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
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
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
. 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
'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
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
&
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
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
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
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 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
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