Just for info:
There is new version of the dictionary that is compliant with pdb v3.
It works with new version of refmac and should work with phenix also.
It seemed to work with coot also.
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/remfac_dictionary_v5.18.tar.gz
I should warn that
Yes. It should and I will add it now. I do not think refmac writes
this info into the output file but it will do in one or two days time.
GArib
On 30 Nov 2009, at 11:32, Bernhard Lohkamp wrote:
Alexander,
Do you see a way to include in the refmac-from-coot logfile which
mtz columns were
At the moment refmac does extremely simple selection. First structure
factor label and the first sigma that has similar name to the first
structure factor, if not then the first sigma.
It works for a class of cases but it cannot be universal. While we are
on this matter I think it would be go
Hi all
I have struggled with backward compatability for some time and without
any solution. Only way so far I have found is what Graeme describes.
Compile on Mac Os 10.4 then it works on 10.5.
If anybody has a better solution please let me know. Perhaps gcc 4.5
will sort it out but it is st
On 3 Jun 2009, at 09:19, Kevin Cowtan wrote:
Hi!
Hybrid-36 (initial idea from Ralph Grosse Kunstleve, I think) works
around this problem by allowing higher numbered atoms to be numbered
in base 36 starting from A. CCP4 v6.1.1 and recent versions of
Coot support this, as does phenix.re
We are working on this. We are changing to pdb v3 (or whatever) there
we have a lot of peptides.
If you see in the current version some residue that should be L-
peptide but has not been declared so then it should be corrected.
Garib
On 19 Feb 2009, at 09:22, Paul Emsley wrote:
Garib
Have you declared your modified LYS as L-peptide. It should be be done
in the beginning like:
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
LYS LYS 'LYSINE
- I'll see what I can do about that.
Regards,
Paul.
Garib Murshudov wrote:
You can use a link for this. The name of the link is
CYS-BME
To make sure that you have this link in the dictionary have a look:
$CLIBD_MON/list/mon_lib_list.cif
and search for CYS-BME
If you have this i
You can use a link for this. The name of the link is
CYS-BME
To make sure that you have this link in the dictionary have a look:
$CLIBD_MON/list/mon_lib_list.cif
and search for CYS-BME
If you have this in the dictionary then you can just add a link record
in your pdb file. Example how to u
