Re: [ccp4bb] Bond length and angle outlier fixing

[Vipul Panchal]

Thanks all for the reply. I will follow your suggestion and will get back.

Sincerely,

On Thu, May 18, 2017 at 5:02 AM, Paul Adams  wrote:

> To add to Pavel’s comments, it is also possible to do the automated model
> building in Phenix:
>
> http://www.phenix-online.org/documentation/reference/map_
> to_model.html
>
> As Pavel said: there is Phenix mailing list for Phenix-specific questions
>
>
> > On May 17, 2017, at 10:24 AM, Paul Emsley 
> wrote:
> >
> > Hi, all.
> >
> > I have collected cryoEM data and want to use Coot and CCP4 program to
> build model and to refine it.
> >
> > 1. What is the steps to do this?
> > 2. How do I convert cryoEM map file to MTZ file?
> > 3. Can I also use Phenix for this purpose?
> >
> > Thanks to all for your help in advance.
>
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence
> Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
>
> Building 33, Room 347
> Building 80, Room 247
> Building 978, Room 4126
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][
> 1-510-495-2506 ]
> --
>



-- 
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372

Re: [ccp4bb] Bond length and angle outlier fixing

[Paul Adams]

To add to Pavel’s comments, it is also possible to do the automated model 
building in Phenix:

http://www.phenix-online.org/documentation/reference/map_to_model.html

As Pavel said: there is Phenix mailing list for Phenix-specific questions


> On May 17, 2017, at 10:24 AM, Paul Emsley  wrote:
> 
> Hi, all.
> 
> I have collected cryoEM data and want to use Coot and CCP4 program to  build 
> model and to refine it.
> 
> 1. What is the steps to do this?
> 2. How do I convert cryoEM map file to MTZ file?
> 3. Can I also use Phenix for this purpose?
> 
> Thanks to all for your help in advance.

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence 
Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ]
--

Re: [ccp4bb] CYS modification and choice of PEG

[Keller, Jacob]

If you were collecting at a long-ish wavelength (for NaI phasing, perhaps?) you 
might be able to see a peak there in an anomalous difference Fourier map. This 
would be a pretty cool discovery!

JPK

From: Keller, Jacob
Sent: Wednesday, May 17, 2017 4:52 PM
To: Antonio Ariza ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: CYS modification and choice of PEG

Where would it get the sulphate to make sulphonate? Was there sulphate 
somewhere in the purification?

Maybe it's a phosphate gotten off the FMN? I guess the phospho-cys bond might 
be a bit longer?

JPK

Analyst. 2014 Sep 
7;139(17):4118-23. doi: 10.1039/c4an00724g.
Puzzling over protein cysteine phosphorylation--assessment of proteomic tools 
for S-phosphorylation profiling.
Buchowiecka 
AK1.
Author information
Abstract
Cysteine phosphorylation has recently been discovered in both prokaryotic and 
eukaryotic systems, and is thought to play crucial roles in signaling and 
regulation of cellular responses. This article explores the topics of chemical 
stability of this type of structural modification and the resulting issues 
regarding affinity enrichment of S-phosphopeptides and their mass 
spectrometry-based detection in the course of general proteomics studies. 
Together, this work suggests that the current advances in phosphoproteomic 
methodologies provide adequate tools for investigating protein cysteine 
phosphorylation and appear to be immediately available for practical 
implementation. The article provides useful information necessary for designing 
experiments in the emerging cysteine phosphoproteomics. The examples of 
methodological proposals for S-linked phosphorylation detection are included 
herein in order to stimulate development of new approaches by the 
phosphoproteomic community.





From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Antonio 
Ariza
Sent: Wednesday, May 17, 2017 4:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CYS modification and choice of PEG

I haven't asked anything for a loong time, so here are a couple of question 
"for the honourable members of the esteemed CCP4 bulletin board" ... or as I'd 
usually say: "for y'all".  ;)

1)  I have this modified CYS in one of the structures I'm working on and ... 
I'm quite unhappy with it (see attached pics). At first I thought it was 
cacodylate ... but alas, no cacodylate was used during purification or 
crystallisation. So I looked up possible modifications on CYS residues and I 
came up with cysteine-s-sulfonic acid (CSU). This looks good in principle but 
it doesn't quite fit the electron density as the bond between the two sulphur 
atoms is too short. The average length for an S-S bond is about 2.05 Ang and 
refmac refines this one to 1.97 Ang, but it looks like it should be at least 
2.5 Ang to sit correctly in the electron density. Also, there is some negative 
density in there, suggesting that maybe it's something with fewer electrons 
than a sulfonic acid ... or maybe it has less than 100% occupancy. Any 
suggestions?

The condition contains TRIS, bicine, NaCl, NaFl, NaI, DTT, FMN, PEG 500 MME and 
PEG 20,000.

2)  There are two partial PEG molecules in this structure. I've initially 
modeled two PEG 400 (PE4) molecules into the density (simply because I 
remembered the 3 -letter code for it) and removed the excess atoms from them. 
However, since there is a mixture of PEG 500 MME and PEG 20,000 in the 
condition, what would you recommend I use instead of PE4?

Cheers,

Tony

--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE
e-mail: antonio.ar...@path.ox.ac.uk
Tel: 00 +44 1865 285655

Links to my public profiles:
ResearchGate
LinkedIn
GoogleScholar
Twitter

Check out my latest paper!!!
The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of 
DNA

Re: [ccp4bb] CYS modification and choice of PEG

[Keller, Jacob]

Where would it get the sulphate to make sulphonate? Was there sulphate 
somewhere in the purification?

Maybe it's a phosphate gotten off the FMN? I guess the phospho-cys bond might 
be a bit longer?

JPK

Analyst. 2014 Sep 
7;139(17):4118-23. doi: 10.1039/c4an00724g.
Puzzling over protein cysteine phosphorylation--assessment of proteomic tools 
for S-phosphorylation profiling.
Buchowiecka 
AK1.
Author information
Abstract
Cysteine phosphorylation has recently been discovered in both prokaryotic and 
eukaryotic systems, and is thought to play crucial roles in signaling and 
regulation of cellular responses. This article explores the topics of chemical 
stability of this type of structural modification and the resulting issues 
regarding affinity enrichment of S-phosphopeptides and their mass 
spectrometry-based detection in the course of general proteomics studies. 
Together, this work suggests that the current advances in phosphoproteomic 
methodologies provide adequate tools for investigating protein cysteine 
phosphorylation and appear to be immediately available for practical 
implementation. The article provides useful information necessary for designing 
experiments in the emerging cysteine phosphoproteomics. The examples of 
methodological proposals for S-linked phosphorylation detection are included 
herein in order to stimulate development of new approaches by the 
phosphoproteomic community.





From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Antonio 
Ariza
Sent: Wednesday, May 17, 2017 4:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CYS modification and choice of PEG

I haven't asked anything for a loong time, so here are a couple of question 
"for the honourable members of the esteemed CCP4 bulletin board" ... or as I'd 
usually say: "for y'all".  ;)

1)  I have this modified CYS in one of the structures I'm working on and ... 
I'm quite unhappy with it (see attached pics). At first I thought it was 
cacodylate ... but alas, no cacodylate was used during purification or 
crystallisation. So I looked up possible modifications on CYS residues and I 
came up with cysteine-s-sulfonic acid (CSU). This looks good in principle but 
it doesn't quite fit the electron density as the bond between the two sulphur 
atoms is too short. The average length for an S-S bond is about 2.05 Ang and 
refmac refines this one to 1.97 Ang, but it looks like it should be at least 
2.5 Ang to sit correctly in the electron density. Also, there is some negative 
density in there, suggesting that maybe it's something with fewer electrons 
than a sulfonic acid ... or maybe it has less than 100% occupancy. Any 
suggestions?

The condition contains TRIS, bicine, NaCl, NaFl, NaI, DTT, FMN, PEG 500 MME and 
PEG 20,000.

2)  There are two partial PEG molecules in this structure. I've initially 
modeled two PEG 400 (PE4) molecules into the density (simply because I 
remembered the 3 -letter code for it) and removed the excess atoms from them. 
However, since there is a mixture of PEG 500 MME and PEG 20,000 in the 
condition, what would you recommend I use instead of PE4?

Cheers,

Tony

--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE
e-mail: antonio.ar...@path.ox.ac.uk
Tel: 00 +44 1865 285655

Links to my public profiles:
ResearchGate
LinkedIn
GoogleScholar
Twitter

Check out my latest paper!!!
The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of 
DNA

[ccp4bb] Associate Researcher Position at the University of Kansas Protein Structure Laboratory

[Lovell, Scott W]

The Protein Structure Laboratory at the University of Kansas is seeking a 
full-time Associate Researcher to assist with various structural biology 
projects.  For a full description and to apply, GO TO: 
https://employment.ku.edu/staff/8691BR

Review of applications begins 5/30/17


Regards,
Scott

__
Scott Lovell Ph.D., Director
Protein Structure Laboratory
University of Kansas
Del Shankel Structural Biology Center
2034 Becker Drive
Lawrence, KS 66047
Office: SBC 1015
Email: swlov...@ku.edu
Website: https://psf.cobre.ku.edu/cores/psl/about
Phone: 785-864-3772
__

Re: [ccp4bb] CYS modification and choice of PEG

[Ethan A Merritt]

On Wednesday, 17 May, 2017 20:03:42 Antonio Ariza wrote:
> I haven't asked anything for a loong time, so here are a couple of 
> question "for the honourable members of the esteemed CCP4 bulletin board" ... 
> or as I'd usually say: "for y'all".  ;)
> 
> 1)  I have this modified CYS in one of the structures I'm working on and ... 
> I'm quite unhappy with it (see attached pics). At first I thought it was 
> cacodylate ... but alas, no cacodylate was used during purification or 
> crystallisation. So I looked up possible modifications on CYS residues and I 
> came up with cysteine-s-sulfonic acid (CSU). This looks good in principle but 
> it doesn't quite fit the electron density as the bond between the two sulphur 
> atoms is too short. The average length for an S-S bond is about 2.05 Ang and 
> refmac refines this one to 1.97 Ang, but it looks like it should be at least 
> 2.5 Ang to sit correctly in the electron density. Also, there is some 
> negative density in there, suggesting that maybe it's something with fewer 
> electrons than a sulfonic acid ... or maybe it has less than 100% occupancy. 
> Any suggestions?

Could it be that a cloning error introduced a Cys->Arg mutation?

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

Re: [ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

[Tanner, John J.]

I’m not aware of a wide study on NAD carboxamide conformation. Lacking atomic 
resolution, optimizing the hydrogen bonding can be used to determine the 
orientation of the carboxamide, as you wrote. You may have to consider 
intramolecular hydrogen bonding within NAD+ as well as intermolecular hydrogen 
bonding with the protein. For example, Fig. 5 from below shows a case in which 
the carboxamide of NADPH donates a hydrogen bond to a backbone carbonyl, while 
accepting a hydrogen bond from the NADPH pyrophosphate.

https://www.ncbi.nlm.nih.gov/pubmed/28258219


John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On May 17, 2017, at 2:46 PM, Jorge Iulek 
> wrote:

Dear all,

I came across some difficulty to refine a NAD molecule in a structure, 
specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to point that not so 
ever the C2N-C3N-C7N-N7N dihedral is close to either 0 or 180 degrees, but in 
most cases it is to one of these, with a preference towards 0 degrees. Another 
search in the literature, and I could not find any study on either NAD or even 
the nicotinamide alone to calculate the energy barrier to rotate around this 
bond (in vacuum, eg).
My data quality and resolution do not put much confidence on B-factor 
differences, but they seem to indicate that the cited dihedral angle should be 
close to 180 degrees, id est, O7N is "closer" to C2N (and, consequently, to 
N1N) than N7N is. In fact, I have a glutamine nearby whose terminal amide is 
interacting with the nicotinamide amide, so my idea is to make one's nitrogen 
to interact with other's oxygen. Concerning b-factor differences for this 
glutamine, they favor its NE2 to point to nicotinamide amide, what would imply 
that the C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees rather than 
0 degree.
Is there any wide study on NAD nicotinamide amide conformation? Specially, 
bound to protein structures?
Thanks,

Jorge

[ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

[Jorge Iulek]

  
  
Dear all,

    I came across some difficulty to refine a NAD molecule in a
structure, specially its amide of the nicotinamide moiety.
    A (very) brief search in deposited structures seems to point
that not so ever the C2N-C3N-C7N-N7N dihedral is close to either
0 or 180 degrees, but in most cases it is to one of these, with
a preference towards 0 degrees. Another search in the
literature, and I could not find any study on either NAD or even
the nicotinamide alone to calculate the energy barrier to rotate
around this bond (in vacuum, eg). 
    My data quality and resolution do not put much confidence on
B-factor differences, but they seem to indicate that the cited
dihedral angle should be close to 180 degrees, id est, O7N is
"closer" to C2N (and, consequently, to N1N) than N7N is. In
fact, I have a glutamine nearby whose terminal amide is
interacting with the nicotinamide amide, so my idea is to make
one's nitrogen to interact with other's oxygen. Concerning
b-factor differences for this glutamine, they favor its NE2 to
point to nicotinamide amide, what would imply that the C2N-C3N-C7N-N7N


dihedral to would be close to 180 degrees rather than 0 degree.
    Is there any wide study on NAD nicotinamide amide
conformation? Specially, bound to protein structures?
    Thanks,

Jorge

  
  

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

[Petr Leiman]

If your signal goes all the way to the half Nyquist frequency, oversample your 
map to have the pixel size equal to 1/3rd of the highest resolution. Your map 
will look much better in coot. Real space fitting will work much better as 
well. 

Best,

Petr

> On May 17, 2017, at 11:24 AM, MyeongSeon Lee 
> <0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi, all.
> 
> I have collected cryoEM data and want to use Coot and CCP4 program to  build 
> model and to refine it.
> 
> 1. What is the steps to do this?
> 2. How do I convert cryoEM map file to MTZ file?
> 3. Can I also use Phenix for this purpose?
> 
> Thanks to all for your help in advance.

Re: [ccp4bb] Poor density fit.

[Eleanor Dodson]

It sometimes help to use the coot tool NCS ghost control to fit the good
chain over the weak. Obviously you must work at a lower contour level than
for the good chain..

Of course be careful about the basics.. Is the space group right? is there
twinning? Check data quality - anisotropy - tc..

Eleanor



On 4 May 2017 at 16:38, Vipul Panchal  wrote:

> Thanks Bert,
>
> I did understand not to delete such atoms or set occupancy to zero from
> forum and literature. However, colleagues in the vicinity informed to take
> approaches i mentioned earlier. Therefore, I thought to take opinion from
> forum if something has changed recently.
>
> Thanking,
>
>
>
> On Thu, May 4, 2017 at 8:55 PM, Bert Van-Den-Berg <
> bert.van-den-b...@newcastle.ac.uk> wrote:
>
>> This has been discussed before, I guess more than once
>>
>> I think most people (I'm sure i'll be corrected if wrong) would favor not
>> removing any atoms or setting occupancies to zero and let the invisible
>> atoms be accounted for by high B-factors (either set manually or just
>> letting refinement do its thing).
>>
>>
>> Bert
>>
>>
>> --
>> *From:* CCP4 bulletin board  on behalf of Vipul
>> Panchal 
>> *Sent:* 04 May 2017 16:12
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] Poor density fit.
>>
>> HI all.
>>
>> I am solving protein structure with 2.16A resolution. There are two chain
>> in an asymmetric unit. I see that in one of the chain, many residues'
>> density for side chains is incomplete and therefore results in poor density
>> fit.
>>
>> *I want to know your opinions for the approach I have taken. Figures
>> relevant to each approach have been attached herewith.*
>>
>> *Case1*: There is no experimental density at all. Therefore, i have
>> deleted side chains to Gly.
>> *Case2*: Though there is incomplete density for Leu, it is enough to
>> suggest its rotamer. In this case, as may be seen, i have just set
>> occupancy for atoms without density(CG, CD1, CD2) to zero.
>>
>> Hopeful for the response.
>>
>> --
>> Vipul Panchal
>> Senior Research Fellow,
>> Respiratory disease and biology,
>> CSIR-IGIB
>> (M)-9540113372
>>
>
>
>
> --
> Vipul Panchal
> Senior Research Fellow,
> Respiratory disease and biology,
> CSIR-IGIB
> (M)-9540113372
>

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

[Tom Burnley]

Hi,

CCP-EM (CCP4 sister project for cryoEM) can help you here.  We have a EM
specific interface for several CCP4 programs as well as some others and
will handle map to mtz conversions for you.

You can download the suite here:
http://www.ccpem.ac.uk/download.php

We recently ran a workshop on high resolution modelling building and the
course material may be useful for you:
http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

Finally we also have an EM mailing list:
https://www.jiscmail.ac.uk/ccpem

All the best,

Tom

On 17 May 2017 at 17:24, MyeongSeon Lee <
0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi, all.
>
> I have collected cryoEM data and want to use Coot and CCP4 program to
> build model and to refine it.
>
> 1. What is the steps to do this?
> 2. How do I convert cryoEM map file to MTZ file?
> 3. Can I also use Phenix for this purpose?
>
> Thanks to all for your help in advance.
>

Re: [ccp4bb] Bond length and angle outlier fixing

[Paul Emsley]

On 17/05/2017 13:34, Vipul Panchal wrote:


I am solving protein structure with 2.16A resolution. There are two chain in an 
asymmetric
unit.
While submitted to PDB validation server, i could see few ligand bond -length 
and -angle
outlier. Coot doesn't have any module that can help me with these


h? :-)


as per my best understanding.



Kindly find the image of relevant details attached herewith.


I see a list of outliers for residues.  What's more interesting are the outliers in the 
ligand - I don't see them. What are the ideal metrics for the outliers? Are they correct? 
How to they compare to the same metrics in the dictionary? Did you generate your dictionary? 
If so how? Did you use Acedrg?



Paul.

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

[Paul Emsley]

On 17/05/2017 17:24, MyeongSeon Lee wrote:

Hi, all.

I have collected cryoEM data and want to use Coot and CCP4 program to  build 
model and to refine it.

1. What is the steps to do this?
2. How do I convert cryoEM map file to MTZ file?


CCPEM provides an increasingly sophisticated tool-set aimed at use with Cryo-EM 
data.

http://www.ccpem.ac.uk/download.php

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

[Pavel Afonine]

Hi,

2. How do I convert cryoEM map file to MTZ file?
>

While technically you can do it, normally there is absolutely no need to do
it. In cryo-EM the map is your data, not reflection data (structure
factors!). So no need to 'massage' your data (the map) by converting it
into "Fobs" and storing as reflection data in MTZ file.


> 3. Can I also use Phenix for this purpose?
>

Yes. Some relevant information:
http://phenix-online.org/presentations/latest/real_space_refine_web.pdf
http://phenix-online.org/documentation/


 Pavel

P.S.: there is Phenix mailing list for Phenix-specific questions (which
applies to your question #3 above).

[ccp4bb] Using Coot and CCP4 program for cryoEM data

[MyeongSeon Lee]

Hi, all.

I have collected cryoEM data and want to use Coot and CCP4 program to  build 
model and to refine it.

1. What is the steps to do this?
2. How do I convert cryoEM map file to MTZ file?
3. Can I also use Phenix for this purpose?

Thanks to all for your help in advance.

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Edward A. Berry]

Couple of wuestions:
What is the procedure for updating an entry? Start a new submission, or mail 
revised coordinates along with an explanation of changes to deposit@rcsb?

"unchanged experimental data" - does this mean the exact same structure 
factors, or will newly reduced data from the same original diffraction images be 
acceptable?

Thanks,
Ed

On 05/17/2017 09:28 AM, Jasmine Young wrote:

*Use CAUTION opening attachments or clicking on links in emails - IMT Help 
Desk, 4-4115*



The wwPDB is planning to introduce in 2017 a new procedure for the management 
by the Depositor of Record (where the Depositor of Record is defined as the 
Principal Investigator for the entry) of substantial revisions to previously 
released PDB archival entries.

At present, revised atomic coordinates for an existing released PDB entry are 
assigned a new accession code, and the prior entry is obsoleted. This 
long-standing wwPDB policy had the unintended consequence of breaking 
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The wwPDB is introducing a file versioning system that allows Depositors of 
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--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] AW: [ccp4bb] Bond length and angle outlier fixing

[Herman . Schreuder]

Hi Vipul,

The first thing to do is to check whether the fit of the offending residues in 
the electron density maps is correct. If it is not, you have to do rebuilding. 
If the fit is correct, I would leave them as they are. Assuming the 
distribution of bond lengths and angles has a bell-shape, there will always be 
some residues at the extreme ends.

Best, Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Vipul 
Panchal
Gesendet: Mittwoch, 17. Mai 2017 14:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Bond length and angle outlier fixing

HI all.

I am solving protein structure with 2.16A resolution. There are two chain in an 
asymmetric unit.
While submitted to PDB validation server, i could see few ligand bond -length 
and -angle outlier. Coot doesn't have any module that can help me with these as 
per my best understanding.
Kindly find the image of relevant details attached herewith.

Can somebody suggest me how to fix them?

Sincerely,
--
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372

[ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Jasmine Young]

The wwPDB is planning to introduce in 2017 a new procedure for the 
management by the Depositor of Record (where the Depositor of Record is 
defined as the Principal Investigator for the entry) of substantial 
revisions to previously released PDB archival entries.


At present, revised atomic coordinates for an existing released PDB 
entry are assigned a new accession code, and the prior entry is 
obsoleted. This long-standing wwPDB policy had the unintended 
consequence of breaking connections with publications and usage of the 
prior set of atomic coordinates, resulting in a non-trivial barrier to 
submission of atomic coordinate revisions by our Depositors of Record.


The wwPDB is introducing a file versioning system that allows Depositors 
of Record to update their own previously released entries. Please note, 
in the first phase, file versioning will be applied to the atomic 
coordinates refined versus unchanged experimental data.


Version numbers of each PDB archive entry will be designated using a #-# 
identifier. The first digit specifies the major version, and the second 
designates the minor version. The Structure of Record (i.e., the initial 
set of released atomic coordinates) is designated as Version 1-0. 
Thereafter, the major version digit is incremented with each substantial 
revision of a given entry (e.g., Version 2-0, when the atomic 
coordinates are replaced for the first time by the Depositor of Record). 
“Major version changes” are defined as updates to the atomic 
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All other changes are defined as “minor changes”. When a major change is 
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--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Bond length and angle outlier fixing

[Vipul Panchal]

HI all.

I am solving protein structure with 2.16A resolution. There are two chain
in an asymmetric unit.
While submitted to PDB validation server, i could see few ligand bond
-length and -angle outlier. Coot doesn't have any module that can help me
with these as per my best understanding.
Kindly find the image of relevant details attached herewith.

Can somebody suggest me how to fix them?

Sincerely,
-- 
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372

[ccp4bb] 3D graphics under linux for coot, pymol and chimera

[Wim Burmeister]

  
  

Hello,
 
we just wanted to share our experience in finding
  a configuration which allows to use 3D graphics under linux
  using Nvidia GeForce 3D glasses.
 
We had quite a hard time to find a configurations
  which works correctly.
 
We finally used Debian linux with a xfce desktop.
  Other recent desktops use a tiling which is not compatible
  with 3D graphics.
 
The hardware consists of


  a DELL Precision T5810 
  desktop computer with an Nvidia Quadro M4000 (8 Gbyte memory,
  4 DP) graphics card
  Nvidia
  GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
  active stereo glasses
  a stereo
  connector PNY Quadro 4000 3D for the synchronization of
  graphics card and glasses
  an ASUS 24"
  LED 3D - VG248QE display
  a
  DisplayPort-DisplayPort cable


The Nvidia linux drivers from version 367.57 can
  handle the current version of the Nvidia glasses.
 
For an obscure reason a direct DP-DP connection
  between graphics card and display is absolutely required in
  order to obtain fully working stereo. If a DP-DVI dual link
  adapter is used, the stereo does not work on the top and the
  bottom part of the screen. This is true for a native DELL
  active adaptor or generic models. The exact reason remains
  unresolved, but the solution is to use a direct DP-DP
  connection. This limits the available choice of displays which
  require 120 Hz for 1080*1980 screen resolution and a DP input.
  We have been choosing a “Nvidia 3D ready” model.
 
There has been a considerate about of exchange
  about this problem on
 
https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
 
The setup comes with a price tag of about 1600 €
  free of taxes.
 
coot, pymol and chimera work straight without
  problems in hardware stereo mode. The experience is absolutely
  great.
 
Best
 
Wim 









-- 
  
  
Wim Burmeister
  Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS
20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94
  00
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