[ccp4bb] Phenix refinement with modified amino acids

[Jan van Agthoven]

Dear all,
I'm refining a structure with three modified amino, ccp4 code: CY3, DTR,
and MPT respectively. However I don't know how to give phenix.refine the
adequate libraries as to obtain the correct geometry for three amino acids.
I tried to add the cif libraries downloaded from ccp4 to the command, but
it doesn't seem to work.
Thanks in advance for your help,

[ccp4bb] Second announcement for the (Pacific) Northwest Crystallography Workshop

[Dale Tronrud]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

 Second announcement for the
  (Pacific) Northwest Crystallography Workshop
   http://oregonstate.edu/conferences/event/nwcw2014/
   June 20-22, 2014

   Registration is continuing for this year's edition of the Northwest
Crystallography Workshop.  It is being hosted at Oregon State University
in Corvallis in the heart of the Willamette Valley surrounded by wine
country, wildlife refuges, and with both the Cascade Mountains and the
Pacific Ocean within easy driving distance.  It can be easily accessed
from either the Portland or Eugene airports.

   The "workshop" part of the name will be taken seriously.  We will
have talks and posters with priority for speaking slots given to
students and post-docs who focus on methodologies or interesting
structure determination stories, and/or how structural observations
provide insight into function and biology.

   Oregon State is the home of the Ava Helen and Linus Pauling Papers,
which is a fascinating collection that goes far beyond papers.  We
have arranged two tours of this collection for Friday afternoon before
the workshop.  If you can make it to Corvallis for either the 2 PM or
4 PM tour you will be amazed by this collection.  Let us know if you
plan to attend and we will reserve a spot.

   On May 1st the registration fee will increase by $25 from the
current $75 for students and $100 for others.

   And get those abstracts in!

   We look forward to a great meeting and celebration of the International
Year of Crystallography.

Dale and Andy

Dale E. Tronrud and P. Andrew Karplus
Department of Biochemistry & Biophysics
2011 ALS Bldg
Oregon State University
Corvallis, OR 97331
USA
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22 (MingW32)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iEYEARECAAYFAlNFojcACgkQU5C0gGfAG13evACfWzJo2D/RQEGT6xeYICJl/kTI
4eYAn0m4YyqkOajtKkuY6zojeic1+9Il
=lYDp
-END PGP SIGNATURE-

[ccp4bb] Job Opening: Postdoctoral Position at the NIH Bethesda

[esserlo]

Job

Position Type : Postdoctoral Position At the NIH NCI Bethesda, MD USA

Position Title: Structural Mechanism of Multi-Drug Resistance

Position Description:
Applications are invited for a postdoctoral position to investigate the
structures and functional mechanisms of the macromolecular machines that are
involved in cellular multidrug resistance. The position is associated with the
Crystallography Section (http://ccr.cancer.gov/staff/staff.asp?profileid=5719)
in the Laboratory of Cell Biology, National Cancer Institute, NIH, which is
located in the Bethesda Campus, Maryland.

The successful candidate should have a recent Ph.D. and have practical
experiences in both molecular biology and protein purification. Experience in
membrane protein and protein crystallization is a plus, but not required.
Applications, consisting of a CV, a statement of research, and three letters
of recommendation, should be sent to:

Dr. Di Xia via Email at x...@mail.nih.gov

Employer Name: National Cancer Institute, NIH

Position Location: Bethesda, MD 20892, USA

Disclaimers: The NIH is dedicated to building a diverse community in its
training and employment programs and this position is subject to a background
investigation.

[Sent on behalf of Dr. Di Xia by L. Esser]

[ccp4bb] PhD Studentship at UCL

[Alun R Coker]

Dear All,

I'd like to draw your attention to the following PhD studentship.
http://www.findaphd.com/search/ProjectDetails.aspx?PJID=53965
Crystallography will form a large part of the project.

The deadline for applications is tomorrow Thursday April 10th.

Alun

--
Alun R. Coker
Senior Lecturer
Centre for Amyloidosis and Acute Phase Proteins
Division of Medicine (Royal Free Campus)
University College London
Rowland Hill Street
London
NW32PF

Tel: +44(0)20 7433 2764
Fax: +44(0)20 7433 2776
Web: www.ucl.ac.uk/pxmed

Re: [ccp4bb] CCP4i aimless problem, no HKLIN

[Björn Kauppi]

Hi Phil,

If I make a new project among my old projects, aimless fails (no HKLIN is 
written to the script).

But if I just mv-ed the ".CCP4" directory to  ".CCP4-backup" and started ccp4i 
and it made the setup, i.e made the missing .CCP4 directory and content. Then I 
made a new project and and can run aimless without any problem.
So somehow my orignial .CPP4 content is corupted but it seem only to manifest 
it self on the missing HKLIN when running aimless, so there is clearly some 
difference how that script is generated compared to scala or refmac for 
example. 
I do not understand either and had hope to have this sorted out in some update, 
but since nobody else seem to have this problem I am stuck. 


--Björn

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Phil Evans
> Sent: den 9 april 2014 10:57
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] CCP4i aimless problem, no HKLIN
> 
> I don't understand this. Does it happen in a new project? Or if you "Restore
> default parameters" (in "Save or Restore" panel at the bottom)?
> 
> AFAIK, the general .CCP4 directory just points to different projects (in
> .CCP4/unix/directories.def) and doesn't store anything specific to any
> particular task: task data is in the PROJECT/CCP4_DATABASE/ directory
> 
> I'm not really an expert on ccp4i
> 
> Phil
> 
> On 9 Apr 2014, at 07:32, Björn Kauppi  wrote:
> 
> > Thanks Phil,
> >
> > It works fine if I just start with a new fresh ".CCP4" directory, so I 
> > guess it is
> a general CCP4i interface problem.
> > But it is just the aimless program that does this, all other ccp4 progs I 
> > use
> with ccp4i works fine to the best of my knowledge with my old .CCP4
> directory.
> >
> > Anything else to try?
> > I am reluctant to give up my old .CCP4-directory and the information I have
> collected during the years.
> >
> > --Björn
> >
> >> -Original Message-
> >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
> Of
> >> Phil Evans
> >> Sent: den 8 april 2014 16:50
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] CCP4i aimless problem, no HKLIN
> >>
> >> Just tested with a clean binary install on a Mac (running 10.8), and
> >> it works for me
> >>
> >> Phil
> >>
> >>
> >> On 8 Apr 2014, at 15:19, Björn Kauppi 
> wrote:
> >>
> >>>
> >>> Hi
> >>>
> >>> I run latest CCP4 as of today, 6.4.0 update 12 and CCP4i 2.2.1 When
> >>> trying to run pointless/aimless from the interface the script
> >>> generated
> >> show no HKLIN and hence program fails running. If I do "Run&View Com-
> file"
> >> and manually add HKLIN at proper place in the script, it runs fine.
> >>> This problem was introduced a few updates ago.
> >>>
> >>> Scala has no problem
> >>>
> >>> Is it just me or something general.
> >>> What do do?
> >>>
> >>> --Björn
> >>>
> >>>
> >>>
> >>>
> >>
> __
> >> 
> >>> This e-mail may contain confidential information proprietary to Karo
> >>> Bio AB and is meant for the intended addressee(s) only. Any
> >>> unauthorized review, use, disclosure or distribution is prohibited.
> >>> If you have received this message in error, please advise the sender
> >>> and delete the e-mail and any attachments from your files. Thank you!
> >>>
> >>
> __
> >> 
> >>>

[ccp4bb] Job opening for a structural biologist to join the Structural Motility team at the Curie Institute Paris, France.

[Houdusse-Juille Anne]

Job opening for a structural biologist to join the Structural Motility team at 
the Curie Institute Paris, France.

We are looking for a post-doctoral fellow to join the team Structural Motility 
at the Curie Institute (Paris Center) directed by Anne Houdusse. The position 
is immediately available (preference for a start in September 2014).

The Structural Motility group at the Institut Curie uses structural biology 
approaches combined with cell and biochemical approaches to understand how 
molecular motors produce force, how their activity is regulated and how they 
are recruited to their cellular targets. Many of these motors are also involved 
in human pathologies and they are thus good targets for new therapies which we 
are helping to develop.
The research project of the new candidate aims at a better understanding of how 
molecular motors coordinate their action in the cell and what adaptation 
acquired by some of these motors allow specific functions to be performed. It 
consists of a biochemical, crystallogenesis and structural determination study 
of several complexes that involve molecular motors. Coupled with functional and 
cellular studies, this project will elucidate how these motors are regulated 
and what role they play in the context of a cell.
A solid experience in crystallization and X-ray structural determination is 
required. Experience in the production and purification of recombinant proteins 
is a plus but we are ready to train a dynamic and motivated candidate.

If you are interested, please send a CV and a letter of motivation as well as 
letters of recommendation of your previous employers.

Contact : Anne Houdusse (anne.houdu...@curie.fr)
http://umr144.curie.fr/en/research-groups/structural-motility-anne-houdusse/structural-motility-00199

Some recent publications
1- Pylypenko O, Attanda W, Gauquelin C, Lahmani M, Coulibaly D, Baron B, Hoos 
S, Titus MA, England P, Houdusse A. Structural basis of human Myosin V 
Rab-dependent cargo recognition. Proc Natl Acad Sci USA  110:20443-8, 2013.
2- Ménétrey J*, Isabet T*, Ropars V, Mukherjea M, Pylypenko O, Liu X, Perez J, 
Vachette P, Sweeney HL, Houdusse AM. Processive steps in the reverse direction 
require uncoupling of the lead head lever arm of myosin VI. Mol Cell. 48,75-86, 
2012.
3- Mukherjea M, Llinas P, Kim H-J, Travaglia M, Safer D, Zong AB, Ménétrey J, 
Franzini-Armstrong C, Selvin PR, Houdusse A and Sweeney HL. Myosin VI 
dimerization triggers an unfolding of a 3-helix bundle in order to extend its 
reach.  Molecular Cell, 35:305-15, 2009.
4- Houdusse A, Carter AP. Dynein swings into action. Cell, 136:395-6, 2009.
5- Ménétrey J*, Llinas P*, Mukherjea M, Sweeney HL and Houdusse A. The 
structural basis for the large powerstroke of myosin VI. Cell 131:300-308, 2007.
6- Ménétrey J, Bahloul A, Wells AL, Yengo CM, Morris CA, Sweeney HL, Houdusse 
A. The structure of the myosin VI motor reveals the mechanism of directionality 
reversal. Nature (London) 435, 779-85, 2005.
7- Sweeney HL and Houdusse A, Myosin VI rewrites the rules for myosin motors, 
Cell, 141:573-82, 2010.


Anne Houdusse-Juillé, Directeur de Recherche CNRS
Institut Curie - UMR 144
Team Leader of the Structural motility Team
26 rue  d'Ulm
F-75248 Paris cedex 05

Tel: +33-1-5624-6395
FAX: +33-1-5624-6319
E-mail: anne.houdu...@curie.fr
http://umr144.curie.fr/fr/profile/anne-houdusse-00484

Re: [ccp4bb] Create Links in PDB

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Remie,

there is a difference between the bonds you see in Coot and the bonds
that are recognised by e.g. refmac5. Can you measure the bond length
after refinement and compare it with the expected value? Does the bond
length deviate from the target value? If not, your bond is probably
recognised, i.e. restrained during refinement, although it is not
displayed as such.

Regards,
Tim

On 04/09/2014 06:02 AM, Remie Fawaz-Touma wrote:
> Thanks to Maisam and Paul (answers below) but I still could not see
> the links in coot after refining.
> 
> In coot before refinement, the glucoses are connected, but when I
> refine, they become disconnected, then if I add a link in coot by
> doing Extension>Modeling>Add a link, I get disconnected bonds.
> 
> The LINK I see in pdb as text is for Arg and other residues but not
> for the sugars
> 
> Please advise on what I should do to see the sugars connected after
> refinement,
> 
> Thank you so much,
> 
> Remie
> 
> 
> On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma
>  wrote:
> 
>> Hi all,
>> 
>> I need help creating links between units of sugar (ligands) in
>> the PDB file before refining so that CCP4 recognizes the sugars
>> are attached.
>> 
>> I tried the one suggestion I got before Extension > Make a Link,
>> but I get discontinued bonds instead of full bonds.
>> 
>> Thanks so much for all your help in advance.
>> 
>> Remie
> 
> A dotted line is how Coot represents a LINK.  It will not use solid
> lines for LINKs. You don't need a solid line for Coot and Refmac to
> consider the residues as bonded.
> 
> If you examine the output PDB file, you will see a LINK record.
> 
> Paul.
> 
> If you open the pdb that Refmac generates ( As text file ) you will
> see that there is an "R" added to your link and it is "linkR", you
> need to delete that "R" and press the space button one time to
> correct for the spacing in your link description, and then coot
> will show that dotted line.
> 
> If you want to see a solid line in coot for the links, your sugar
> molecules should be defined as the residues of the same chain, but
> to be honest I have never tried that myself.
> 
> And if you run the refmac, and the pdb that is generated does not
> show the description of your link that means that the description
> of your link is not right.
> 
> Hope this helped.
> 
> Meisam
> 

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFTRQ7gUxlJ7aRr7hoRAksaAKCAmHEeeNOn/43a8mmgEn5G66m4fgCfbBLt
0LzZN7nh5trn2iPZEj4OjZw=
=yDiy
-END PGP SIGNATURE-

Re: [ccp4bb] CCP4i aimless problem, no HKLIN

[Phil Evans]

I don't understand this. Does it happen in a new project? Or if you "Restore 
default parameters" (in "Save or Restore" panel at the bottom)?

AFAIK, the general .CCP4 directory just points to different projects (in 
.CCP4/unix/directories.def) and doesn't store anything specific to any 
particular task: task data is in the PROJECT/CCP4_DATABASE/ directory

I'm not really an expert on ccp4i

Phil

On 9 Apr 2014, at 07:32, Björn Kauppi  wrote:

> Thanks Phil,
> 
> It works fine if I just start with a new fresh ".CCP4" directory, so I guess 
> it is a general CCP4i interface problem.
> But it is just the aimless program that does this, all other ccp4 progs I use 
> with ccp4i works fine to the best of my knowledge with my old .CCP4 directory.
> 
> Anything else to try? 
> I am reluctant to give up my old .CCP4-directory and the information I have 
> collected during the years.
> 
> --Björn
> 
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Phil Evans
>> Sent: den 8 april 2014 16:50
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] CCP4i aimless problem, no HKLIN
>> 
>> Just tested with a clean binary install on a Mac (running 10.8), and it 
>> works for
>> me
>> 
>> Phil
>> 
>> 
>> On 8 Apr 2014, at 15:19, Björn Kauppi  wrote:
>> 
>>> 
>>> Hi
>>> 
>>> I run latest CCP4 as of today, 6.4.0 update 12 and CCP4i 2.2.1 When
>>> trying to run pointless/aimless from the interface the script generated
>> show no HKLIN and hence program fails running. If I do "Run&View Com-file"
>> and manually add HKLIN at proper place in the script, it runs fine.
>>> This problem was introduced a few updates ago.
>>> 
>>> Scala has no problem
>>> 
>>> Is it just me or something general.
>>> What do do?
>>> 
>>> --Björn
>>> 
>>> 
>>> 
>>> 
>> __
>> 
>>> This e-mail may contain confidential information proprietary to Karo
>>> Bio AB and is meant for the intended addressee(s) only. Any
>>> unauthorized review, use, disclosure or distribution is prohibited.
>>> If you have received this message in error, please advise the sender
>>> and delete the e-mail and any attachments from your files. Thank you!
>>> 
>> __
>> 
>>> 

Re: [ccp4bb] AW: [ccp4bb] Create Links in PDB

[Campeotto, Ivan]

Dear Remie,

There is an alternative route, which requires the usage of the JLigand program 
of Andrey Lebedev, which is part of the CCP4 suite.
You can search for the two sugars in the JLigand library by inserting  their 
letter code in the "Load Ligand" window or you can use the drawing tools, if 
they are new. When both sugars are displayed in JLigand, you can link them 
together with the tool "Link" (left menu) and minimise the obtained molecule 
(Ligand > Regularise). At this point you can save the molecule as a monomer and 
this will generate the corresponding dictionary cif file.
After obtaining the cif file, you will have to restart JLigand, open the cif 
file and save the molecule as PDB this time (" Save Coordinates").
You will have the option to include or not hydrogens.
Now you have cif file and PDB file for the joint sugars, both ready to be used 
in COOT and in REFMAC and everything should run smoothly. 

Good luck!

Dr Ivan Campeotto
Imperial College London
UK



On 9 Apr 2014, at 08:47, 
 wrote:

> Sorry, I made a typo. One should of course delete the O1!
> Herman
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Schreuder, Herman R&D/DE
> Gesendet: Mittwoch, 9. April 2014 09:17
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] AW: [ccp4bb] Create Links in PDB
> 
> Dear Remie,
> 
> The first thing I would do is to download a random file form the pdb with 
> sugars attached and examine how the link looks like in coot and in an editor. 
> You could use e.g. (shameless plug)  4ci9.
> The next thing to do is to check the link record you created. Here the 
> punch-card heritage of the pdb format is still very prominent: one space too 
> much or too little and things will not work. I even have had mysterious cases 
> where the link would not work, although it looked ok in the editor. I would 
> copy and paste a link record from an official pdb file and edit that one, 
> making sure that the positions of the atom names etc. stay exactly the same 
> (do not move to the left or right). 
> 
> An alternative, which may even be better is to start from scratch. For 
> N-linked sugars this would go as follows:
> 
> go to to the linked sugar in coot
> delete the NAG attached to the Asn
> get monomer NAG
> merge molecules (to get the NAG in the same pdb file as your protein) 
> delete the O4 (delete item Atom) 
> fit and real space refine the NAG 
> make link (between ASN ND2 and NAG C1)
> 
> The same you should do for the other linked sugars. Make sure to delete the 
> right oxygen which gets lost in the link. In this way you are sure your NAG 
> has the right atom names and the correct cif file with restraints.
> 
> Good luck!
> Herman
> 
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Remie 
> Fawaz-Touma
> Gesendet: Mittwoch, 9. April 2014 06:03
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Create Links in PDB
> 
> Thanks to Maisam and Paul (answers below) but I still could not see the links 
> in coot after refining.
> 
> In coot before refinement, the glucoses are connected, but when I refine, 
> they become disconnected, then if I add a link in coot by doing 
> Extension>Modeling>Add a link, I get disconnected bonds.
> 
> The LINK I see in pdb as text is for Arg and other residues but not for the 
> sugars
> 
> Please advise on what I should do to see the sugars connected after 
> refinement, 
> 
> Thank you so much,
> 
> Remie
> 
> 
> On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma  wrote:
> 
>> Hi all,
>> 
>> I need help creating links between units of sugar (ligands) in the PDB file 
>> before refining so that CCP4 recognizes the sugars are attached.
>> 
>> I tried the one suggestion I got before Extension > Make a Link,  but I get 
>> discontinued bonds instead of full bonds.
>> 
>> Thanks so much for all your help in advance.
>> 
>> Remie
> 
> A dotted line is how Coot represents a LINK.  It will not use solid lines for 
> LINKs. You don't need a solid line for Coot and Refmac to consider the 
> residues as bonded.
> 
> If you examine the output PDB file, you will see a LINK record.
> 
> Paul.
> 
> If you open the pdb that Refmac generates ( As text file ) you will see that 
> there is an "R" added to your link and it is "linkR", you need to delete that 
> "R" and press the space button one time to correct for the spacing in your 
> link description, and then coot will show that dotted line.
> 
> If you want to see a solid line in coot for the links, your sugar molecules 
> should be defined as the residues of the same chain, but to be honest I have 
> never tried that myself.
> 
> And if you run the refmac, and the pdb that is generated does not show the 
> description of your link that means that the description of your link is not 
> right.
> 
> Hope this helped.
> 
> Meisam

[ccp4bb] AW: [ccp4bb] Create Links in PDB

[Herman . Schreuder]

Sorry, I made a typo. One should of course delete the O1!
Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Schreuder, Herman R&D/DE
Gesendet: Mittwoch, 9. April 2014 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] Create Links in PDB

Dear Remie,

The first thing I would do is to download a random file form the pdb with 
sugars attached and examine how the link looks like in coot and in an editor. 
You could use e.g. (shameless plug)  4ci9.
The next thing to do is to check the link record you created. Here the 
punch-card heritage of the pdb format is still very prominent: one space too 
much or too little and things will not work. I even have had mysterious cases 
where the link would not work, although it looked ok in the editor. I would 
copy and paste a link record from an official pdb file and edit that one, 
making sure that the positions of the atom names etc. stay exactly the same (do 
not move to the left or right). 

An alternative, which may even be better is to start from scratch. For N-linked 
sugars this would go as follows:

go to to the linked sugar in coot
delete the NAG attached to the Asn
get monomer NAG
merge molecules (to get the NAG in the same pdb file as your protein) 
delete the O4 (delete item Atom) 
fit and real space refine the NAG 
make link (between ASN ND2 and NAG C1)

The same you should do for the other linked sugars. Make sure to delete the 
right oxygen which gets lost in the link. In this way you are sure your NAG has 
the right atom names and the correct cif file with restraints.

Good luck!
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Remie 
Fawaz-Touma
Gesendet: Mittwoch, 9. April 2014 06:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Create Links in PDB

Thanks to Maisam and Paul (answers below) but I still could not see the links 
in coot after refining.

In coot before refinement, the glucoses are connected, but when I refine, they 
become disconnected, then if I add a link in coot by doing 
Extension>Modeling>Add a link, I get disconnected bonds.

The LINK I see in pdb as text is for Arg and other residues but not for the 
sugars

Please advise on what I should do to see the sugars connected after refinement, 

Thank you so much,

Remie


On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma  wrote:

> Hi all,
> 
> I need help creating links between units of sugar (ligands) in the PDB file 
> before refining so that CCP4 recognizes the sugars are attached.
> 
> I tried the one suggestion I got before Extension > Make a Link,  but I get 
> discontinued bonds instead of full bonds.
> 
> Thanks so much for all your help in advance.
> 
> Remie

A dotted line is how Coot represents a LINK.  It will not use solid lines for 
LINKs. You don't need a solid line for Coot and Refmac to consider the residues 
as bonded.

If you examine the output PDB file, you will see a LINK record.

Paul.

If you open the pdb that Refmac generates ( As text file ) you will see that 
there is an "R" added to your link and it is "linkR", you need to delete that 
"R" and press the space button one time to correct for the spacing in your link 
description, and then coot will show that dotted line.

If you want to see a solid line in coot for the links, your sugar molecules 
should be defined as the residues of the same chain, but to be honest I have 
never tried that myself.

And if you run the refmac, and the pdb that is generated does not show the 
description of your link that means that the description of your link is not 
right.

Hope this helped.

Meisam

[ccp4bb] AW: [ccp4bb] Create Links in PDB

[Herman . Schreuder]

Dear Remie,

The first thing I would do is to download a random file form the pdb with 
sugars attached and examine how the link looks like in coot and in an editor. 
You could use e.g. (shameless plug)  4ci9.
The next thing to do is to check the link record you created. Here the 
punch-card heritage of the pdb format is still very prominent: one space too 
much or too little and things will not work. I even have had mysterious cases 
where the link would not work, although it looked ok in the editor. I would 
copy and paste a link record from an official pdb file and edit that one, 
making sure that the positions of the atom names etc. stay exactly the same (do 
not move to the left or right). 

An alternative, which may even be better is to start from scratch. For N-linked 
sugars this would go as follows:

go to to the linked sugar in coot
delete the NAG attached to the Asn
get monomer NAG
merge molecules (to get the NAG in the same pdb file as your protein)
delete the O4 (delete item Atom)
fit and real space refine the NAG
make link (between ASN ND2 and NAG C1)

The same you should do for the other linked sugars. Make sure to delete the 
right oxygen which gets lost in the link. In this way you are sure your NAG has 
the right atom names and the correct cif file with restraints.

Good luck!
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Remie 
Fawaz-Touma
Gesendet: Mittwoch, 9. April 2014 06:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Create Links in PDB

Thanks to Maisam and Paul (answers below) but I still could not see the links 
in coot after refining.

In coot before refinement, the glucoses are connected, but when I refine, they 
become disconnected, then if I add a link in coot by doing 
Extension>Modeling>Add a link, I get disconnected bonds.

The LINK I see in pdb as text is for Arg and other residues but not for the 
sugars

Please advise on what I should do to see the sugars connected after refinement, 

Thank you so much,

Remie


On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma  wrote:

> Hi all, 
> 
> I need help creating links between units of sugar (ligands) in the PDB file 
> before refining so that CCP4 recognizes the sugars are attached.
> 
> I tried the one suggestion I got before Extension > Make a Link,  but I get 
> discontinued bonds instead of full bonds.
> 
> Thanks so much for all your help in advance.
> 
> Remie

A dotted line is how Coot represents a LINK.  It will not use solid lines for 
LINKs. You don't need a solid line for Coot and Refmac to consider the residues 
as bonded.

If you examine the output PDB file, you will see a LINK record.

Paul.

If you open the pdb that Refmac generates ( As text file ) you will see that 
there is an "R" added to your link and it is "linkR", you need to delete that 
"R" and press the space button one time to correct for the spacing in your link 
description, and then coot will show that dotted line.

If you want to see a solid line in coot for the links, your sugar molecules 
should be defined as the residues of the same chain, but to be honest I have 
never tried that myself.

And if you run the refmac, and the pdb that is generated does not show the 
description of your link that means that the description of your link is not 
right.

Hope this helped.

Meisam