I want to summarize my findings about the heme library and finish this
thread:
1)The heme coordinates in HEC.cif contain errors for B ring: it is turned
by 90 degrees relatively to heme plane.
2)HEC in PHENIX is not the same as in CCP4. It does not contain coordinates
for heme and could not be
This is interesting. If the parameters for heme C reflect the molecule before
linking
to cysteines in the protein, and the modifications will be made as specified by
link information in the dictionary, then actually heme C (HEC) should be the
same
as HEM (heme b, protoheme). HEC is superfluous,
---
> *From:* Edward A. Berry <ber...@upstate.edu>
> *Sent:* Tuesday, May 15, 2018 8:07:38 PM
> *To:* Robbie Joosten; CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] Problems with HEC in CCP4
>
> Does this mean- if the pdb file has standard PDB link records
edu>
Sent: Tuesday, May 15, 2018 8:07:38 PM
To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4
Does this mean- if the pdb file has standard PDB link records involving HEC,
like
LINK SG CYS A 32 CAB HEM A 93 1555 1555 1.8
Vonrhein <vonrh...@globalphasing.com>
Sent: Tuesday, May 15, 2018 6:21:35 PM
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4
Hi,
On Tue, May 15, 2018 at 02:21:59PM +, Robbie Joosten wrote:
> A link describes a chemical bond between two
the
appropriate LINK records.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robbie
Joosten
Sent: Tuesday, May 15, 2018 10:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4
Hi Eugene,
The problem is not in the H
?
>
> Cheers,
> Robbie
>
> Sent from my Windows 10 phone
>
>
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene Osipov
> <e.m.osi...@gmail.com>
> Sent: Tuesday, May 15, 2018 2:53:49 PM
> To: CCP4BB@JISCMAIL.AC.
s,
>
> Robbie
>
>
>
> Sent from my Windows 10 phone
>
>
> --
> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene
> Osipov <e.m.osi...@gmail.com>
> *Sent:* Tuesday, May 15, 2018 2:53:49 PM
>
> *To:* CCP4BB@JISCMAIL.AC.UK
&
com>
Sent: Tuesday, May 15, 2018 2:53:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4
Hi Robbie,
I thought LINK just adds another bond restrain to the refinement procedure and
does not affect already existing restrains in library cif file. Am I wrong?
Also, what
day, May 15, 2018 10:51
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb] Problems with HEC in CCP4
>
> Hi Eugene,
>
> The problem is not in the HEC.cif file but with the LINKs which modify
the
> chemistry. The
K records.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robbie
> > Joosten
> > Sent: Tuesday, May 15, 2018 10:51
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Proble
AIL.AC.UK> On Behalf Of Robbie
> Joosten
> Sent: Tuesday, May 15, 2018 10:51
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Problems with HEC in CCP4
>
> Hi Eugene,
>
> The problem is not in the HEC.cif file but with the LINKs which modify the
> chemistry. These we
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