Dear All,
I have a set of data, in which there are very nice electron density for
several Arg residues. However MolProbity analysis demonstrated that the
percentage of the Arg rotamer in my data is 0%. Although there is the
possibility that the Arg rotamer in my data is 0%, I still wonder is an
Dear All,
Real space refinement in COOT is one important strategy to reduce Ramachandran
outlier, right?
Dialing
Dear All,
If I rebuild a 4-residue peptide, and the first 1 is leu. When I rebuild the
first one, the sidechain of leu occupies the electron density of the first 3
residues. Can you tell me the method to turn the side chain of Leu from
position of the first 3 residues to its sidechain position i
Dear All,
Suppose I delete a residue ( residue 100 for example) for outlier refinement,
then I add the same residue at the C-terminal of residue 99 (by Add terminal
residue function of the Coot). By coot, how can I connect the C-terminal of
residue 100 to the N-terminal of residue 101?
I am look
Dear All，
If an initial PDB has only 86% residues in the Ramachandran favored region, it
would mean there is a significant error (for example significant length of
protein fragment in the total protein assigned to the wrong electron density
map position) , right?
Dialing
Dear All,
Will you please introduce me the ways to correct Ramachandran outlier by Coot?
Dialing
Dear All,
When I use WinCoot 0.8.1 to open a PDB file, it comes,
Fix Nomenclature Errors. Correct them?
Asp [spec: 1 "A" 128 ""]PHE[spec: 1 "A" 134""]PHE [spec: 1 "A" 371""]
But when I check the 3 residues, I cannot find any error.
Will you let me know the issue?
Dialing
nement. Is any bug in my CCP4? Or there is something I do not understand?
Dialing
On Tuesday, 6 January 2015, 10:10, CHAVAS Leonard
wrote:
Dear Dialing
are you talking about the 'creating date' or the 'modified date'?
Leo
On Jan 6, 2015, at 2:55 AM, Dialing P
Dear All,
When I run Refmac, it would produce a refined PDB file and mtz file. My
question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, I
find the refined PDB file and mtz file were created in the target directory at
perhaps 6:30 pm. I think from 6:30 pm the created PDB f
Dear All,
Will you please tell me what should I input for the LIB in for refmac5? How can
I get the LIB in?
Dialing
Dear All,
After I got the initial MTZ file without the structure factors, will you please
tell me by which CCP4 program I can get the MTZ file with the structure factors?
I am looking forward to getting your reply.
Dialing
Dear All,
Will you please show your opinion on the standards or qualifications to serve
as the co-author for a protein 3D structure stored in RCSB?
Cheers,
Dialing
I just have it successfully done:
Import reflection file in mmCIF format and create MTZ file
In 1w2i-sf.cif
- Forwarded Message -
From: Jayashankar
To: Dialing Pretty
Cc: CCP4BB@jiscmail.ac.uk
Sent: Wednesday, 29 February 2012 7:05 PM
Subject: Re: [ccp4bb] CCP4i Reflection
Dear All,
I want to use "CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ" to
change a RCSB mmCIF file into MTZ file.
It shows there are a lot of data name (related to _pdbx_.or something else) not
present in dictionary, and shows CCP4I termination status 0 "child process
excited
Dear All,
Will you please tell me a server of software which can draw a curve for the B
factor of the atoms in a protein PDB file from the first residue to the
residue?Or a server or software by which we can easily order the B factors of
the atoms in the PDB file according to the B factor in
Dear All,
For the PDB_extract, one item to be filled is "Deposit Structure Factor
Used for Final Refinement". If this way the structure factor which could be
downloaded from RCSB after depositation will be not the final
structure factor corresponding to the final deposited PDB file, as for wha
Dear All,
After we refine the structure of the protein to satisfactory with
satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree
always increases slightly after the water picking refinment.
Do you have nay idea to solve this problem or any comment?
Cheers,
Diali
Dear All,
Can anyone tell me how to change the position of Cbeta of Ser by Coot?
Cheers,
Dialing
Dear All,
For the 3.4 M sodium malonate of Hampton Research, will you please tell me how
the pH was regulated to 6.0, 7.0 and 8.0 separately?
Cheers,
Dialing
Dear All,
For the electronic density of LEU and Pro in the electronic density map, which
is much stronger?
For the electronic density of LEU and Lys in the electronic density map, which
is much stronger?
The reason I ask the above questions is I need to distinguish them in the
electronic de
Dear All,
Can the CCP4 software get mixed with the PHE and ARG?
I use the Coot to build a peptide. 2 fragments of peptides are suitable for one
specific part of electronic density map, and there is only one residue can
distinguish which fragment of peptide is the real peptide fragment for that
Dear All,
For the RCSB depositation report, it gives the "Average Occupancy-weighted avg
temperature factor (Deviation)".
Will you please tell me what range the "Average Occupancy-weighted avg
temperature factor (Deviation)" should be and what is the significance of that
value?
I am lookin
Dear All,
I am trying to convert a PDB and the corresponding mtz file to the mmcif file,
and I got the following message:
"Converting structure factor to mmCIF format
Error! No labels are written for MTZ to mmCIF conversion Structure factor
conversion is done.
Header of the mtz file can
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