethan Lai]

Dear all,

I have recently installed Coot version 0.5 on Fedora 9. However, when I
tried to open a mtz file, the following error occurs.

 CCP4 library signal library_file:Bad mode (Error)
 raised in ccp4_file_readchar 

Any advices? Thanks!

Re: [ccp4bb] COOT Problem

[Jayashankar]

since its a same coot problem,
i have one more,

i am using mac 10.5 leopord osx  the thing is, i dont get any pop upped
 table even after i do a translate and do a real space refinement .
is it a bug  or is it a problem in setups of other supportive libraries


S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.


On Fri, Dec 12, 2008 at 2:22 AM, Ethan Lai tf...@imcb.a-star.edu.sg wrote:

 Dear all,

 I have recently installed Coot version 0.5 on Fedora 9. However, when I
 tried to open a mtz file, the following error occurs.

  CCP4 library signal library_file:Bad mode (Error)
 raised in ccp4_file_readchar 

 Any advices? Thanks!