[ccp4bb] pdb/mmcif to cif

[Pascal]

Hi,

Is anyone know how I can convert a pdb or mmcif file into the cif format ?
I am trying to convert this file:
http://pdb.org/pdb/explore/explore.do?structureId=3NIR

Thanks,
Pascal



smime.p7s
Description: Signature cryptographique S/MIME

Re: [ccp4bb] Puzzling Structure

[MARTYN SYMMONS]

Dear Robbie

A shame then that these 'helpful' annotators did not make use of  Pavel's basic 
sanity on the space group (*mentioned below) and check back to the one listed 
in the uploaded PDB file. 

I often wonder why the PDB does not make the deposited coordinate file publicly 
available so that these sorts of issues can be checked and tracked. Depositors' 
coordinate files nowadays are the output of reputable, documented programs.  

The whole PDB data (excluding the EMDB that was recently merged into it) 
amounts to about a laptop hard drive's worth of data  - so surely space can be 
made for the deposited coordinates? (and restraint files which will be very 
useful for other workers including pdb-redo).

Structural genomic groups could also take a lead here by making their final 
refined coordinates and restraint files available alongside the PDB data. 

Having the depositors' uploaded data would help me understand other puzzling 
features of structures such as the current 4GRV.pdb which seems to have a list 
of TLS groups but contains not a single ANISOU line!...  

Cheers
  Martyn 

*In this particular case attempting to calculate R-factor using data and model 
files and making sure that the R you get is not twice as large as published one 
would entirely suffice -:)

Pavel



 From: Robbie Joosten 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Friday, 12 April 2013, 22:57
Subject: Re: [ccp4bb] Puzzling Structure
 

Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group, then the
annotation pipeline understandably messes things up. If the originally
uploaded PDB file was kept by PDBe, then the problem can be recovered quite
easily by the annotators. Perhaps the topic starter, Michel Fodje, can send
a bug report to PDBe. In my experience, the annotators are very helpful
resolving these matters.  


Hoping that the depositors solve the problem by themselves, is probably in
vain: There are many crystallographers who do not read the CCP4BB (which is
a shame, really); they didn't notice the enormous amount of water related
bumps in their final model (which is in the validation report you get after
deposition and in REMARK 500 of the PDB file you have to approve); they also
didn't notice the huge number of symmetry-related bumps; the R-factors in
the PDB file are different from (and better than) the ones in Table 1. Also
notice that the paper was submitted on April 21st 2009 and the model was
deposited on June 29th 2009. Paper accepted on July 8th 2009. But I'm sure
the referees had a chance to properly assess the quality of the structure
model ;-)


Cheers,
Robbie

P.S. It's pretty awesome that the problem was solved in less than 20 minutes
by the CCP4BB (that is, by Phoebe Rice)


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Garib N Murshudov
> Sent: Friday, April 12, 2013 21:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Puzzling Structure
> 
> It is typo:
> R factor for p212121 - 0.4
>                for p21212    - around 0.18
> 
> Although water seem to have been moved around using p212121
> 
> 
> 
> 
> On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:
> 
> 
>     Looks like a typo to me: if you change the CRYST space group record
> from P212121 to P21212, as the paper says it is, the packing problem goes
> away.
> 
>     ++
> 
>     Phoebe A. Rice
>     Dept. of Biochemistry & Molecular Biology
>     The University of Chicago
> 
>     773 834 1723; pr...@uchicago.edu
>     http://bmb.bsd.uchicago.edu/Faculty_and_Research/
> 
>     http://www.rsc.org/shop/books/2008/9780854042722.asp
> 
>     
>     From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> Michel Fodje [michel.fo...@lightsource.ca]
>     Sent: Friday, April 12, 2013 2:17 PM
>     To: CCP4BB@JISCMAIL.AC.UK
>     Subject: Re: [ccp4bb] Puzzling Structure
> 
>     By the way, you will need to show symmetry atoms to see the
> problem.
> 
> 
> 
>         -Original Message-
> 
> 
>         From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
> On Behalf Of
> 
> 
>         Michel Fodje
> 
> 
>         Sent: April-12-13 1:14 PM
> 
> 
>         To: CCP4BB@JISCMAIL.AC.UK
> 
> 
>         Subject: [ccp4bb] Puzzling Structure
> 
> 
> 
>         Has anyone else noticed a problem with the structure  of the
> N-terminal
> 
> 
>         capsid domain of HIV-2  PDB 2wlv.
> 
> 
> 
>         Load it up to in coot and navigate to residue B118.
> 
> 
> 
> 
> 
>         /Michel.
> 
> 
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology Francis Crick Avenue
> Cambridge Biomedical Campus Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk
> Web http://www.mrc-lmb.cam.ac.uk 
> 
> 
> 
> 
> 
> 

Re: [ccp4bb] Puzzling Structure

[Robbie Joosten]

Hi Martyn,

> A shame then that these 'helpful' annotators did not make use of  Pavel's
> basic sanity on the space group (*mentioned below) and check back to the
> one listed in the uploaded PDB file.
As far as I know, EDS is run on all new depositions at PDBe. I don't know
whether they already did that when this model was deposited. Even if they
did, this may not solve the problem because the PDB does not refuse models.
Possible scenarios (there may be more):

1) Pretty bad case
- Annotator: We cannot reproduce your R-factors in EDS. Could you check the
annotated coordinate and reflection files?
- Depositor: Not interested (the paper is almost accepted anyway). Approve
model as-is.

2) Worst case
- Annotator: ... (doesn't notice the problem)
- Depositor: ... (doesn't notice the problem)

> I often wonder why the PDB does not make the deposited coordinate file
> publicly available so that these sorts of issues can be checked and
tracked.
Good point, I wonder about that as well. Also about whether depositors would
like that?

> The whole PDB data (excluding the EMDB that was recently merged into it)
> amounts to about a laptop hard drive's worth of data  - so surely space
can be
> made for the deposited coordinates? (and restraint files which will be
very
> useful for other workers including pdb-redo).
Yes, having access to certain restraint files (particularly for LINKs) would
be very nice. That said, a proper repository of consensus-restraints for
hetero compounds and LINKs would be more reliable than potentially different
restraints for each PDB entry.

 > Having the depositors' uploaded data would help me understand other
> puzzling features of structures such as the current 4GRV.pdb which seems
to
> have a list of TLS groups but contains not a single ANISOU line!...
I'm not a big fan of using ANISOU records for TLS contributions anyway ;-)
But, more seriously, PDB entries should adhere to the PDB standard.

Cheers,
Robbie


> 
> 
> Cheers
>   Martyn
> 
> *In this particular case attempting to calculate R-factor using data and
model
> files and making sure that the R you get is not twice as large as
published one
> would entirely suffice -:)
> 
> Pavel
> 
> 
> 
> From: Robbie Joosten 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Friday, 12 April 2013, 22:57
> Subject: Re: [ccp4bb] Puzzling Structure
> 
> 
> Waters are moved during annotation using the perceived space group's
> symmetry operation. So if the authors give the wrong space group, then the
> annotation pipeline understandably messes things up. If the originally
> uploaded PDB file was kept by PDBe, then the problem can be recovered
> quite
> easily by the annotators. Perhaps the topic starter, Michel Fodje, can
send
> a bug report to PDBe. In my experience, the annotators are very helpful
> resolving these matters.
> 
> 
> Hoping that the depositors solve the problem by themselves, is probably in
> vain: There are many crystallographers who do not read the CCP4BB (which
is
> a shame, really); they didn't notice the enormous amount of water related
> bumps in their final model (which is in the validation report you get
after
> deposition and in REMARK 500 of the PDB file you have to approve); they
> also
> didn't notice the huge number of symmetry-related bumps; the R-factors in
> the PDB file are different from (and better than) the ones in Table 1.
Also
> notice that the paper was submitted on April 21st 2009 and the model was
> deposited on June 29th 2009. Paper accepted on July 8th 2009. But I'm sure
> the referees had a chance to properly assess the quality of the structure
> model ;-)
> 
> 
> Cheers,
> Robbie
> 
> P.S. It's pretty awesome that the problem was solved in less than 20
minutes
> by the CCP4BB (that is, by Phoebe Rice)
> 
> 
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> > Garib N Murshudov
> > Sent: Friday, April 12, 2013 21:39
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Puzzling Structure
> >
> > It is typo:
> > R factor for p212121 - 0.4
> >for p21212- around 0.18
> >
> > Although water seem to have been moved around using p212121
> >
> >
> >
> >
> > On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:
> >
> >
> > Looks like a typo to me: if you change the CRYST space group record
> > from P212121 to P21212, as the paper says it is, the packing problem
goes
> > away.
> >
> > ++
> >
> > Phoebe A. Rice
> > Dept. of Biochemistry & Molecular Biology
> > The University of Chicago
> >
> > 773 834 1723; pr...@uchicago.edu
> > http://bmb.bsd.uchicago.edu/Faculty_and_Research/
> >
> > http://www.rsc.org/shop/books/2008/9780854042722.asp
> >
> > 
> > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Michel Fodje [michel.fo...@lightsource.ca]
> > Sent: Friday, April 12, 2013 2:17 PM
> >