[ccp4bb] CCP4 Study Weekend 2015

[Charles Ballard]

The CCP4 Study Weekend (7 - 9 January 2015)
East Midlands Conference Centre, University of Nottingham
 
Wednesday 7 - MX User Meeting
Thursday 8 / Friday 9 - CCP4 Study Weekend
 
"Advances in Experimental Phasing"
 
We cordially invite you to participate in this year's Study Weekend at the the 
East Midlands Conference Centre, University of Nottingham. The annual CCP4 
Study Weekend is a chance to shake off the post-New Year torpor, and work hard 
and play hard with your fellow crystallographers. Once again, we have put 
together an exciting scientific programme for the Thursday and Friday, either 
side of the traditional conference dinner. Please also check out the satellite 
meetings which may be of interest. The Study Weekend is a chance to catch up 
with old friends, but is also a chance to meet the CCP4 staff who will be there 
in force to demonstrate the latest software and to answer questions - please 
say hello!
 
This year, the topic for the Study Weekend is "Advances in Experimental 
Phasing". In keeping with previous CCP4 meetings, the lectures will focus on 
the presentation and discussion of advanced methods and techniques developed 
and used by the leaders in the field.
 
Scientific Organisers
Thomas Schneider - EMBL Hamburg (Germany)
Airlie McCoy - University of Cambridge (UK)

Further details of the program and the registration are at 
http://www.cse.scitech.ac.uk/events/CCP4_2015

Terms and Conditions apply.  Please read the cancellation policy before 
applying.


-- 
Scanned by iCritical.

[ccp4bb] Postdoc in Barcelona

[F.Xavier Gomis-Rüth]

*/Postdoctoral position in protein biochemistry/molecular biology/*

A senior postdoctoral position is available to work on peptidases, their 
inhibitors and their complexes. The hosting place is the
Proteolysis Lab of the Molecular Biology Institute of Barcelona (IBMB) 
from the Spanish Research Council (CSIC) in Barcelona (Spain).
The IBMB is located within the premises of the Barcelona Science Park 
(PCB), one of the two major poles for excellence in biosciences

in the Barcelona area.

Applications are invited from candidates with proven expertise in 
large-scale production of proteinsby mammalian cell cultures, insect
cells, and otherrecombinant hosts, as well as in protein biochemistry or 
enzymology. The candidate must be extremely self-motivated
and dedicated, be able to work very hard independently but also to 
synergetically interact with other lab members. The tentative starting

date would be in January, 2015.

Interested persons should apply exclusively per e-mail and send a 
detailed CV, as well as a covering letter including motivation, details on
their expertise in protein production, and contact details of three 
referees to F. Xavier Gomis-Rüth (xgr...@ibmb.csic.es 
).


Relevant links:

Proteolysis Lab:www.ibmb.csic.es/home/xgomis 



PCB:www.pcb.ub.es/homePCB/live/en/p1.asp 



Barcelona city:www.bcn.cat/en/ihome.htm 




--

[ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Andrew Leslie]

Does anyone know if Molprobity has recently changed the standard bond lengths 
and angles that it uses ?  

Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond 
angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new 
structure refined with Refmac. I then tried Molprobity on a deposited PDB 
structure that also contains AMPPNP and it reported the same errors. I am sure 
that these errors were not reported when this structure (2JDI) was deposited in 
2007.

This would suggest that the standard dictionary that Molprobity uses has 
changed, but I cannot find any reference to this on the Molprobity pages. 

I would be very grateful if anyone can throw some light on this.

Thanks,

Andrew

[ccp4bb] Selenium in AreaImol

[Carter, Charlie]

I want to have a quantitative estimate for the accessible solvent area for a 
Selenocysteine residue in a tripeptide, gly-Sec-gly. AreaImol doesn't recognize 
Selenium, at least in the version I'm using (6.1.1). The online documentation 
for Areaimol doesn't include the text Selenium. Do newer versions of CCP4 
recognize selenium? 

Are there work-arounds for this problem?

Thanks,

Charlie

[ccp4bb] Technician / Research assistant at the technology platform ŒProtein Crystallography Core Facility¹ of EPFL (Switzerland)

[Pojer Florence]

The technology platform ‘Protein Crystallography Core Facility’ 
(http://pcrycf.epfl.ch) of Life Sciences Faculty is 
opening a fixed-term position for a highly motivated

Technician / Research assistant
The mission of the platform is to provide instrumentation and expertise at 
every stage of the protein structure determination process for research groups, 
both in-house and in the Lake Geneva Area.
The suitable candidate will be involved in the complete crystal structure 
determination pipeline, in close collaboration with researchers leading the 
projects. This includes crystallization and crystal optimization, as well as 
X-ray crystal screening, data collection, data processing and structure 
determination and analysis. He/She will operate, provide training and maintain 
the heavy instruments of the platform. The successful candidate will also be 
responsible for ordering consumables and keeping the laboratory in good 
condition.
The candidate is expected to have a technical or masters degree in 
Biochemistry, Biology or related disciplines. Computational skills for 
performing structure determination and analysis will be an asset.
The applicant should be rigorous, reliable, well organized and have the 
flexibility needed for working in a service-oriented context. Fluency in 
reading and speaking English is anecessity in the EPFL multicultural 
environment.
The suitable candidate will be initially hired on a two-year contract, with a 
salary commensurate with qualifications and experience. EPFL is an equal 
opportunity employer.
Starting date:September 1st, 2014 or to be discussed.  Activity rate: 50-70%.  
Duration: 2 years, renewable.
Sending of applications (full CV, a statement of interest and relevant 
references from previous positions) electronically to: 
candidature...@epfl.ch, by email only. Please 
use the position title and the reference 4278/SV in the “subject” field.
http://emploi.epfl.ch/page-111893-en.html

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Ethan Merritt]

On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote:
> Does anyone know if Molprobity has recently changed the standard bond lengths 
> and angles that it uses ?  
> 
> Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond 
> angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new 
> structure refined with Refmac. I then tried Molprobity on a deposited PDB 
> structure that also contains AMPPNP and it reported the same errors. I am 
> sure that these errors were not reported when this structure (2JDI) was 
> deposited in 2007.
> 
> This would suggest that the standard dictionary that Molprobity uses has 
> changed, but I cannot find any reference to this on the Molprobity pages. 
> 
> I would be very grateful if anyone can throw some light on this.

I suspect, though I cannot say for sure, that the difference is
whether ANP is [correctly] treated as a ligand or [incorrectly]
treated as a monomer in a nucleic acid polymer.   We have seen
similar cases recently.   For now I would say it is safe to
disregard Molprobity scores for ligands that just happen to be
nucleic acids.

Ethan  




> Thanks,
> 
> Andrew

-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[C]

Isn't Molprobity too tight anyway for high resolution structures? I have often (for proteins) found it highlighting "outliers" when in fact that is what the density shows.Isn't it a trade off between molprobity and what the measurements show, especially at high resolutions?-Original Message-From: merr...@u.washington.eduSent: Mon, 15 Sep 2014 08:35:37 -0700To: ccp4bb@jiscmail.ac.ukSubject: Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)
On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote:
> Does anyone know if Molprobity has recently changed the standard bond lengths and angles that it uses ?  
> 
> Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new structure refined with Refmac. I then tried Molprobity on a deposited PDB structure that also contains AMPPNP and it reported the same errors. I am sure that these errors were not reported when this structure (2JDI) was deposited in 2007.
> 
> This would suggest that the standard dictionary that Molprobity uses has changed, but I cannot find any reference to this on the Molprobity pages. 
> 
> I would be very grateful if anyone can throw some light on this.
 
I suspect, though I cannot say for sure, that the difference is
whether ANP is [correctly] treated as a ligand or [incorrectly]
treated as a monomer in a nucleic acid polymer.   We have seen
similar cases recently.   For now I would say it is safe to
disregard Molprobity scores for ligands that just happen to be
nucleic acids.
 
	Ethan  
 
 
 
 
> Thanks,
> 
> Andrew
 
-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Tim Gruene]

Hi Andrew,

the ccp4 ANP.cif entry for C4'-C5' is 1.528A, but both the Phenix and
Grade cif list 1.508A. The distance in 2JDI is 1.53, so if molprobity
relies on one of the latter two sources, this might be the source of the
flag. Also some shelxl dictionary lists 1.509A, so it's 3:1 for the flag
being correct.

Well, this doesn't answer your actual question, but it may still be
informative.

Cheers,
Tim

On 09/15/2014 04:24 PM, Andrew Leslie wrote:
> Does anyone know if Molprobity has recently changed the standard bond lengths 
> and angles that it uses ?  
> 
> Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond 
> angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new 
> structure refined with Refmac. I then tried Molprobity on a deposited PDB 
> structure that also contains AMPPNP and it reported the same errors. I am 
> sure that these errors were not reported when this structure (2JDI) was 
> deposited in 2007.
> 
> This would suggest that the standard dictionary that Molprobity uses has 
> changed, but I cannot find any reference to this on the Molprobity pages. 
> 
> I would be very grateful if anyone can throw some light on this.
> 
> Thanks,
> 
> Andrew
> 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Dale Tronrud]

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Hash: SHA1


   In general the word "outlier" should not be read as "error".  It
simply means that this thing is interesting.  You have to judge, based
on all information at hand, if it is interesting because it is rare or
because it is wrong.

   It is true that the rmsd of high resolution models tend to be
higher than those of low resolution.  The libraries we use are
distillations of high resolution structures and do not contain all of
the true variability of reality.  We have to use libraries when the
diffraction data is insufficient for the model to stand on its own,
but you have to keep in mind the library's limitations.

Dale Tronrud

On 9/15/2014 8:42 AM, C wrote:
> Isn't Molprobity too tight anyway for _high resolution_ structures?
> 
> 
> I have often (for proteins) found it highlighting "outliers" when
> in fact that is what the density shows.
> 
> Isn't it a trade off between molprobity and what the measurements
> show, especially at high resolutions?
> 
> 
> -Original Message- *From:* merr...@u.washington.edu *Sent:*
> Mon, 15 Sep 2014 08:35:37 -0700 *To:* ccp4bb@jiscmail.ac.uk 
> *Subject:* Re: [ccp4bb] Bond lengths and angles used by Molprobity 
> for ANP (AMPPNP)
> 
> On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote:
> 
>> Does anyone know if Molprobity has recently changed the standard
> bond lengths and angles that it uses ?
> 
>> 
> 
>> Molprobity is reporting errors in the C4-C5 bond length and the
> C5-C4-N3 bond angle (deviations of 8-10 sigma) for AMPPNP (monomer 
> code ANP) for a new structure refined with Refmac. I then tried 
> Molprobity on a deposited PDB structure that also contains AMPPNP 
> and it reported the same errors. I am sure that these errors were 
> not reported when this structure (2JDI) was deposited in 2007.
> 
>> 
> 
>> This would suggest that the standard dictionary that Molprobity
> uses has changed, but I cannot find any reference to this on the 
> Molprobity pages.
> 
>> 
> 
>> I would be very grateful if anyone can throw some light on this.
> 
> 
> 
> I suspect, though I cannot say for sure, that the difference is
> 
> whether ANP is [correctly] treated as a ligand or [incorrectly]
> 
> treated as a monomer in a nucleic acid polymer. We have seen
> 
> similar cases recently. For now I would say it is safe to
> 
> disregard Molprobity scores for ligands that just happen to be
> 
> nucleic acids.
> 
> 
> 
> Ethan
> 
> 
> 
> 
> 
> 
> 
> 
> 
>> Thanks,
> 
>> 
> 
>> Andrew
> 
> 
> 
> --
> 
> mail: Biomolecular Structure Center, K-428 Health Sciences Bldg
> 
> MS 357742, University of Washington, Seattle 98195-7742
> 
> 
>
> 
Can't remember your password? Do you need a strong and secure password?
> Use Password manager! It stores your passwords & protects your
> account. 
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Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Huw Jenkins]

On 15 Sep 2014, at 15:24, Andrew Leslie  wrote:

> This would suggest that the standard dictionary that Molprobity uses has 
> changed, but I cannot find any reference to this on the Molprobity pages. 
> 
> I would be very grateful if anyone can throw some light on this.

MolProbity now uses the same target values as Phenix:

"MolProbity4 structure validation now provides many of its validation metrics 
through CCTBX, the open-source component of the Phenix crystallographic 
package. CCTBX allows for consistent validation results with Phenix, as well as 
added functionality, such as geometry regularization of NQH flips” 

The target values for the C4-C5 bond length and the C5-C4-N3 bond angle are 
quite different in the two libraries:


ccp4-6.4.0/lib/data/monomers/a/ANP.cif 

ANP  C4 C5double  1.4900.020

ANP  C5 C4 N3  120.0003.000

phenix-1.9-1692/chem_data/geostd/a/data_ANP.cif 

ANP   C5  C4aromatic  1.386 0.010

ANP   N3  C4  C5  126.80 0.741

That explains the 8-10 sigma deviations reported by MolProbity but it doesn’t 
explain which target values are (more) correct. 



Huw

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Andrew Leslie]

Dear Huw,

Many thanks for this information. I had seen the notice about Molprobity using 
CCTBX validation metrics, but I mistakenly thought that Phenix used the CCP4 
monomer library, which I think was true once but is clearly no longer the case. 

Given the very small sigma values associated with the Phenix C4-C5 bond length, 
it could be said to differ by 10.4 standard deviations from the CCP4 monomer 
library value !

Many thanks to all others who have responded too. 

In response to Dale's comment, the frustrating thing is that this is not 
interesting at all, it is merely confusing. The resolution of the new structure 
is only ~3 Å, so there is no way that one can make meaningful statements about 
distortions from standard geometry. The warnings merely highlight the fact that 
we do not have adequate library entries.

Best wishes,

Andrew



On 15 Sep 2014, at 17:14, Huw Jenkins  wrote:

>   
> On 15 Sep 2014, at 15:24, Andrew Leslie  wrote:
> 
>> This would suggest that the standard dictionary that Molprobity uses has 
>> changed, but I cannot find any reference to this on the Molprobity pages. 
>> 
>> I would be very grateful if anyone can throw some light on this.
> 
> MolProbity now uses the same target values as Phenix:
> 
> "MolProbity4 structure validation now provides many of its validation metrics 
> through CCTBX, the open-source component of the Phenix crystallographic 
> package. CCTBX allows for consistent validation results with Phenix, as well 
> as added functionality, such as geometry regularization of NQH flips” 
> 
> The target values for the C4-C5 bond length and the C5-C4-N3 bond angle are 
> quite different in the two libraries:
> 
> 
> ccp4-6.4.0/lib/data/monomers/a/ANP.cif 
> 
> ANP  C4 C5double  1.4900.020
> 
> ANP  C5 C4 N3  120.0003.000
> 
> phenix-1.9-1692/chem_data/geostd/a/data_ANP.cif 
> 
> ANP   C5  C4aromatic  1.386 0.010
> 
> ANP   N3  C4  C5  126.80 0.741
> 
> That explains the 8-10 sigma deviations reported by MolProbity but it doesn’t 
> explain which target values are (more) correct. 
> 
> 
> 
> Huw

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Ian Tickle]

Andrew, GRADE gives:

ANP   C5  C4aromatic  1.388  0.011

ANP   C5  C4  C3  126.8  0.7

i.e. essentially the same as Phenix, so I would go with that.

The CCP4 values definitely could do with a re-examination: I've never heard
of a "double bond" with a length of 1.49, and the angle looks like it's
just been guessed!

Cheers

-- Ian


On 15 September 2014 17:42, Andrew Leslie  wrote:

> Dear Huw,
>
> Many thanks for this information. I had seen the notice about Molprobity
> using CCTBX validation metrics, but I mistakenly thought that Phenix used
> the CCP4 monomer library, which I think was true once but is clearly no
> longer the case.
>
> Given the very small sigma values associated with the Phenix C4-C5 bond
> length, it could be said to differ by 10.4 standard deviations from the
> CCP4 monomer library value !
>
> Many thanks to all others who have responded too.
>
> In response to Dale's comment, the frustrating thing is that this is not
> interesting at all, it is merely confusing. The resolution of the new
> structure is only ~3 Å, so there is no way that one can make meaningful
> statements about distortions from standard geometry. The warnings merely
> highlight the fact that we do not have adequate library entries.
>
> Best wishes,
>
> Andrew
>
>
>
> On 15 Sep 2014, at 17:14, Huw Jenkins  wrote:
>
> >
> > On 15 Sep 2014, at 15:24, Andrew Leslie 
> wrote:
> >
> >> This would suggest that the standard dictionary that Molprobity uses
> has changed, but I cannot find any reference to this on the Molprobity
> pages.
> >>
> >> I would be very grateful if anyone can throw some light on this.
> >
> > MolProbity now uses the same target values as Phenix:
> >
> > "MolProbity4 structure validation now provides many of its validation
> metrics through CCTBX, the open-source component of the Phenix
> crystallographic package. CCTBX allows for consistent validation results
> with Phenix, as well as added functionality, such as geometry
> regularization of NQH flips”
> >
> > The target values for the C4-C5 bond length and the C5-C4-N3 bond angle
> are quite different in the two libraries:
> >
> >
> > ccp4-6.4.0/lib/data/monomers/a/ANP.cif
> >
> > ANP  C4 C5double  1.4900.020
> >
> > ANP  C5 C4 N3  120.0003.000
> >
> > phenix-1.9-1692/chem_data/geostd/a/data_ANP.cif
> >
> > ANP   C5  C4aromatic  1.386 0.010
> >
> > ANP   N3  C4  C5  126.80 0.741
> >
> > That explains the 8-10 sigma deviations reported by MolProbity but it
> doesn’t explain which target values are (more) correct.
> >
> >
> >
> > Huw
>

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Dale Tronrud]

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On 9/15/2014 9:42 AM, Andrew Leslie wrote:
> Dear Huw,
> 
> Many thanks for this information. I had seen the notice about
> Molprobity using CCTBX validation metrics, but I mistakenly thought
> that Phenix used the CCP4 monomer library, which I think was true
> once but is clearly no longer the case.
> 
> Given the very small sigma values associated with the Phenix C4-C5
> bond length, it could be said to differ by 10.4 standard deviations
> from the CCP4 monomer library value !
> 
> Many thanks to all others who have responded too.
> 
> In response to Dale's comment, the frustrating thing is that this
> is not interesting at all, it is merely confusing. The resolution
> of the new structure is only ~3 Å, so there is no way that one can
> make meaningful statements about distortions from standard
> geometry. The warnings merely highlight the fact that we do not
> have adequate library entries.
> 
   Which is interesting.  ;-)

   To be serious, I do think this is interesting.  Apparently someone
looking at this molecule has decided that this bond should be 1.49 A
with a sigma of 0.02 A while someone else looking at the same molecule
concluded it should be 1.386 A with sigma 0.01 A.  The most
significant source of uncertainty in this target value (whether it is
a double bond or an aromatic bond) has been ignored.  Each library is
constructed ignoring the possibility of error in categorizing the type
of bond.

   I think the lesson is that the sigmas are being seriously under
estimated when the target values are not derived from real high
resolution structures.

   Isn't it also interesting that the double bond of ccp4 is longer
than the aromatic bond of phenix?  Not what I would have expected.

Dale

> Best wishes,
> 
> Andrew
> 
> 
> 
> On 15 Sep 2014, at 17:14, Huw Jenkins  wrote:
> 
>>  On 15 Sep 2014, at 15:24, Andrew Leslie
>>  wrote:
>> 
>>> This would suggest that the standard dictionary that Molprobity
>>> uses has changed, but I cannot find any reference to this on
>>> the Molprobity pages.
>>> 
>>> I would be very grateful if anyone can throw some light on
>>> this.
>> 
>> MolProbity now uses the same target values as Phenix:
>> 
>> "MolProbity4 structure validation now provides many of its
>> validation metrics through CCTBX, the open-source component of
>> the Phenix crystallographic package. CCTBX allows for consistent
>> validation results with Phenix, as well as added functionality,
>> such as geometry regularization of NQH flips”
>> 
>> The target values for the C4-C5 bond length and the C5-C4-N3 bond
>> angle are quite different in the two libraries:
>> 
>> 
>> ccp4-6.4.0/lib/data/monomers/a/ANP.cif
>> 
>> ANP  C4 C5double  1.4900.020
>> 
>> ANP  C5 C4 N3  120.0003.000
>> 
>> phenix-1.9-1692/chem_data/geostd/a/data_ANP.cif
>> 
>> ANP   C5  C4aromatic  1.386 0.010
>> 
>> ANP   N3  C4  C5  126.80 0.741
>> 
>> That explains the 8-10 sigma deviations reported by MolProbity
>> but it doesn’t explain which target values are (more) correct.
>> 
>> 
>> 
>> Huw
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Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Paul Emsley]

On 15/09/14 18:05, Dale Tronrud wrote:

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On 9/15/2014 9:42 AM, Andrew Leslie wrote:

Dear Huw,

Many thanks for this information. I had seen the notice about
Molprobity using CCTBX validation metrics, but I mistakenly thought
that Phenix used the CCP4 monomer library, which I think was true
once but is clearly no longer the case.

Given the very small sigma values associated with the Phenix C4-C5
bond length, it could be said to differ by 10.4 standard deviations
from the CCP4 monomer library value !

Many thanks to all others who have responded too.

In response to Dale's comment, the frustrating thing is that this
is not interesting at all, it is merely confusing. The resolution
of the new structure is only ~3 Å, so there is no way that one can
make meaningful statements about distortions from standard
geometry. The warnings merely highlight the fact that we do not
have adequate library entries.


One wonders what is meant by "we" here? LMB? CCP4 users? Macromolecular 
crystallographers (that also use Phenix)?  Each of these constituencies 
would give a different response...





Which is interesting.  ;-)

To be serious, I do think this is interesting.  Apparently someone
looking at this molecule has decided that this bond should be 1.49 A
with a sigma of 0.02 A while someone else looking at the same molecule
concluded it should be 1.386 A with sigma 0.01 A.


Which is strange.  I'd imagine that the refmac monomer library was 
constructed by libcheck. The input bond order is "double" - but a decent 
dictionary generating program would determine that this is actually 
aromatic - and thus should pick up the distance for an aromatic 
CR56-CR56, i.e. 1.38 (0.02)A. In this case, this has not happened and 
(it seems to me) that the value for a single bond has been used instead, 
i.e. 1.49 (0.02)A.




The most
significant source of uncertainty in this target value (whether it is
a double bond or an aromatic bond) has been ignored.  Each library is
constructed ignoring the possibility of error in categorizing the type
of bond.


It seems so.  But is that so bad?  In this case, is there really any 
doubt that this bond order should be "aromatic"?




I think the lesson is that the sigmas are being seriously under
estimated when the target values are not derived from real high
resolution structures.


I would have said the opposite - the Refmac monomer library usually 
overestimates the esds compared to the distributions from small molecule 
crystal structures (I am presuming that the bond orders are unambiguous).




Isn't it also interesting that the double bond of ccp4 is longer
than the aromatic bond of phenix?  Not what I would have expected.


Nor I. I suspect a bug in libcheck.

For the record, the results from pyrogen are:

 ANP   C5  C4aromatic   1.384940.0198269 # pyrogen
c.f
 ANP   C5  C4aromatic   1.3880.011 # grade

 ANP   C5  C4  N3  126.781.33586# pyrogen
c.f.
 ANP   C5  C4  C3  126.8  0.7# grade


(I could trim the sfs a bit, I suppose, hmmm...)

Paul.

Re: [ccp4bb] ligand mismathces in pdb deposit

[Wang, Bing]

The problem keeps during the deposition! I tried to replace all 'HEM' atoms 
with the pdb published before and run refinement. The mismatch is still there. 
Here is a picture cut from pdb deposition website.

The 3 letter of my heme is 'HEM' which is exactly the 'PROTOPORPHYRIN IX 
CONTAINING FE '. I also checked the pdb CCD in which the 'HEM' image model does 
contain ion but not in the SMILES. My question: if this is the problem cause 
the mismatch, how to fix it?

Thank you guys!!

Bing

From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit

On 12/09/14 23:28, Wang, Bing wrote:
> Hi guys,

Hello.

>
> A quick question about pdb deposition! My protein has a common ligand
> 'heme' which mismatches with the ligand in pdb CCD (/Chemical
> Component Dictionary/).

What makes you think so?

> However i didn't find any differences in it. Is that because of the
> positions of double bonds or hydrogen atoms,

unlikely.

> since my model don't have hydrogen atoms. Actually i replace the heme
> with exact one from CCD and run refmac which give me a new pdb file.
> Unfortunately, CCD still didn’t recognize the heme.

It is not clear to me what test you are performing.  I do note that the
SMILES for HEM in the CCD doesn't contain Fe - that might be related.

HTH,

Paul.

Re: [ccp4bb] ligand mismathces in pdb deposit

[Wang, Bing]

Forgot the picture! Here is it!


From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit

On 12/09/14 23:28, Wang, Bing wrote:
> Hi guys,

Hello.

>
> A quick question about pdb deposition! My protein has a common ligand
> 'heme' which mismatches with the ligand in pdb CCD (/Chemical
> Component Dictionary/).

What makes you think so?

> However i didn't find any differences in it. Is that because of the
> positions of double bonds or hydrogen atoms,

unlikely.

> since my model don't have hydrogen atoms. Actually i replace the heme
> with exact one from CCD and run refmac which give me a new pdb file.
> Unfortunately, CCD still didn’t recognize the heme.

It is not clear to me what test you are performing.  I do note that the
SMILES for HEM in the CCD doesn't contain Fe - that might be related.

HTH,

Paul.

Re: [ccp4bb] ligand mismathces in pdb deposit

[Katherine Sippel]

Hi Bing,

This is the result of the new PDB deposition system being buggy. I had a
similar problem with imidazole recently. This is the solution given to me
by the PDB annotators.

>Please choose from the instance page:

>type of ligand: heterogen,

>then give alternate ligand ID as IMD, (in your case HEM)

>then click finish button address the issue.

>It should solve the problem, if not, please let us know.

Hope this helps,
Katherine


On Mon, Sep 15, 2014 at 3:03 PM, Wang, Bing  wrote:

> Forgot the picture! Here is it!
>
> 
> From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
> Sent: Sunday, September 14, 2014 6:16 PM
> To: Wang, Bing
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
>
> On 12/09/14 23:28, Wang, Bing wrote:
> > Hi guys,
>
> Hello.
>
> >
> > A quick question about pdb deposition! My protein has a common ligand
> > 'heme' which mismatches with the ligand in pdb CCD (/Chemical
> > Component Dictionary/).
>
> What makes you think so?
>
> > However i didn't find any differences in it. Is that because of the
> > positions of double bonds or hydrogen atoms,
>
> unlikely.
>
> > since my model don't have hydrogen atoms. Actually i replace the heme
> > with exact one from CCD and run refmac which give me a new pdb file.
> > Unfortunately, CCD still didn’t recognize the heme.
>
> It is not clear to me what test you are performing.  I do note that the
> SMILES for HEM in the CCD doesn't contain Fe - that might be related.
>
> HTH,
>
> Paul.
>
>
>


-- 
"Nil illegitimo carborundum"* - *Didactylos

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[Ian Tickle]

On 15 September 2014 17:48, Ian Tickle  wrote:

>
>
> ANP   C5  C4  C3  126.8  0.7
>
> Oops sorry, typo:
>

 ANP   C5  C4  N3  126.8  0.7

I.

Re: [ccp4bb] ligand mismathces in pdb deposit

[Wang, Bing]

Thank you very one here! Got fixed from Katherine's solution!

You guys are really helpful!

Bing

From: Katherine Sippel [katherine.sip...@gmail.com]
Sent: Monday, September 15, 2014 3:17 PM
To: Wang, Bing
Cc: ccp4bb
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit

Hi Bing,

This is the result of the new PDB deposition system being buggy. I had a 
similar problem with imidazole recently. This is the solution given to me by 
the PDB annotators.

>Please choose from the instance page:

>type of ligand: heterogen,

>then give alternate ligand ID as IMD, (in your case HEM)

>then click finish button address the issue.

>It should solve the problem, if not, please let us know.

Hope this helps,
Katherine


On Mon, Sep 15, 2014 at 3:03 PM, Wang, Bing 
mailto:bingw...@ou.edu>> wrote:
Forgot the picture! Here is it!


From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit

On 12/09/14 23:28, Wang, Bing wrote:
> Hi guys,

Hello.

>
> A quick question about pdb deposition! My protein has a common ligand
> 'heme' which mismatches with the ligand in pdb CCD (/Chemical
> Component Dictionary/).

What makes you think so?

> However i didn't find any differences in it. Is that because of the
> positions of double bonds or hydrogen atoms,

unlikely.

> since my model don't have hydrogen atoms. Actually i replace the heme
> with exact one from CCD and run refmac which give me a new pdb file.
> Unfortunately, CCD still didn’t recognize the heme.

It is not clear to me what test you are performing.  I do note that the
SMILES for HEM in the CCD doesn't contain Fe - that might be related.

HTH,

Paul.





--
"Nil illegitimo carborundum" - Didactylos