Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

2014-07-15 Thread Sabine Schneider 

Hello Wei,

is the modified base defined as DNA in the cif? (see below)
Is the O3* or O3'? You need the latter.
And check whether there are three hydrogens on the O3. You need to 
either remove one from the cif file manually, or name them according to 
a normal DNA base. (In the latter case, by making the phosphodiester 
bond, one should be removed, if coot/refmac/phenix know that this is DNA...)


Hope that helps!
Sabine


# ---   LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
GdX  G   'Guanosine   ' DNA
35  23 .

#

On 15/07/14 11:14, Wang, Wei wrote:

Hi,

There is a problem about modified DNA refinement.

I generated one CIF file of a modified DNA base using eLBOW software 
of PHENIX. However I found the modified DNA could not be linked to the 
downstream DNA when I refined it in the COOT. Then I generated another 
CIF file using sketcher of CCP4, but the problem still existed.


Is there any expert to help me?

Thanks!!
Best

Wei

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

2014-07-15 Thread Ed Pozharski 
You may need to

1) modify _chem_comp.group to be "DNA" in the cif-file
2) import the resulting cif-file in coot

Cheers


Sent on a Sprint Samsung Galaxy S® III

 Original message From: "Wang, Wei" 
 Date:07/15/2014  5:14 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] The modified 
DNA could not be linked to the downstream DNA in the COOT? 
Hi,

There is a problem about modified DNA refinement.

I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. 
However I found the modified DNA could not be linked to the downstream DNA when 
I refined it in the COOT. Then I generated another CIF file using sketcher of 
CCP4, but the problem still existed.

Is there any expert to help me?

Thanks!!
Best

Wei

[ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

2014-07-15 Thread Wang, Wei 
Hi,

There is a problem about modified DNA refinement.

I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. 
However I found the modified DNA could not be linked to the downstream DNA when 
I refined it in the COOT. Then I generated another CIF file using sketcher of 
CCP4, but the problem still existed.

Is there any expert to help me?

Thanks!!
Best

Wei