[ccp4bb] Refmac- riding hydrogen

[Sasha Pausch]

Dear CCP4bb,

When we select 'generate all hydrogen atoms' option in Refmac5, does it use
riding hydrogen model in refinement?




-- 
Regards,

Sasha Pausch

[ccp4bb] Detwin program

[Sasha Pausch]

Dear CCP4bb,

I am facing a problem in generating .mtz output file from DETWIN program in
CCP4 (version 6.5). Program is finishing successfully with log file but not
mtz file.

Please suggest me a way out!

Thanks in advance,


-- 
Regards,

Sasha Pausch

[ccp4bb] Amino acid side chains without density

[Sasha Pausch]

Dear CCP4bb,

Sorry for asking a naive question.

I am trying to deposit a structure in PDB. I would like to know whether we
have to delete the side chains of amino acids for which we are not finding
density or people prefer keeping the side chains occupancy zero? Is there
any other way to do this?

Re: [ccp4bb] Calculating over all bend in a DNA

[Sasha Pausch]

Hello CCP4bb,


Based on suggestions from the members of CCP4bb, I used program
Curves+ to check the bend (angle) in DNA.

I have given my DNA which has two strands and 13 bases each as an
input. I got an output file where I can see other parameters inferred
from the structure.

But I am getting a message at the end of the output file which I
believe gives me answer for my question.


 (E) Groove parameters

No groove analysis: Pabsent in strand = 1 at level =  11


Please indicate to me what could be the error in this?


Thank you all for answers,


On Wed, Oct 22, 2014 at 2:20 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 Dear Sasha,

 you can select two pairs of three corresponding atoms at either end of
 the stand and calculate the plane normal of each set. The angle between
 the normals would be the overall bend.

 Best,
 Tim

 On 10/21/2014 09:53 PM, Sasha Pausch wrote:
  Hello CCP4bb,
 
  May I know how can we calculate or use any server which can calculate the
  overall bend in a DNA (crystal structure)?
 

 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

[ccp4bb] Calculating over all bend in a DNA

[Sasha Pausch]

Hello CCP4bb,

May I know how can we calculate or use any server which can calculate the
overall bend in a DNA (crystal structure)?

[ccp4bb] How to rename nucleic acid residues in PDB files

[Sasha Pausch]

Hello All,

I would like to know how to change the nomenclature of bases (for example
from Ad to DA for adenosine triphosphate) in PDB file.

[ccp4bb] Protein-DNA structure solution

[Sasha Pausch]

Hello CCP4bb

I am solving a 3.2A resolution crystal data for a protein DNA complex.
I would like to know-
1) How to validate the DNA constraints in the crystal structure?
2) How to fit DNA into density? How different it is from protein fitting
into density?
3) What kind of parameters to consider for refining DNA in Refmac for a
Protein-DNA complex?
4) Which versions of refmac and COOT support DNA refining and model
building?

Thank you in advance,


Sasha Pausch