Re: [ccp4bb] Google Gets it Right

[Tim Gruene]

Dear Javier,

without the analysis of the anomalous signal you have a 50:50 chance to
get the correct configuration, and those times were too early for that.
The comment may have been added later and/or from using a different type
of experiment.

Best,
Tim

On 05/13/2014 02:21 AM, Javier Gonzalez wrote:
> Interestingly, that molecule has the opposite configuration. The actual
> modelhas
> a posting saying "(wrong absolute configuration)".
> I wonder what's the story behind it...
> 
> 
> 
> 
> On Mon, May 12, 2014 at 2:28 PM, Gregg Crichlow 
> wrote:
> 
>> Actually, it was noticing penG that made me mouse over it myself. After
>> spending many years completing a thesis on beta-lactamases, I was very
>> surprised - and excited - to see that on something as main-stream as
>> Google. But then when I paid attention more closely, I saw that they even
>> have a good representation of the electron density in three orthogonal
>> planes surrounding the molecule!  Dr. James Knox (my thesis advisor) just
>> informed me that the density maps are on exhibit at the British Museum of
>> Science.
>>   I have heard so much about Dorothy Hodgkin from my thesis advisor,
>> that I became very familiar with her name and legacy, although I never had
>> met her.
>>
>> Gregg
>>
>>
>> On Mon, May 12, 2014 at 9:39 AM, Robert Sweet  wrote:
>>
>>> Check out google.com.  They're announcing what would have been Dorothy
>>> Hodgkin's 104th b-day.  I saw the molecule, and said to myself, "My
>>> goodness, that's penicillin G," and the mouseover announced the big day.
>>>
>>> She was a great scientist and a friend to thousands of us.
>>>
>>> Bob
>>>
>>> =
>>> Robert M. Sweet E-Dress: sw...@bnl.gov
>>> Group Leader, PXRR: Macromolecular   ^ (that's L
>>>   Crystallography Research Resource at NSLSnot 1)
>>>   http://px.nsls.bnl.gov/
>>> Photon Sciences and Biosciences Dept
>>> Office and mail, Bldg 745, a.k.a. LOB-5
>>> Brookhaven Nat'l Lab.   Phones:
>>> Upton, NY  11973631 344 3401  (Office)
>>> U.S.A.  631 344 2741  (Facsimile)
>>> =
>>>
>>
>>
> 
> 

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

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] Google Gets it Right

[Felix Frolow]

Anomalous signal analysis is quite early development in structural biology. 
There are couple of classical papers by Bijvoet in
the first issues oaf Acta Crystallographica. Presently I am  out of ability to 
find exact references :-/
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 13, 2014, at 10:38 , Tim Gruene  wrote:

> Dear Javier,
> 
> without the analysis of the anomalous signal you have a 50:50 chance to
> get the correct configuration, and those times were too early for that.
> The comment may have been added later and/or from using a different type
> of experiment.
> 
> Best,
> Tim
> 
> On 05/13/2014 02:21 AM, Javier Gonzalez wrote:
>> Interestingly, that molecule has the opposite configuration. The actual
>> modelhas
>> a posting saying "(wrong absolute configuration)".
>> I wonder what's the story behind it...
>> 
>> 
>> 
>> 
>> On Mon, May 12, 2014 at 2:28 PM, Gregg Crichlow 
>> wrote:
>> 
>>> Actually, it was noticing penG that made me mouse over it myself. After
>>> spending many years completing a thesis on beta-lactamases, I was very
>>> surprised - and excited - to see that on something as main-stream as
>>> Google. But then when I paid attention more closely, I saw that they even
>>> have a good representation of the electron density in three orthogonal
>>> planes surrounding the molecule!  Dr. James Knox (my thesis advisor) just
>>> informed me that the density maps are on exhibit at the British Museum of
>>> Science.
>>>  I have heard so much about Dorothy Hodgkin from my thesis advisor,
>>> that I became very familiar with her name and legacy, although I never had
>>> met her.
>>> 
>>> Gregg
>>> 
>>> 
>>> On Mon, May 12, 2014 at 9:39 AM, Robert Sweet  wrote:
>>> 
 Check out google.com.  They're announcing what would have been Dorothy
 Hodgkin's 104th b-day.  I saw the molecule, and said to myself, "My
 goodness, that's penicillin G," and the mouseover announced the big day.
 
 She was a great scientist and a friend to thousands of us.
 
 Bob
 
 =
Robert M. Sweet E-Dress: sw...@bnl.gov
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Photon Sciences and Biosciences Dept
Office and mail, Bldg 745, a.k.a. LOB-5
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
 =
 
>>> 
>>> 
>> 
>> 
> 
> -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 

Re: [ccp4bb] Google Gets it Right

[Tim Gruene]

Dear Felix,

I now, of course. The molecule on the picture look like consisting of
rather light atoms, and I would be very impressed if the instrumentation
and software at that time allowed the reliable detection of the hand
from that particular molecule.

I don't assume Dorothy Hodgkin made a mistake leading to that note but
rather realised of what was available to her and made the best of it
(which was clearly very outstanding). But of course I may be wrong and I
am happy to learn.

Best,
Tim

On 05/13/2014 10:12 AM, Felix Frolow wrote:
> Anomalous signal analysis is quite early development in structural biology. 
> There are couple of classical papers by Bijvoet in
> the first issues oaf Acta Crystallographica. Presently I am  out of ability 
> to find exact references :-/
> Dr Felix Frolow   
> Professor of Structural Biology and Biotechnology, Department of Molecular 
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
> 
> Acta Crystallographica F, co-editor
> 
> e-mail: mbfro...@post.tau.ac.il
> Tel:  ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
> 
> On May 13, 2014, at 10:38 , Tim Gruene  wrote:
> 
>> Dear Javier,
>>
>> without the analysis of the anomalous signal you have a 50:50 chance to
>> get the correct configuration, and those times were too early for that.
>> The comment may have been added later and/or from using a different type
>> of experiment.
>>
>> Best,
>> Tim
>>
>> On 05/13/2014 02:21 AM, Javier Gonzalez wrote:
>>> Interestingly, that molecule has the opposite configuration. The actual
>>> modelhas
>>> a posting saying "(wrong absolute configuration)".
>>> I wonder what's the story behind it...
>>>
>>>
>>>
>>>
>>> On Mon, May 12, 2014 at 2:28 PM, Gregg Crichlow 
>>> wrote:
>>>
 Actually, it was noticing penG that made me mouse over it myself. After
 spending many years completing a thesis on beta-lactamases, I was very
 surprised - and excited - to see that on something as main-stream as
 Google. But then when I paid attention more closely, I saw that they even
 have a good representation of the electron density in three orthogonal
 planes surrounding the molecule!  Dr. James Knox (my thesis advisor) just
 informed me that the density maps are on exhibit at the British Museum of
 Science.
  I have heard so much about Dorothy Hodgkin from my thesis advisor,
 that I became very familiar with her name and legacy, although I never had
 met her.

 Gregg


 On Mon, May 12, 2014 at 9:39 AM, Robert Sweet  wrote:

> Check out google.com.  They're announcing what would have been Dorothy
> Hodgkin's 104th b-day.  I saw the molecule, and said to myself, "My
> goodness, that's penicillin G," and the mouseover announced the big day.
>
> She was a great scientist and a friend to thousands of us.
>
> Bob
>
> =
>Robert M. Sweet E-Dress: sw...@bnl.gov
>Group Leader, PXRR: Macromolecular   ^ (that's L
>  Crystallography Research Resource at NSLSnot 1)
>  http://px.nsls.bnl.gov/
>Photon Sciences and Biosciences Dept
>Office and mail, Bldg 745, a.k.a. LOB-5
>Brookhaven Nat'l Lab.   Phones:
>Upton, NY  11973631 344 3401  (Office)
>U.S.A.  631 344 2741  (Facsimile)
> =
>


>>>
>>>
>>
>> -- 
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
> 
> 

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

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] Google Gets it Right

[Richard Fearn]

http://www.google.com/doodles/dorothy-hodgkins-104th-birthday has more 
information about the doodle... though I don't think "cryptographer" was the 
right word to use :-)

Rich

-- 

Richard Fearn
Senior Software Engineer
Diamond Light Source Ltd.
Tel: +44 1235 778655



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[ccp4bb]

[Sanjit Roy]

Dear All
  I am planning to purify monoclonal antibody.  In this concern
I found Pseudospecific ligands such as histidine, tryptophan,phenylalanine
etc. can be used to purify a wide range of bio-molecules and especially
immunoglobulin. I wish to know the structural mode of binding of Histidine
(as affinity ligand) with Immunoglobulin.
Sanjit Kumar

[ccp4bb] Helix alignment and movement

[R. M. Garavito]

Dear Eugene and other CCP4ers

The recent discussion about superposition has prompted me to ask about a 
different kind of superposition problem.  We are working on a small dimeric 
protein that is entirely made up of helices.  Instead of large, concerted 
domain movements, which I am quite familiar with, we have 3 structures for the 
dimer that display slightly, but significantly different helical conformations. 
 I have been able to find the minimal substructure that allows the best 
superposition (lowest RSMD and maximum number of aligned/superimposed C-alphas).

The problem is that none of the superposition programs available outputs a list 
of residue by residue deviations OUTSIDE of the alignment set (for good reason 
as there may not be 1 to 1 correspondence outside of this set).  I can do some 
of this in a piecemeal fashion with Moleman2, but not everything I want.  My 
question is, after creating an "optimal" structural alignment, are there newer 
programs that:

(1) Create a list of residue by residue deviations over different subsets of 
the structure, particularly OUTSIDE of an alignment set? 

(2) Localize and measure "movement" of secondary structure (helix tilt or 
bending)?

I can't seem to find what I need, but I may not be searching with the right key 
words.

Thanks,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





On May 11, 2014, at 7:14 AM, Eugene Krissinel  
wrote:

> My guess is that only atom pairs that are superposed to some measure of 
> distance between them, are output. Can't say that I checked lsqkab code this 
> weekend, but documentation does not suggest anything like that.
> 
> Is this a problem for you? note that you can use other aligners/superposers 
> in CCP4, ssm or Gesamt which will output all coordinates.
> 
> Eugene
> 

Re: [ccp4bb] Helix alignment and movement

[Andrew Leslie]

Dear Mike,

   I think that the "old" CCP4 "superpose" program used to be 
able to do this ? (This was a FORTRAN program, based on code from Wayne 
Hendrickson's PROLSQ program). With this program you specify one set of 
residues to do the alignment with and another set to do the statistics on 
(after alignment).

I don't know if this is still in the CCP4 archive somewhere, but I do have a 
copy of the source code that I could let you have.

Best wishes,
Andrew

On 13 May 2014, at 14:59, R. M. Garavito  wrote:

> Dear Eugene and other CCP4ers
> 
> The recent discussion about superposition has prompted me to ask about a 
> different kind of superposition problem.  We are working on a small dimeric 
> protein that is entirely made up of helices.  Instead of large, concerted 
> domain movements, which I am quite familiar with, we have 3 structures for 
> the dimer that display slightly, but significantly different helical 
> conformations.  I have been able to find the minimal substructure that allows 
> the best superposition (lowest RSMD and maximum number of 
> aligned/superimposed C-alphas).
> 
> The problem is that none of the superposition programs available outputs a 
> list of residue by residue deviations OUTSIDE of the alignment set (for good 
> reason as there may not be 1 to 1 correspondence outside of this set).  I can 
> do some of this in a piecemeal fashion with Moleman2, but not everything I 
> want.  My question is, after creating an "optimal" structural alignment, are 
> there newer programs that:
> 
> (1) Create a list of residue by residue deviations over different subsets of 
> the structure, particularly OUTSIDE of an alignment set? 
> 
> (2) Localize and measure "movement" of secondary structure (helix tilt or 
> bending)?
> 
> I can't seem to find what I need, but I may not be searching with the right 
> key words.
> 
> Thanks,
> 
> Michael
> 
> 
> R. Michael Garavito, Ph.D.
> Professor of Biochemistry & Molecular Biology
> 603 Wilson Rd., Rm. 513   
> Michigan State University  
> East Lansing, MI 48824-1319
> Office:  (517) 355-9724 Lab:  (517) 353-9125
> FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
> 
> 
> 
> 
> 
> On May 11, 2014, at 7:14 AM, Eugene Krissinel  
> wrote:
> 
>> My guess is that only atom pairs that are superposed to some measure of 
>> distance between them, are output. Can't say that I checked lsqkab code this 
>> weekend, but documentation does not suggest anything like that.
>> 
>> Is this a problem for you? note that you can use other aligners/superposers 
>> in CCP4, ssm or Gesamt which will output all coordinates.
>> 
>> Eugene
>> 
> 

[ccp4bb]

[David Blum]

Sanjit,

We routinely use Protein G coupled resins for purification of monoclonals
produced in the facility.  On a structural level, antibodies typically
recognize 5 or more residues in a protein unless the immunogen, such as a
single amino acid in your case, is a hapten conjugated to a carrier
molecule.

Could you be more specific regarding your rationale and why conventional
methods (e.g. Protein A or G) are not appropriate for purifying a
monoclonal antibody?

Best,
David
-- 
David L. Blum, Ph.D.
Bioexpression and Fermentation Facility
Department of Biochemistry and Molecular Biology
University of Georgia
120 Green Street room A414A
Athens, GA 30602
http://bff.uga.edu/
(706) 542-1035 (Office)


On Tue, May 13, 2014 at 7:32 AM, Sanjit Roy  wrote:

> Dear All
>   I am planning to purify monoclonal antibody.  In this
> concern I found Pseudospecific ligands such as histidine,
> tryptophan,phenylalanine etc. can be used to purify a wide range of
> bio-molecules and especially immunoglobulin. I wish to know the structural
> mode of binding of Histidine (as affinity ligand) with Immunoglobulin.
> Sanjit Kumar
>

[ccp4bb] puzzle of reference zone in HKL2000

[林世强]

Hi everybody! I met with a problem when I was reading the HKL2000 online
manual. It's the reference zone setup in the "Step 11: What is the
reference zone? How is this useful? (page 38, figure 38)". Does anybody
know the definition of reference zone, and why the reference zone setup
window seems always contain the same 10 options, h0l, hk0, l0h, kh0, ...,
0-kl? Thanks.

Best regards,

Shiqiang Lin

Re: [ccp4bb] puzzle of reference zone in HKL2000

[Felix Frolow]

these are symmetry  alternative choices of the cell axes 
they sure are the same as there are 14 Bravais lattices
I guess it is not space group related.
they were introduced to maintain a precision of calculationI guess, so to 
choose and alternative orientation were trigonometric parameters
are in the region were small change in angle does not bring large change in the 
trigonometric function (or vice versa)

FF

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 13, 2014, at 23:19 , 林世强  wrote:

> Hi everybody! I met with a problem when I was reading the HKL2000 online 
> manual. It's the reference zone setup in the "Step 11: What is the reference 
> zone? How is this useful? (page 38, figure 38)". Does anybody know the 
> definition of reference zone, and why the reference zone setup window seems 
> always contain the same 10 options, h0l, hk0, l0h, kh0, ..., 0-kl? Thanks.
> 
> Best regards,
> 
> Shiqiang Lin
> 
> 

[ccp4bb] TER in PDB file

[Felix Frolow]

Community!
I am in the process of PDB deposition. 
I have used for refinement Refmac.
I enter to refinement cycle PDB file with TER separators.
After refinement they disappear.
PDB validation server (option 1 with geometrical parameters report ) DEMAND TER 
separator.
In my structure there are 28 hetero-mers.
Is it sane:
 To demand such thing?
Not to supply  such thing?
Do I miss something ?
Does community punch in TER cards manually ?

FF

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

[ccp4bb] OFF TOPIC - zebra printer labels for SBS format plates

[Eric Larson]

Hello all,

Sorry for the off topic post.  I am looking for alternate (and more
reasonably priced) sources for label rolls for our Zebra printer for
labeling crystallization experiments.  We use Formulatrix rock imagers and
rock maker software but am interested in hearing from anyone that uses
Zebra printers for labeling SBS format plates about your source and
approximate cost/roll.  Please respond to me privately and I will post a
follow-up summary.  U.S. sources would be most appropriate for my purposes
but I am happy to collect sources from elsewhere in the world to compile in
my summary.

thanks in advance for your suggestions/advice.

sincerely,
Eric

Eric Larson
Structural Research
Boehringer Ingelheim Pharmaceuticals
Ridgefield, CT USA

[ccp4bb] High B-factors

[Kgosisejo, Oarabile]

Hi all,

We have solved the structure of a protein at 2.3 A with the final R-work and 
R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with an 
average of 72. There are 3 molecules in the asymmetric unit and the 3rd 
molecule is very disordered and I believe is the main contributor to high 
B-factors.

I was wondering if there is a way I can look at the B-factors of the molecules 
individually. Also is there a way I can improve the B-factors of my model?

Best Regards,

Oarabile Kgosisejo

Re: [ccp4bb] High B-factors

[Ethan A Merritt]

On Tuesday, 13 May, 2014 22:49:15 Kgosisejo, Oarabile wrote:
> Hi all,
> 
> We have solved the structure of a protein at 2.3 A with the final R-work and 
> R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with 
> an average of 72. There are 3 molecules in the asymmetric unit and the 3rd 
> molecule is very disordered and I believe is the main contributor to high 
> B-factors.
> 
> Also is there a way I can improve the B-factors of my model?

The first thing I suggest is to check what is the Wilson B from your data 
processing.
If the data intensity distribution already indicates that the expected mean B 
is high,
then I wouldn't worry about it.

You could then test whether the high B factors are due to bulk motion of the 
molecules
rather than disorder or large motions of individual residues.  Do this by 
placing each
chain into a single TLS group and refining the structure again in the presence 
of this
3-group TLS model. 

> I was wondering if there is a way I can look at the B-factors of the 
> molecules individually. 

If you do go ahead and refine a 3-group TLS model, you can feed it to the 
server at
http://skuld.bmsc.washington.edu/parvati/
Among other things, it will create a nice picture of your 3 chains colored by
B factor.

Ethan


> 
> Best Regards,
> 
> Oarabile Kgosisejo
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] TER in PDB file

[Robbie Joosten]

Dear Felix,

I recently had the same problem. I didn't think TER records were a big deal. I 
never had a program that did weird thing because of missing TER records. But 
well, orders are orders, so we need TER records for deposition. It would be 
nice if all refinement programs would write those. AFAIK, Phenix already does.

Rather then putting them in manually, I ended up using pdb_extract to convert 
my pdb file to mmCIF. A nice bonus is that you can throw in the log files from 
indexing and phasing which saves a lot of typing later in the deposition 
process.

Cheers,
Robbie

Sent from my Windows Phone

Van: Felix Frolow
Verzonden: 13-5-2014 23:26
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] TER in PDB file

Community!
I am in the process of PDB deposition.
I have used for refinement Refmac.
I enter to refinement cycle PDB file with TER separators.
After refinement they disappear.
PDB validation server (option 1 with geometrical parameters report ) DEMAND TER 
separator.
In my structure there are 28 hetero-mers.
Is it sane:
 To demand such thing?
Not to supply  such thing?
Do I miss something ?
Does community punch in TER cards manually ?

FF

Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

Re: [ccp4bb] TER in PDB file

[Felix Frolow]

Phenix does even more, it adds TER after ions and ligands, so again manual 
messing is needed.
However they may have a jiffy to fix it.

FF

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 14, 2014, at 07:23 , Robbie Joosten  wrote:

> Dear Felix,
> 
> I recently had the same problem. I didn't think TER records were a big deal. 
> I never had a program that did weird thing because of missing TER records. 
> But well, orders are orders, so we need TER records for deposition. It would 
> be nice if all refinement programs would write those. AFAIK, Phenix already 
> does.
> 
> Rather then putting them in manually, I ended up using pdb_extract to convert 
> my pdb file to mmCIF. A nice bonus is that you can throw in the log files 
> from indexing and phasing which saves a lot of typing later in the deposition 
> process.
> 
> Cheers,
> Robbie
> 
> Sent from my Windows Phone
> Van: Felix Frolow
> Verzonden: 13-5-2014 23:26
> Aan: CCP4BB@JISCMAIL.AC.UK
> Onderwerp: [ccp4bb] TER in PDB file
> 
> Community!
> I am in the process of PDB deposition. 
> I have used for refinement Refmac.
> I enter to refinement cycle PDB file with TER separators.
> After refinement they disappear.
> PDB validation server (option 1 with geometrical parameters report ) DEMAND 
> TER separator.
> In my structure there are 28 hetero-mers.
> Is it sane:
>  To demand such thing?
> Not to supply  such thing?
> Do I miss something ?
> Does community punch in TER cards manually ?
> 
> FF
> 
> Dr Felix Frolow   
> Professor of Structural Biology and Biotechnology, Department of Molecular 
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
> 
> Acta Crystallographica F, co-editor
> 
> e-mail: mbfro...@post.tau.ac.il
> Tel:  ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
> 

Re: [ccp4bb] TER in PDB file

[Nat Echols]

On Tue, May 13, 2014 at 9:20 PM, Felix Frolow wrote:

> Phenix does even more, it adds TER after ions and ligands, so again manual
> messing is needed.
> However they may have a jiffy to fix it.
>

phenix.sort_hetatms will remove them for you, although why this "problem"
was apparently beyond the capability of the PDB itself to handle is a
mystery.  When I encountered this a couple of years ago I spent longer
arguing with the annotator than writing the code.  Fortunately mmCIF
deposition does indeed seem to work more smoothly.

-Nat