On 13/03/2018 07:36, M T wrote:
So finally the solution was easy access...
Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that
session, and it was fine.
Then I went back on my session, I removed the files below:
0-coot-history.py
0-coot-histor
So finally the solution was easy access...
Thanks to someone who suggest me to do that, I created a new user, to
verify if coot was ok under that session, and it was fine.
Then I went back on my session, I removed the files below:
0-coot-history.py
0-coot-history.scm
0-coot.state.py
0-coot.state.s
On 12/03/18 14:05, M T wrote:
> Dear all,
>
> I restart this topic because the problem was finally not solved...
You give me an opportunity to comment, I had previously missed the boat
while traveling.
>
> Summary:
> - I am working on a structure with an unnatural ligand and I want to
> refine th
thing:
>>>
>>> Start with COOT with the DRG coordinates and ProDRG dictionary and try a
>>> bit of real space refinement.
>>> Coot should move the coodinates a bit and you should see something
>>> happen.
>>>
>>> Then read out those new co
or otherwise it will find
>> something which is not appropriate for your problem..
>> Eleeanor
>>
>> On 5 March 2018 at 13:36, wrote:
>>
>>> PS: If you have two different home-brewn ligands, you have to rename one
>>> of them (pdb and cif), otherwise t
erent ligands. Also make sure your cif file is a dictionary and not
>> just a coordinate file.
>>
>> HS
>>
>>
>>
>> *Von:* Schreuder, Herman /DE
>> *Gesendet:* Montag, 5. März 2018 14:31
>> *An:* 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK
&
'Colin Levy'; CCP4BB@JISCMAIL.AC.UK
> *Betreff:* AW: [ccp4bb] Small molecule not refined in coot.
>
>
>
> Hi Colin and Michel,
>
>
>
> In my experience, both refmac and coot will use the most recently read-in
> cif dictionary and there is no need to try to
. März 2018 14:31
An: 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [ccp4bb] Small molecule not refined in coot.
Hi Colin and Michel,
In my experience, both refmac and coot will use the most recently read-in cif
dictionary and there is no need to try to find an unique identifier for
residue and atom names in the cif dictionary.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Colin
Levy
Gesendet: Montag, 5. März 2018 13:38
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot.
Hi Michel,
If your ligand
Hi Michel,
If your ligand is designated as DRG in your pdb then refinement programs will
anticipate that it is:
Chemical Description
Name5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
Formula C12 H11 N3
Formal charge 0
Molecular weight197.236 g/mol
Component type NON-POLYMER
If this is
Dear all,
I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual
pre-fit in the map using coot and I manually merged the pdf file of my
protein with the one of the ligand.
After that I did few cycles of refinem
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