[ccp4bb] Third CCP4-OIST workshop in Okinawa, third call

[Charles Ballard]

Dear Colleagues,

a reminder,  the third  CCP4 structure solution school at the Okinawa Institute 
of Science and Technology (OIST), Okinawa. All details can be found at 
http://www.ccp4.ac.uk/schools/OIST-2015 or contact ccp4_okin...@oist.jp

Title:
"CCP4 school: From data processing to structure refinement and beyond"
Dates: November 2 to 7, 2015
Site: Okinawa Institute of Science and Technology, Okinawa, Japan

The school content:

Software workshop: the workshop will be taught by authors and other experts, 
including Garib Murshudov (refmac), Victor Lamzin (arp/warp), Robbie Joosten 
(pdb_redo) and Phil Evans (aimless).  It will be organized in three Sections - 
lectures, tutorials and hands-on trouble-shooting.  We will also be covering 
the use of DIALS for data processing and the new ccp4 interface.

There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 25 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets so the problems can be 
addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 22 August. Application form, the program, contact info 
and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015

Fees: 

There is no fee for the workshop. The students will be responsible for their 
transportation costs outside Okinawa.  Lodging will be provided at the OIST 
Guest House "Seaside House".  The workshop will also cover the expenses for all 
meals and refreshments.

Fadel Samatay, Charles Ballard

e-mail contact: 

ccp4_okin...@oist.jp

[ccp4bb] Research Technician (Structural biology) position at University of Oxford

[Wyatt W. Yue]

Dear all,

We are advertising a research technician position in the Metabolic and Rare
Diseases group at SGC University of Oxford, which processes a variety of
human medically-relevant proteins in recombinant expression systems, and
purifies the proteins for structural and biophysical studies.


Closing date: Wednesday 15th July 2015, 12pm GMT


Interested candidates please apply via University of Oxford job page that
is accessible here (vacation ID 118978):

http://www.thesgc.org/careers/oxford/sgc-oxford-laboratory-technician-%E2%80%93-protein-structural-biology


Visit the SGC Metabolic & Rare Diseases group page:

http://www.thesgc.org/science/mob


Informal inquiries to:

wyatt@sgc.ox.ac.uk

-

Assoc Prof Wyatt W. Yue

PI in Metabolic & Rare Diseases

Structural Genomics Consortium

Nuffield Department of Medicine

University of Oxford OX3 7DQ

+44 (0)1865 617757

http://www.thesgc.org/wyatt

Re: [ccp4bb] Rfree below Rwork

[Boaz Shaanan]

Just wondering about Eleanor's interesting remark: would the Rf & Rw go as low as reported by Wolfram (0.22) in case of a wrong space group?


 Boaz

 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk]
Sent: Tuesday, June 30, 2015 8:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree below Rwork




I suppose if I was the referee for this structure and your FreeR is so close to the Rfactor I would ask you to ensure you had the right space group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3 fold..
Cases occur where R32 is indexed as C2.. 


Certainly if the Rfree set is assigned randomly to reflections which are symmetry equivalents then you see this phenomena of Rfree = Rfactor


Eleanor


On 30 June 2015 at 18:26, Gerard Bricogne 
 wrote:

Dear Wolfram,

     I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a "problem". People
have agonised to extreme degrees over the "difficulty" of choosing a
free set of reflections that would produce the expected gap between
Rwork and Rfree, and some of the conclusions were that you would need
to hide almost half of your data in some cases!

     I think it is best to remember that the idea of cross-validation
by Rfree is to prevent overfitting, i.e. ending up with a model that
fits the amplitudes too well compared to how well it determines the
phases. In the case of high-order NCS (in your case, the U/V ratio
that the old papers on NCS identified as the key quantity to measure
the phasing power of NCS would be less than 0.1!) the phases and the
amplitudes are so tightly coupled that it is simply impossible to fit
the amplitudes without delivering phases of an equally good quality.
In other words there is no overfitting problem (provided you do have
good and complete data) and the difference between Rfree and Rwork is
simply within the bounds of the statistical spread of Rfree depending
on the free set chosen.

     You are lucky to have 6-fold NCS, so don't let any reviewer
convince you that it is a curse, and make you suffer for it :-) .


     With best wishes,

          Gerard.

--

On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
> Hello,
> my question concerns refinement of a structure with 6-fold NCS (local
> automatic restraints in REFMAC) against 2.8 A data. The size of my free set
> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
> 4.3 % of reflections.
> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes,
> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
> I understand that NCS stresses the independence assumption of the free set.
> Am I correct in believing that Rfree *may* be smaller than Rcryst even in
> the absence of a major mistake? My hope is that the combined wisdom of
> ccp4bb followers can point out my possible mistake,  suggest tests that I
> may perform to avoid them and, possibly, arguments in defense of a
> crystallographic model with Rfree < Rcryst.
> Many thanks,
> Wolfram Tempel



--

     ===
     *                                                             *
     * Gerard Bricogne                     g...@globalphasing.com  *
     *                                                             *
     * Global Phasing Ltd.                                         *
     * Sheraton House, Castle Park         Tel: 
+44-(0)1223-353033 *
     * Cambridge CB3 0AX, UK               Fax: 
+44-(0)1223-366889 *
     *                                                             *
     ===

[ccp4bb] Research technician position at the University of Leicester

[Echalier, Aude M.P.C. (Dr.)]

Dear all,

A research technician position (Ref. MBP01379) is opening in my group to 
support a biochemical and structural biology project on the 
ubiquitin-proteasome system. Further details can be found at ; 
http://www2.le.ac.uk/offices/jobs/opportunities/
Informal enquiries are welcome and should be made to Dr Aude Echalier on 
amp...@le.ac.uk

Interested candidates should apply via the University of Leicester page 
(http://www2.le.ac.uk/offices/jobs/account-login) before July 20th 2015

Kind regards,
Aude

M5 Structural Biology: 
https://www2.le.ac.uk/departments/biochemistry/staff/cyril-dominguez/research/M5-Network-Event
-
Aude Echalier, Ph.D.
Lecturer in Structural Biology
Departments of Biochemistry and of Cancer Studies,
University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, 
LE1 9HN, UK

T. +44(0)116 229 7120
E. aude.echal...@le.ac.uk
[https://email.le.ac.uk/owa/attachment.ashx?id=RgBM4xSId5YtSpz6cDaVIIwsBwA%2bfW0enQplRo0dZMAx9BCyq2kCAAA%2bfW0enQplRo0dZMAx9BCyq47YAAAJ&attcnt=1&attid0=BAAA&attcid0=image001.jpg%4001CFA4D7.0C95C6E0]


[CRUKcentre]

Elite without being elitist

[ccp4bb] AW: [ccp4bb] Rfree below Rwork

[Herman . Schreuder]

Dear Boaz,

One can equally well describe a R32 crystal with one molecule in the asymmetric 
unit as P1 and 6 molecules in the asymmetric unit. In this case, the NCS in P1 
is identical to the crystallographic symmetry in R32.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Boaz 
Shaanan
Gesendet: Mittwoch, 1. Juli 2015 12:10
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Rfree below Rwork

Just wondering about Eleanor's interesting remark: would the Rf & Rw go as low 
as reported by Wolfram (0.22) in case of a wrong space group?

 Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[eleanor.dod...@york.ac.uk]
Sent: Tuesday, June 30, 2015 8:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree below Rwork
I suppose if I was the referee for this structure and your FreeR is so close to 
the Rfactor I would ask you to ensure you had the right space group - is the 6 
fold NCS actually 2 fold NCS with a crystallographic 3 fold..
Cases occur where R32 is indexed as C2..

Certainly if the Rfree set is assigned randomly to reflections which are 
symmetry equivalents then you see this phenomena of Rfree = Rfactor

Eleanor

On 30 June 2015 at 18:26, Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear Wolfram,

 I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a "problem". People
have agonised to extreme degrees over the "difficulty" of choosing a
free set of reflections that would produce the expected gap between
Rwork and Rfree, and some of the conclusions were that you would need
to hide almost half of your data in some cases!

 I think it is best to remember that the idea of cross-validation
by Rfree is to prevent overfitting, i.e. ending up with a model that
fits the amplitudes too well compared to how well it determines the
phases. In the case of high-order NCS (in your case, the U/V ratio
that the old papers on NCS identified as the key quantity to measure
the phasing power of NCS would be less than 0.1!) the phases and the
amplitudes are so tightly coupled that it is simply impossible to fit
the amplitudes without delivering phases of an equally good quality.
In other words there is no overfitting problem (provided you do have
good and complete data) and the difference between Rfree and Rwork is
simply within the bounds of the statistical spread of Rfree depending
on the free set chosen.

 You are lucky to have 6-fold NCS, so don't let any reviewer
convince you that it is a curse, and make you suffer for it :-) .


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
> Hello,
> my question concerns refinement of a structure with 6-fold NCS (local
> automatic restraints in REFMAC) against 2.8 A data. The size of my free set
> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
> 4.3 % of reflections.
> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes,
> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
> I understand that NCS stresses the independence assumption of the free set.
> Am I correct in believing that Rfree *may* be smaller than Rcryst even in
> the absence of a major mistake? My hope is that the combined wisdom of
> ccp4bb followers can point out my possible mistake,  suggest tests that I
> may perform to avoid them and, possibly, arguments in defense of a
> crystallographic model with Rfree < Rcryst.
> Many thanks,
> Wolfram Tempel
--

 ===
 * *
 * Gerard Bricogne 
g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: 
+44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: 
+44-(0)1223-366889 *
 * *
 ===

Re: [ccp4bb] AW: [ccp4bb] Rfree below Rwork

[Eleanor Dodson]

I wasn't suggesting the space group was wrong - just a lower symmetry
equivalent of the true SG. e.g. all structures can be solved in P1 but
several of the molecules in the cell will be related by crystal symmetry
operators. The same is true for the associated P1 intensities. So IF you
had assigned FreeR flags as for P1 it is more than likely that say h k l
and -h k -l will have different FreeR status..

And then the FreeR is not really free and it is very likely they will
refine to much the same value.

However if you had been careful to assign the FreeRs to the highest
possible Laue symmetry then expand them to cover P1 you usually find that
the freeR and R differ as expected


On 1 July 2015 at 12:33,  wrote:

>  Dear Boaz,
>
>
>
> One can equally well describe a R32 crystal with one molecule in the
> asymmetric unit as P1 and 6 molecules in the asymmetric unit. In this case,
> the NCS in P1 is identical to the crystallographic symmetry in R32.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Boaz Shaanan
> *Gesendet:* Mittwoch, 1. Juli 2015 12:10
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Rfree below Rwork
>
>
>
> Just wondering about Eleanor's interesting remark: would the Rf & Rw go as
> low as reported by Wolfram (0.22) in case of a wrong space group?
>
>
>
>  Boaz
>
>
>
>
>
> *Boaz Shaanan, Ph.D. *
>
>
>
>
>
>
>
> * Dept. of Life Sciences  Ben-Gurion
> University of the Negev  Beer-Sheva
> 84105
> Israel
> E-mail:
> bshaa...@bgu.ac.il  Phone: 972-8-647-2220  Skype:
> boaz.shaanan  Fax:   972-8-647-2992 or 972-8-646-1710*
>
>
>
>
>
>
>--
>
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
> Dodson [eleanor.dod...@york.ac.uk]
> *Sent:* Tuesday, June 30, 2015 8:55 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Rfree below Rwork
>
> I suppose if I was the referee for this structure and your FreeR is so
> close to the Rfactor I would ask you to ensure you had the right space
> group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3
> fold..
>
> Cases occur where R32 is indexed as C2..
>
>
>
> Certainly if the Rfree set is assigned randomly to reflections which are
> symmetry equivalents then you see this phenomena of Rfree = Rfactor
>
>
>
> Eleanor
>
>
>
> On 30 June 2015 at 18:26, Gerard Bricogne  wrote:
>
> Dear Wolfram,
>
>  I have a perhaps optimistic view of the effect of high-order NCS
> on Rfree, in the sense that I don't view it as a "problem". People
> have agonised to extreme degrees over the "difficulty" of choosing a
> free set of reflections that would produce the expected gap between
> Rwork and Rfree, and some of the conclusions were that you would need
> to hide almost half of your data in some cases!
>
>  I think it is best to remember that the idea of cross-validation
> by Rfree is to prevent overfitting, i.e. ending up with a model that
> fits the amplitudes too well compared to how well it determines the
> phases. In the case of high-order NCS (in your case, the U/V ratio
> that the old papers on NCS identified as the key quantity to measure
> the phasing power of NCS would be less than 0.1!) the phases and the
> amplitudes are so tightly coupled that it is simply impossible to fit
> the amplitudes without delivering phases of an equally good quality.
> In other words there is no overfitting problem (provided you do have
> good and complete data) and the difference between Rfree and Rwork is
> simply within the bounds of the statistical spread of Rfree depending
> on the free set chosen.
>
>  You are lucky to have 6-fold NCS, so don't let any reviewer
> convince you that it is a curse, and make you suffer for it :-) .
>
>
>  With best wishes,
>
>   Gerard.
>
> --
>
> On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
> > Hello,
> > my question concerns refinement of a structure with 6-fold NCS (local
> > automatic restraints in REFMAC) against 2.8 A data. The size of my free
> set
> > is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
> > 4.3 % of reflections.
> > A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> > Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224.
> Yes,
> > Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
> > I understand that NCS stresses the independence assumption of the free
> set.
> > Am I correct in believing that Rfree *may* be smaller than Rcryst even in
> > the absence of a major mistake? My hope is that the combined wisdom of
> > ccp4bb followers can point out my possible mistake,  suggest tests that I
> > may perform to avoid them and, possibly, arguments in defense of a
> > crystallographic model with Rfree < Rcryst.
>

Re: [ccp4bb] Rfree below Rwork

[wtempel]

A valid concern particularly in this case, and related to a question
someone asked off-list. The model came from a collaborator when it was at
early stages of refinement (Rwork/Rfree 0.244/0.296). I followed up with
steps I knew would additionally confound cross-validation:

   1. I assigned a new free flag in thin shells to allow for the effect of
   NCS on free set independence (Kleywegt & Jones, 1996)
   .
   2. I selected one of the NCS mates from coordinates I received and used
   PHASER to position 6 copies of it in the asymmetric unit.

Afterward, I annealed the model (PHENIX.REFINE) to “remove the memory”
(Brunger,
1993)  of free reflections, to
the extent possible given inherent interdependencies of between reflections
and NCS.
Further to several suggestions about the space group, I am refining the
structure in R3 (hexagonal setting). XDS’s CORRECT.LP “SYMMETRY OF
REFLECTION INTENSITIES” shows Rmeas(146) as 21% v Rmeas(155) 53%. The fact
that I have experimented with both SCALEPACK and XDS intensities throughout
my refinement should not matter in this context as the MTZ files have
consistent indices and the same FREE flag.
Additional testing has shown that mere omission of TLS parameterization
will give Rwork/Rfree of 0.209/0.215 (versus 0.207/0.206 with 10 cycles TLS
refinement). For that comparison, I had to adjust REFMAC’s WEIGHT MATRIX to
achieve similar bond/angle RMSDs. The latter is relevant here since, as
another off-list respondent suggested, Rfree positively correlates with
those RMSDs. I further suspect (but have not tested yet) that omission of
explicit NCS restraints would also cause Rfree to rise.
I tend toward following Gerard Bricogne’s intuition about sample variance
of Rfree. It is mentioned briefly by Brunger (1993). Would this be the
variance
corresponding to Cruickshank’s expected value
?
​

On Tue, Jun 30, 2015 at 2:07 PM, Robbie Joosten 
wrote:

> Hi Wolfram,
>
>
>
> You didn’t tell us where your model came from but 10 cycles of TLS and 10
> cycles of restrained refinement is not enough for a refinement to converge
> if you just picked your test set. Try resetting your B-factor and doing
> 30-40 cycles refinement in REFMAC.
>
>
>
> Cheers,
>
> Robbie
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> wtempel
> *Sent:* Tuesday, June 30, 2015 18:59
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Rfree below Rwork
>
>
>
> Hello,
>
> my question concerns refinement of a structure with 6-fold NCS (local
> automatic restraints in REFMAC) against 2.8 A data. The size of my free set
> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
> 4.3 % of reflections.
>
> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes,
> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
>
> I understand that NCS stresses the independence assumption of the free
> set. Am I correct in believing that Rfree *may* be smaller than Rcryst even
> in the absence of a major mistake? My hope is that the combined wisdom of
> ccp4bb followers can point out my possible mistake,  suggest tests that I
> may perform to avoid them and, possibly, arguments in defense of a
> crystallographic model with Rfree < Rcryst.
>
> Many thanks,
>
> Wolfram Tempel
>

[ccp4bb] Reindexing of lattice

[Bonsor, Daniel]

Hi,

I am trying to reindex a P212121 lattice to change the axis order from 32.62, 
64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't 
find how to reindex the lattice. Does anyone know how I should do this and an 
example of the execute script that I should use?

Thanks


Dan

[ccp4bb] Reindexing lattice

[D Bonsor]

Hi,

I am trying to reindex a P212121 lattice to change the axis order from 32.62, 
64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't 
find how to reindex the lattice. Does anyone know how I should do this and an 
example of the execute script that I should use? 

Thanks 


Dan

Re: [ccp4bb] Reindexing lattice

[Phil Evans]

reindex k, l, h

you can use Pointless or Reindex

Phil

On 1 Jul 2015, at 16:04, D Bonsor  wrote:

> Hi,
> 
> I am trying to reindex a P212121 lattice to change the axis order from 32.62, 
> 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I 
> can't find how to reindex the lattice. Does anyone know how I should do this 
> and an example of the execute script that I should use? 
> 
> Thanks 
> 
> 
> Dan

Re: [ccp4bb] Reindexing of lattice

[Todd Jason Green]

I think if you chose option "entering reflection transformation" from the 
define transformation matrix button under reindexing details and then use:

h->k, k->l, l->h

i think you should be ok.

-Todd



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bonsor, Daniel 
[dbon...@som.umaryland.edu]
Sent: Wednesday, July 01, 2015 10:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Reindexing of lattice

Hi,

I am trying to reindex a P212121 lattice to change the axis order from 32.62, 
64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't 
find how to reindex the lattice. Does anyone know how I should do this and an 
example of the execute script that I should use?

Thanks


Dan

[ccp4bb] Real space refinement of alternative conformations

[Isaac Westwood]

This is a cross-post from the cootbb last week, regarding the modelling of
multiple conformations in coot.

I know this has long been a tricky thing to do, and in the past I've always
managed to model multiple alternative conformers by hook or by crook, but
in some current structures I'm having a bit of a nightmare getting things
to refine with reasonable geometry, and was wondering if anyone has noticed
this and/or managed to resolve it satisfactorily.

If you add an alternate conformer in coot, you cannot then do real space
refinement with either sphere refine or real space refine zone (eg i +/- 1
by pressing 'a' or by selecting a zone around the residue with multiple
conformers).
In the case of sphere refine, the i-1 backbone peptide will become
non-planar (or completely flip so the C=O bond overlaps the C-N bond), and
the i peptide will also be distorted though to a lesser extent.
In the case of real space refine zone, the i-1 and i backbone angles are
distorted such that C-N-CA is around 150 degrees.
You can real space refine zone, then just select one of the multiple
conformers, which has worked acceptably in the past (especially when then
fed into a refinement package, which tends to clear things up), but at
least on the several datasets I've tested it on, this is still leading to
distorted geometry, particularly peptide planarity of the i-1 and i
peptides.

I'd really like to get a model with good geometry directly from coot, so I
don't have to rely on maximum likelihood refinement to sort out the
problems - I always find that a rather clunky solution.
Has anyone else noted or documented this behaviour, and is it possible to
fix this? I know I may be asking a lot, here!

To clarify some of the obvious questions up front: I'm using coot 0.8.1 on
Ubuntu 12.04 and coot 0.8 on Max OSX with the same results. The observed
behaviour occurs with and without the following restraints in coot: planar
peptides, torsion and Ramachandran restraints, with a refinement weight
typically of about 10, but I've observed the same problem at any value
between 0.1 and 90 (I haven't tested wider as there's not much point!). You
don't need high res data with genuine alt conf density to test this, you
get the same behaviour by modelling in 2 x 0.5 occ conformers into the same
density.

The only work around so far seems to be real-space refining without the
second conformer to get all the geometries right, then putting in the alt
conf and selecting the nearest rotamer, then do ML refinement to try to fix
the errors and get B-factors. Deleting the alt conf in coot before any
additional real space refinement is then required (but coot cleverly
remembers the B factors for the alt conf when you add it back in, which is
neat).

I'd be extremely grateful for any help to resolve this!

Thanks in advance

Isaac Westwood

Re: [ccp4bb] Reindexing of lattice

[Harry Powell]

hi

You probably don't want to reprocess the data, but there is the "known cell" 
option in iMosflm that would allow this at the indexing stage.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 1 Jul 2015, at 16:33, Todd Jason Green  wrote:
> 
> I think if you chose option "entering reflection transformation" from the 
> define transformation matrix button under reindexing details and then use:
> 
> h->k, k->l, l->h
> 
> i think you should be ok.
> 
> -Todd
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bonsor, Daniel 
> [dbon...@som.umaryland.edu]
> Sent: Wednesday, July 01, 2015 10:14 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Reindexing of lattice
> 
> Hi,
>  
> I am trying to reindex a P212121 lattice to change the axis order from 32.62, 
> 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I 
> can't find how to reindex the lattice. Does anyone know how I should do this 
> and an example of the execute script that I should use?
>  
> Thanks
>  
>  
> Dan
>  

[ccp4bb] Postdoctoral Position

[Jikui Song]

A post-doctoral position is available for highly motivated candidates to
join a research group interested in investigating molecular mechanisms
underlying epigenetic regulation and DNA replication initiation. Projects
will involve structure determination of macromolecular complexes by X-ray
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(Zhang W et al, ACS Chemical Biology 2015, 10:1176-80; Kuo et al, Nature
2012, 484:115-9). Applicants should hold a recent PhD degree and have
significant experience in molecular cloning, protein production and X-ray
crystallography. Additional background in cell biology and/or enzymatic
assay is considered a plus but not essential. Interested applicants should
send curriculum vitae, a summary of past research experience and
accomplishments, and contact information of three references to Jikui Song,
Ph.D. Department of Biochemistry, University of California, Riverside, CA
92521 (Email: jikui.s...@ucr.edu).

[ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Chen Zhao]

Hi all,

Sorry to bother you, but I am trying to fix a long-standing problem that I
cannot run Coot and Pymol through Xming/PUTTY by SSH connection on a
windows client. The error messages are pretty similar for both:
Coot:
PuTTY X11 proxy: unable to connect to forwarded X server: Network error:
Connection refused
(coot-real:23113): Gtk-WARNING **: cannot open display: localhost:10.0
Pymol:
PuTTY X11 proxy: unable to connect to forwarded X server: Network error:
Connection refused
freeglut (pymol): failed to open display 'localhost:10.0'

Does anybody have some ideas?

Thank you so much,
Chen

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Dale Tronrud]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


   Both the ssh client and server must be set up with "X11Forwarding
yes".  The message sounds like your local computer is not set up to
accept X11 tunneling.  (By the way, in the X11 world the remote system
is the "client" and your local system the "server".)

Dale Tronrud

On 7/1/2015 3:40 PM, Chen Zhao wrote:
> Hi all,
> 
> Sorry to bother you, but I am trying to fix a long-standing problem
> that I cannot run Coot and Pymol through Xming/PUTTY by SSH
> connection on a windows client. The error messages are pretty
> similar for both: Coot: PuTTY X11 proxy: unable to connect to
> forwarded X server: Network error: Connection refused 
> (coot-real:23113): Gtk-WARNING **: cannot open display:
> localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to
> forwarded X server: Network error: Connection refused freeglut
> (pymol): failed to open display 'localhost:10.0'
> 
> Does anybody have some ideas?
> 
> Thank you so much, Chen
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22 (MingW32)

iEYEARECAAYFAlWUbgYACgkQU5C0gGfAG10hVgCeLmuE4pHFrapu9biY9nHO/Bpi
5O8An17UN+hgpr7/6A+mny+XOBfJV/T5
=iTfz
-END PGP SIGNATURE-

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Chen Zhao]

Thank you Dale, but when I added " localhost:10.0"  to X display location,
the problem still exist, just without the phrase "localhost:10.0" in the
warning. My X11 forwarding is enabled all the time and all other GUIs work
just fine.

And thank you for your clarification on the concept of server and client
"in the X11 word". It makes a lot of sense and I just didn't give it a
second thought!

Best,
Chen

On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
>
>Both the ssh client and server must be set up with "X11Forwarding
> yes".  The message sounds like your local computer is not set up to
> accept X11 tunneling.  (By the way, in the X11 world the remote system
> is the "client" and your local system the "server".)
>
> Dale Tronrud
>
> On 7/1/2015 3:40 PM, Chen Zhao wrote:
> > Hi all,
> >
> > Sorry to bother you, but I am trying to fix a long-standing problem
> > that I cannot run Coot and Pymol through Xming/PUTTY by SSH
> > connection on a windows client. The error messages are pretty
> > similar for both: Coot: PuTTY X11 proxy: unable to connect to
> > forwarded X server: Network error: Connection refused
> > (coot-real:23113): Gtk-WARNING **: cannot open display:
> > localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to
> > forwarded X server: Network error: Connection refused freeglut
> > (pymol): failed to open display 'localhost:10.0'
> >
> > Does anybody have some ideas?
> >
> > Thank you so much, Chen
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v2.0.22 (MingW32)
>
> iEYEARECAAYFAlWUbgYACgkQU5C0gGfAG10hVgCeLmuE4pHFrapu9biY9nHO/Bpi
> 5O8An17UN+hgpr7/6A+mny+XOBfJV/T5
> =iTfz
> -END PGP SIGNATURE-
>

[ccp4bb] paired refinement

[Eric Karg]

Hi all,

I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do 
"paired refinement" to determine the optimal resolution cutoff. Here is what I 
get at different resolutions set in Phenix:

Final Rfree/Rwork:
2.7—> 0.2498/0.2027
2.6—> 0.2519/0.2009
2.5—> 0.2567/0.2025
2.4 —> 0.2481/0.2042
2.3 —> 0.2493/0.2075

The geometry of all output structures are similar.

1. What is the high resolution cutoff based on these data? I know that 
Rfree/Rwork at different resolution should not be compared, but is there a 
simple way to do the test as described in the K&D 2012 Science paper using 
Phenix GUI?

2. For refining a structure at a lower resolution (lower than the initial 
dataset), do I simply set the resolution limit in the refinement or I need to 
reprocess the data starting from the images? Do I need to do anything with 
Rfree flags? Based on the discussions on this forum I know I should deposit the 
highest resolution dataset but my question is about the mtz file which will be 
used for refinement. 

Thank you very much for your help!

[ccp4bb] ANISOU in pdb and density improvement

[Appu kumar]

Dear CCP4 users,
I am refining a structure at 4A resolution. Crystal diffracted
anisotropically and after refinement in both PHENIX and REFMAC, electron
density in one of the domain of protein is represented by discontinuity and
poor maps. Therefore i did the aniosotropy correction using anisotropy
server. After anisotropy correction using anisotropy server, the electron
density becomes resonable for 4A map as evident by appearance of electron
density around some bulky sidechains and discontinuity in electron density
is diminished. When i look into the pdb, I found that pdb contain ANISOU
records for each atoms.

I tried same things with other data sets and same data set again (data set
described above) of same protein. After refinement, the ANISOU records are
not present for each atoms in refined pdb and the electron density is
discontinuous and poor.

I am wondering why one of the anisotropically corrected MTZ by diffraction
server gives the ANISOU  records with the good density after refinement and
other mtz file do not produce ANISOU record in pdb and poor density map.

I would appreciate your help regarding this issue.
Thank you
Appu

Re: [ccp4bb] ANISOU in pdb and density improvement

[xaravich ivan]

4 Angstrom resolution is pretty low and there has to be other info
associated with that to get more help from here.
How big is your protein? How are you solving the phases? How complete is
your data at that resolution? What kind of multiplicity are you getting? I
think you have other issues that are much more pressing than what you are
asking here!!!
As you are able to get 4A data it is evident that you can crystallize your
protein. Congrats Now, concentrate on that and try to get higher
resolution data from better diffracting crystals and it might be a much
easier experience, (unless you trying to solve a huge ribosomal complex
kind of protein and in that case 4 angs is amazing)
cheers

Ivan

On Wed, Jul 1, 2015 at 5:57 PM, Appu kumar  wrote:

> Dear CCP4 users,
> I am refining a structure at 4A resolution. Crystal diffracted
> anisotropically and after refinement in both PHENIX and REFMAC, electron
> density in one of the domain of protein is represented by discontinuity and
> poor maps. Therefore i did the aniosotropy correction using anisotropy
> server. After anisotropy correction using anisotropy server, the electron
> density becomes resonable for 4A map as evident by appearance of electron
> density around some bulky sidechains and discontinuity in electron density
> is diminished. When i look into the pdb, I found that pdb contain ANISOU
> records for each atoms.
>
> I tried same things with other data sets and same data set again (data set
> described above) of same protein. After refinement, the ANISOU records are
> not present for each atoms in refined pdb and the electron density is
> discontinuous and poor.
>
> I am wondering why one of the anisotropically corrected MTZ by diffraction
> server gives the ANISOU  records with the good density after refinement and
> other mtz file do not produce ANISOU record in pdb and poor density map.
>
> I would appreciate your help regarding this issue.
> Thank you
> Appu
>

Re: [ccp4bb] paired refinement

[Jason Busby]

Hi,

In order to do a paired refinement you need 2 sets of Rwork/Rfree at each 
resolution.  The first is just the normal figures from refinement, the second 
is from the structure refined at higher resolution but with the R/Rfree 
calculated at the lower resolution.  You can calculate this using something 
like phenix.model_vs_data and setting a high resolution cutoff, or I believe 
running Refmac with 0 rounds of refinement will do the same thing.

e.g. refinement at 2.7
refinement at 2.6 with r/rfree calculated using only the reflections to 2.7

That way you can directly compare the two and see if including the extra data 
to 2.6 has made your structure better.  Usually this means either Rfree goes 
down, or Rfree stays the same but Rwork goes up (indicating less overfitting).

Cheers,

Jason.
--
Dr Jason Busby
Laboratory of Structural Biology
School of Biological Sciences
The University of Auckland
Thomas Building 110
3A Symonds St
Private Bag 92019
Auckland Mail Centre
Auckland
New Zealand

ph: +64 9 3737599 ext 88958



On 2/07/2015, at 11:15 am, Eric Karg 
<052044071b36-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi all,

I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do 
"paired refinement" to determine the optimal resolution cutoff. Here is what I 
get at different resolutions set in Phenix:

Final Rfree/Rwork:
2.7—> 0.2498/0.2027
2.6—> 0.2519/0.2009
2.5—> 0.2567/0.2025
2.4 —> 0.2481/0.2042
2.3 —> 0.2493/0.2075

The geometry of all output structures are similar.

1. What is the high resolution cutoff based on these data? I know that 
Rfree/Rwork at different resolution should not be compared, but is there a 
simple way to do the test as described in the K&D 2012 Science paper using 
Phenix GUI?

2. For refining a structure at a lower resolution (lower than the initial 
dataset), do I simply set the resolution limit in the refinement or I need to 
reprocess the data starting from the images? Do I need to do anything with 
Rfree flags? Based on the discussions on this forum I know I should deposit the 
highest resolution dataset but my question is about the mtz file which will be 
used for refinement.

Thank you very much for your help!

Re: [ccp4bb] ANISOU in pdb and density improvement

[Appu kumar]

Hello All,
Sorry for giving incomplete information. The protein is 75KDa membrane
protein and it exists as tetramer in ASU. Structure is solved by MR.
Overall completeness of data is 98% wiith multiplicity of 4.8. Density
looks great after refinement having ANISOU record in PDB.

Any suggestions and guidance will be much appreciated
Thanks you
Appu

On 1 July 2015 at 21:14, xaravich ivan  wrote:

> 4 Angstrom resolution is pretty low and there has to be other info
> associated with that to get more help from here.
> How big is your protein? How are you solving the phases? How complete is
> your data at that resolution? What kind of multiplicity are you getting? I
> think you have other issues that are much more pressing than what you are
> asking here!!!
> As you are able to get 4A data it is evident that you can crystallize your
> protein. Congrats Now, concentrate on that and try to get higher
> resolution data from better diffracting crystals and it might be a much
> easier experience, (unless you trying to solve a huge ribosomal complex
> kind of protein and in that case 4 angs is amazing)
> cheers
>
> Ivan
>
> On Wed, Jul 1, 2015 at 5:57 PM, Appu kumar  wrote:
>
>> Dear CCP4 users,
>> I am refining a structure at 4A resolution. Crystal diffracted
>> anisotropically and after refinement in both PHENIX and REFMAC, electron
>> density in one of the domain of protein is represented by discontinuity and
>> poor maps. Therefore i did the aniosotropy correction using anisotropy
>> server. After anisotropy correction using anisotropy server, the electron
>> density becomes resonable for 4A map as evident by appearance of electron
>> density around some bulky sidechains and discontinuity in electron density
>> is diminished. When i look into the pdb, I found that pdb contain ANISOU
>> records for each atoms.
>>
>> I tried same things with other data sets and same data set again (data
>> set described above) of same protein. After refinement, the ANISOU records
>> are not present for each atoms in refined pdb and the electron density is
>> discontinuous and poor.
>>
>> I am wondering why one of the anisotropically corrected MTZ by
>> diffraction server gives the ANISOU  records with the good density after
>> refinement and other mtz file do not produce ANISOU record in pdb and poor
>> density map.
>>
>> I would appreciate your help regarding this issue.
>> Thank you
>> Appu
>>
>
>

Re: [ccp4bb] paired refinement

[Robbie Joosten]

Hi Eric,

Since you are asking your question on the CCP4 bulletin board, I will give a 
CCP4 answer. Take your model refined to 2.7A and through it into PDB_REDO with 
the full 2.3A dataset. It will automatically do paired refinement and pick a 
resolution cut-off in REFMAC. No mucking about with all sorts of programs. One 
difference with the K&D paper is that the resolution steps are such that they 
contain the same number of reflections.

HTH,
Robbie

Sent with my Windows Phone

Van: Eric Karg
Verzonden: ‎2-‎7-‎2015 01:28
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] paired refinement

Hi all,

I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do 
"paired refinement" to determine the optimal resolution cutoff. Here is what I 
get at different resolutions set in Phenix:

Final Rfree/Rwork:
2.7—> 0.2498/0.2027
2.6—> 0.2519/0.2009
2.5—> 0.2567/0.2025
2.4 —> 0.2481/0.2042
2.3 —> 0.2493/0.2075

The geometry of all output structures are similar.

1. What is the high resolution cutoff based on these data? I know that 
Rfree/Rwork at different resolution should not be compared, but is there a 
simple way to do the test as described in the K&D 2012 Science paper using 
Phenix GUI?

2. For refining a structure at a lower resolution (lower than the initial 
dataset), do I simply set the resolution limit in the refinement or I need to 
reprocess the data starting from the images? Do I need to do anything with 
Rfree flags? Based on the discussions on this forum I know I should deposit the 
highest resolution dataset but my question is about the mtz file which will be 
used for refinement.

Thank you very much for your help!

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[Rose, Peter]

The RCSB PDB is seeking exceptional Developers, and we know we're not alone in 
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Want to write code at scale, let's do it. Everyone at our organization is 
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want to hear from skilled Developers, people passionate about their craft and 
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We are looking for two experienced Developers to join our team of agile 
software Developers at the University of California, San Diego. By joining our 
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projects ranging from:

  *   Front end development using HTML, CSS, Javascript, JSP, and NodeJS
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 *   How we scale to meet tens of thousands of unique users every day
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 *   How we incorporate and add value to the scientific community
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 *   Search using Apache Solr
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world’s leading biological databases with more than 300,000 unique users per 
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Requirements:

  *   BS degree in Computer Science or related field
  *   A minimum of 2 years of experience developing dynamic, highly scalable, 
database-driven web applications using HTML, CSS, JavaScript and Java/JSP
  *   Demonstrable experience with database design and systems
 *   Experience with NoSQL database systems, object-relational mapping 
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  *   Citable experience using agile software development and test-driven design

For more requirements or to apply, please view the UCSD job page 
(https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=75896).

Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West 
(http://www.rcsb.org)
San Diego Supercomputer Center 
(http://bioinformatics.sdsc.edu)
University of California, San Diego
+1-858-822-5497

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Dale Tronrud]

   Then I would worry that your local X11 server doesn't support glut.
 3d graphics is an additional layer to the protocol and not every
server supports it, since the performance over the network is quite
poor in the best of circumstances.

Dale Tronrud

On 7/1/2015 4:05 PM, Chen Zhao wrote:
> Thank you Dale, but when I added " localhost:10.0"  to X display
> location, the problem still exist, just without the phrase
> "localhost:10.0" in the warning. My X11 forwarding is enabled all
> the time and all other GUIs work just fine.
>
> And thank you for your clarification on the concept of server and
> client "in the X11 word". It makes a lot of sense and I just didn't
> give it a second thought!
>
> Best, Chen
>
> On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud
> mailto:de...@daletronrud.com>> wrote:
>
>
> Both the ssh client and server must be set up with "X11Forwarding
> yes".  The message sounds like your local computer is not set up
> to accept X11 tunneling.  (By the way, in the X11 world the remote
> system is the "client" and your local system the "server".)
>
> Dale Tronrud
>
> On 7/1/2015 3:40 PM, Chen Zhao wrote:
>> Hi all,
>
>> Sorry to bother you, but I am trying to fix a long-standing
>> problem that I cannot run Coot and Pymol through Xming/PUTTY by
>> SSH connection on a windows client. The error messages are
>> pretty similar for both: Coot: PuTTY X11 proxy: unable to connect
>> to forwarded X server: Network error: Connection refused
>> (coot-real:23113): Gtk-WARNING **: cannot open display:
>> localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to
>> forwarded X server: Network error: Connection refused freeglut
>> (pymol): failed to open display 'localhost:10.0'
>
>> Does anybody have some ideas?
>
>> Thank you so much, Chen
>
>

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Takanori Nakane]

Hi,

I have successfully forwarded OpenGL applications like PyMOL
using VirtualGL http://www.virtualgl.org/.

Takanori Nakane

On 2015年07月02日 14:09, Dale Tronrud wrote:

Then I would worry that your local X11 server doesn't support glut.
  3d graphics is an additional layer to the protocol and not every
server supports it, since the performance over the network is quite
poor in the best of circumstances.

Dale Tronrud

On 7/1/2015 4:05 PM, Chen Zhao wrote:

Thank you Dale, but when I added " localhost:10.0"  to X display
location, the problem still exist, just without the phrase
"localhost:10.0" in the warning. My X11 forwarding is enabled all
the time and all other GUIs work just fine.

And thank you for your clarification on the concept of server and
client "in the X11 word". It makes a lot of sense and I just didn't
give it a second thought!

Best, Chen

On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud
mailto:de...@daletronrud.com>> wrote:


Both the ssh client and server must be set up with "X11Forwarding
yes".  The message sounds like your local computer is not set up
to accept X11 tunneling.  (By the way, in the X11 world the remote
system is the "client" and your local system the "server".)

Dale Tronrud

On 7/1/2015 3:40 PM, Chen Zhao wrote:

Hi all,



Sorry to bother you, but I am trying to fix a long-standing
problem that I cannot run Coot and Pymol through Xming/PUTTY by
SSH connection on a windows client. The error messages are
pretty similar for both: Coot: PuTTY X11 proxy: unable to connect
to forwarded X server: Network error: Connection refused
(coot-real:23113): Gtk-WARNING **: cannot open display:
localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to
forwarded X server: Network error: Connection refused freeglut
(pymol): failed to open display 'localhost:10.0'



Does anybody have some ideas?



Thank you so much, Chen

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

[Zhijie Li]

Hi Chen,

I followed instructions on this page and it seems to be working:

http://www.geo.mtu.edu/geoschem/docs/putty_install.html

One thing I think is worth mentioning is that in Putty-connection-SSH-X11, I 
put localhost:0.0 instead of 10.0, as for putty itself, it is requesting from 
Xming for the use of display 0.0.

For COOT, it seems that I have to set Xlaunch in “one window” mode or simply 
run Xming.exe. But still there is some issue with refreshing the screen when 
choosing menu items.

My systems are CentOS 6.6 and Windows 7/Putty0.60/Xming6.9.0.31.

Zhijie



From: Chen Zhao 
Sent: Wednesday, July 01, 2015 7:05 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows 
client?

Thank you Dale, but when I added " localhost:10.0"  to X display location, the 
problem still exist, just without the phrase "localhost:10.0" in the warning. 
My X11 forwarding is enabled all the time and all other GUIs work just fine.


And thank you for your clarification on the concept of server and client "in 
the X11 word". It makes a lot of sense and I just didn't give it a second 
thought!


Best,

Chen


On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud  wrote:

  -BEGIN PGP SIGNED MESSAGE-
  Hash: SHA1


 Both the ssh client and server must be set up with "X11Forwarding
  yes".  The message sounds like your local computer is not set up to
  accept X11 tunneling.  (By the way, in the X11 world the remote system
  is the "client" and your local system the "server".)

  Dale Tronrud


  On 7/1/2015 3:40 PM, Chen Zhao wrote:
  > Hi all,
  >
  > Sorry to bother you, but I am trying to fix a long-standing problem
  > that I cannot run Coot and Pymol through Xming/PUTTY by SSH
  > connection on a windows client. The error messages are pretty
  > similar for both: Coot: PuTTY X11 proxy: unable to connect to
  > forwarded X server: Network error: Connection refused
  > (coot-real:23113): Gtk-WARNING **: cannot open display:
  > localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to
  > forwarded X server: Network error: Connection refused freeglut
  > (pymol): failed to open display 'localhost:10.0'
  >
  > Does anybody have some ideas?
  >
  > Thank you so much, Chen

  -BEGIN PGP SIGNATURE-
  Version: GnuPG v2.0.22 (MingW32)

  iEYEARECAAYFAlWUbgYACgkQU5C0gGfAG10hVgCeLmuE4pHFrapu9biY9nHO/Bpi
  5O8An17UN+hgpr7/6A+mny+XOBfJV/T5
  =iTfz
  -END PGP SIGNATURE-

[ccp4bb] [Job] Computational Biologist/Structural Bioinformatics/Big Data Analytics at UC San Diego

[Rose, Peter]

Computational and Data Science Research Specialist

The Structural Bioinformatics Group at the San Diego
Supercomputer Center (SDSC) is seeking an exceptional scientific
software developer to work on our new project “Compressive Structural
Bioinformatics” funded by the US National Institutes of Health (NIH) Big Data 
to Knowledge (BD2K) initiative 
(https://datascience.nih.gov/bd2k/funded-programs/software).
The Challenge is to enable efficient research on the rapidly growing
number of 3D molecular structures of ever increasing size and
complexity, and develop highly scalable 3D structural search, analysis,
workflow, data-exchange, and visualization tools.

Our team values open discussion and contribution. Starting from
your first day, you will shape software and services used by thousands
of people around the world. Have a great idea? Let's hear it. Want to
try a new technology? Let's learn it. Want to write code at scale? Let's
do it. Everyone at our organization is passionate about what we do, and
that is why we are leaders in our field. We want to hear from skilled
scientists and software developers, people passionate about their craft
and what they can bring to the field.

The Structural Bioinformatics Group is involved in research and
development activities centered around 3D structures of proteins and
nucleic acids, the integration of structural data with other domains
such as Medicine, Genomics, Biology, Drug Discovery, and the development
of scalable solution to Big Data problems in Structural Bioinformatics.
Our group leads the RCSB Protein Data Bank (PDB) (http://www.rcsb.org)
west-coast operations, which represents the preeminent source of
experimentally determined macromolecular structure information for
research and teaching in biology, biological chemistry, and medicine.
With over 300,000 unique users from over 160 countries around the world,
the RCSB PDB is one of the leading worldwide Biological Databases.

This position researches, designs, develops, and deploys
innovative, highly scalable solutions for 3D structure visualization,
structural queries, and large-scale analyses of 3D macromolecular
complexes. Develops protocols for the efficient network data transfer
using custom compression and streaming techniques to facilitate 3D
visualization of large complexes on any device from phone, tablet, to
laptop and desktop. Designs distributed parallel workflows for
structural queries and analysis of the PDB archive.

Qualifications:
* Bachelor's degree in Structural Bioinformatics, Bioinformatics,
Computational Biology, Computer Science or comparable combination of
education and experience with considerable focus in scientific software
development demonstrated by publications, participation in open source
or other types of software projects. Strong skills in applied
Mathematics and algorithm design. MS or Ph.D. degree preferred.

* Experience in the representation and data structures of
ligands, proteins, nucleic acids, and associated sequence information.
Experience with 3D structure and sequence analysis algorithms.

* Advanced experience in one or more of the following object
oriented programming languages:Java, JavaScript, C++, or Python.
Experience with software development tools including IDEs, Maven, Git,
and continuous integration tools.

* Experience in one or more of the following: development of 3D
visualization applications and knowledge of OpenGL/WebGL, development of
distributed parallel programming models using "Big Data" frameworks
such as Apache Hadoop or Spark, setup of these frameworks on compute
clusters, or development of workflow applications.

* Demonstrated effective communication and interpersonal skills.
Demonstrated ability to communicate technical information to technical
and non-technical personnel at various levels in the organization and to
external research and education audiences.

For more requirements or to apply, please view the UCSD job page 
(http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=77059).


--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)
San Diego Supercomputer Center (http://bioinformatics.sdsc.edu)
University of California, San Diego
+1-858-822-5497

[ccp4bb] [Job] Postdoctoral Fellows Computational Biology at UC San Diego

[Rose, Peter]

San Diego Supercomputer Center
Postdoctoral Fellow

Summary: We are looking for two highly motivated post-docs as part of our new 
project “Compressive Structural Bioinformatics” funded by the US National 
Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

The Challenge: To enable efficient research on the rapidly growing number of 3D 
molecular structures of ever increasing size and complexity. Develop highly 
scalable 3D structural search, analysis, workflow, data-exchange, and 
visualization tools.

Qualifications: Ph.D. in structural bioinformatics, structural biology, 
bioinformatics, computational biology or chemistry, computer science, or 
related discipline. Experience with scientific software development as 
demonstrated by publications or participation in open source software projects. 
Experience with several programming languages, including Java, JavaScript, C++, 
or Python, and software development tools. Strong skills in applied mathematics 
and algorithm design are required. Experience with distributed parallel 
computing or 3D visualization applications are a plus. Excellent interpersonal, 
written, and oral presentation skills are essential.

Note, this position is reviewed annually on the basis of performance and can be 
renewed for a maximum of three years.

Our Environment:

The Structural Bioinformatics Group 
(http://bioinformatics.sdsc.edu) at the San 
Diego Supercomputer Center (SDSC) (http://www.sdsc.edu) 
is involved in research and development activities centered around 3D 
structures of proteins and nucleic acids, the integration of structural data 
with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the 
development of scalable solution to Big Data problems in Structural 
Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast 
operations. The RCSB PDB (http://www.rcsb.org) represents 
the preeminent source of experimentally determined macromolecular structure 
information for research and teaching in biology, biological chemistry, and 
medicine. With over 300,000 unique users from over 160 countries around the 
world, the RCSB PDB is one of the leading worldwide Biological Databases.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in 
data-intensive computing and cyber infrastructure, providing resources, 
services, and expertise to the national research community, including industry 
and academia.

To apply, please send cover letter and resume to Dr. Peter Rose 
(pwr...@ucsd.edu).

--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West 
(http://www.rcsb.org)
Principal Investigator, Structural Bioinformatics Laboratory 
(http://bioinformatics.sdsc.edu)
San Diego Supercomputer Center (http://www.sdsc.edu)
University of California, San Diego
+1-858-822-5497