*Subject:* [External] Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the
structure using phenix. do I need to turn off the DNA secondary
structure restraints during refinement?
Application of secondary structure
On 30/03/2021 02:52, Srivastava, Dhiraj wrote:
I am sorry about phenix related question. But since the question was
refinement related I thought it will be ok to ask on ccp4bb.
For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and
timely respon
Cc: CCP4BB@jiscmail.ac.uk
Subject: [External] Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure using
phenix. do I need to turn off the DNA secondary structure restraints during
refinement?
Application of secondary
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
Application of secondary structure restraints depends on the quality of the
experimental data. The most basic param
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
probably not, unless you have reasons to do so otherwise.
P.S.: There is a Phenix mailing list for Phenix specifi
Hi
I have structure with bent DNA. I am trying to refine the structure using
phenix. do I need to turn off the DNA secondary structure restraints during
refinement?
Thank you
Dhiraj
To unsubscribe from the CCP4BB list
is5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Nigel Moriarty
À : CCP4BB@JISCMAIL.AC.UK
Envoyé le : Vendredi 2 mars 2018 8h25
Objet : Re: [ccp4bb] phenix refinement about cis-proline
Shijun
You can ask all the questions you like about Phenix on PhenixBB. However,
Shijun
You can ask all the questions you like about Phenix on PhenixBB. However,
to answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {
cis_trans_mod = cis *trans
residue_selection = None
Dear all
I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is
gone when I set the "threshold degrees for cis-peptide " from default 45 to 65,
but still has cis-Pro. While no significant change when I set it to 15. My
question is how to set in phenix refinement to clear
Your .eff file must be explicitly referencing the Ca that you removed. Since it
doesn't
exist, phenix stops. Search your .eff file for the string
"name CA and chain A and resname CA and resseq 1"
(maybe a geometry.edit) and remove the reference.
I think the CCP4 bylines specifically encourage di
Thank you all very much for your replies.
However I am sorry this "ad" was a typing mistake of mine while
transcribing the message.
I have signed up for the phenixbb mailing list.
And I will look up at the restraints that may still be there for this atom
that I removed.
Thanks again,
best wish
Hi Almudena,
I am refining my structure with Phenix refine and I get the following error
> message just before starting:
>
> "no atom selected, "name CA ad chain A and resname CA and resseq 1".
>
this is due to atom selection syntax error that you provided:
after CA must be and not ad .
> I
FYI, there is a phenix BB for phenix questions.
Sent from Jack's iPad
> On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra
> wrote:
>
> Dear all,
>
> I am refining my structure with Phenix refine and I get the following error
> message just before starting:
>
> "no atom selected, "nam
Change "ad" to "and" in selection.
Sent from Jack's iPad
> On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra
> wrote:
>
> Dear all,
>
> I am refining my structure with Phenix refine and I get the following error
> message just before starting:
>
> "no atom selected, "name CA ad chain
Dear all,
I am refining my structure with Phenix refine and I get the following error
message just before starting:
"no atom selected, "name CA ad chain A and resname CA and resseq 1".
I knew how to fix it once but I think I have forgotten now. Anyway, the
only difference between the output mode
Dear all,
I'm refining a structure with three modified amino, ccp4 code: CY3, DTR,
and MPT respectively. However I don't know how to give phenix.refine the
adequate libraries as to obtain the correct geometry for three amino acids.
I tried to add the cif libraries downloaded from ccp4 to the comman
Sent: Friday, December 18, 2009 5:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phenix refinement peptide bond poor geometry
Dear all,
I'm about to deposit a structure into the protein data bank and I'm
encountering a disturbing problem, I have a protein site where the
pept
Hi Mohd,
- if it is a regular peptide bond then they are linked automatically and
this problem should never happen, otherwise there must be something not
right with your input PDB file.
- check in .geo file if this particular bond is restrained;
If you send me (and not to the whole bb) the P
Dear all,
I'm about to deposit a structure into the protein data bank and I'm
encountering a disturbing problem, I have a protein site where the
peptide bond is not properly linked, the distance of C-N bond is 2.23
Angstrom, I tried to restrain that site by modifying my def file but the
problem p
Dear folks:
I am currently using Phenix to refine a structure that has many
carbohydrate chains on it.
I created the cif file according to an old message from Dr.Ralf W like
the following:
refinement.pdb_interpretation {
apply_cif_link {
data_link = NAG-ASN
residue_se
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