Re: [ccp4bb] weekend puzzle

2013-09-17 Thread Andreas Förster 
Thanks to all who engaged with my little puzzle.  The weekend is over 
and I'm not exactly closer to fitting the right pieces into the density. 
 Benzamidine was a good suggestion for the first bit of density. 
However, I didn't use that inhibitor during purification.  The second 
set of blobs doesn't sit on a twofold.  It might just remain undefined.


Thanks anyway for all replies.



Andreas




On 13/09/13 17:50, Andreas Förster wrote:

Dear all,

a structure I'm refining is enjoying a free R factor of 18 but still
suffers from mystery density that nothing in the crystallization
condition could explain.  I can't explain it either.  Maybe you like
to venture some guesses?

The missing ligand is derivatized benzoic acid, nitrobenzene or
benzamide.  I didn't find anything obvious in the PDB.  Any suggestions?
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png

The second ligand is a longer shot, two blobs connected by a
substantial bridge.  The two views are slightly rotated, and a bit of
peptide is shown to give an idea of the size.
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png

Happy guessing!




--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] Postdoctoral Fellow Position Available

2013-09-17 Thread Demet Arac-Ozkan 
Postdoctoral Fellow Position in Biochemistry/Structural Biology

The research group of Demet Arac-Ozkan, Ph.D. at the University of Chicago is 
seeking a postdoctoral fellow with expertise in protein biochemistry. The 
laboratory is housed in the Department of Biochemistry and Molecular Biology. 
The overarching goal of our group is to understand the structure/function 
relationship of cell surface proteins involved in cellular adhesion at the 
central nervous system. We are particularly interested in understanding the 
mechanism by which adhesion-type G-protein coupled receptors function in the 
brain.
 
Postdoctoral fellows will have the opportunity to learn the newest methods in 
biochemistry and biophysics, in addition to complementary functional methods. 
We use various approaches, including X-ray crystallography, molecular biology, 
protein biochemistry, and eukaryotic cell-based studies. For more information, 
please refer to the lab website: arac.uchicago.edu

Candidates must have a Ph.D. degree and a strong background in molecular 
biology and protein expression/purification. Those with experience in x-ray 
crystallography and baculovirus expression are preferred. Interested 
individuals must submit a CV including contact information for three references 
and a cover letter as a single pdf file to: arac at uchicago dot edu


Demet Arac-Ozkan

[ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-17 Thread Peter Keller 

Dear all,

At Global Phasing, we have seen that there are still issues with the way 
that different applications deal with mmCIF-format data, and this continues 
to cause problems for users. I believe that part of the reason for this is 
that the underlying syntax (the STAR format) is not universally understood, 
and that a common and complete understanding of the full STAR syntax amongst 
programmers who deal with the format will help with some of the existing 
problems.


I wrote some code for low-level handling of the STAR format a while ago that 
I have been meaning to release for over a year. Garry Battle's announcement 
on 23 August about the mmCIF/PDBx workshop at the EBI has prompted me into 
action: I have written a short article that discusses some examples of the 
issues that we have encountered, and made my code available for download. 
The references in the article are given primarily as web links: more 
conventional citations can usually be found in the pages that I link to. 
This code has not been used in any released products, but it has had some 
internal use at Global Phasing. There is an MX bias in the article's 
discussion, but the issues are not restricted to MX.


As I explain in the article, the handling of the input data is based on an 
enourmous regular expression that matches STAR data, with only a little 
logic in the code itself. The regular expression should be usable with a 
variety of other languages, not only in Java (which I have used in this 
case). The code, or the regular expression on its own, may be freely used in 
other projects: see the included licencing for details, but basically you 
should: (i) give credit for using it, and (ii) if you choose to modify the 
regular expression, state that you have done so in that credit.


The article, which contains links to a tar file containing the code, and the 
documentation, is here:


   

Hoping that others will find this useful and/or help to resolve or clarify 
outstanding questions,


Peter.

--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom

Re: [ccp4bb] What kind of reflection data to deposit to PDB

2013-09-17 Thread Gerard DVD Kleywegt 

Hi all,

Sorry for contributing to the noise as well as the signal in the discussion. 
To clarify:


It is not an issue of not having a place to put the data as we certainly have 
definitions for this and for intermediate phasing data sets. You cannot simply 
put the data into the current REFLN category which is where we presently 
collect reflection data.


At present, there is no official wwPDB policy in place describing how this 
data is to be processed, validated and distributed. Stuffing it into the 
structure factor files, as has been done informally by some depositors, is not 
a good long term solution as there is no way for people to easily find the 
information. What we'll likely end up doing is store these data in separate 
files (just like for NMR the raw NOE peak lists and distance restraints are 
likely to be archived and distributed as separate files).


As I tried to explain yesterday, the case for both unmerged Is and unassigned 
NOE peak lists has been made, and this will get implemented. It will just take 
a bit of time.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk




On Tue, 17 Sep 2013, Miller, Mitchell D. wrote:


Hi Martyn,

 I too was puzzled by the statement that "unmerged data
cannot be handled properly as part of a PDB deposition."

 We have deposited the unmerged original index intensities
for the refinement wavelength (and for additional wavelengths
used for phasing in the case of MAD) since 2005.

 This was based on recommendation #2 from the "Report of Task Force
on Numerical Criteria in Structural Genomics" from the 2001
Airlie meeting (2nd Intl. Struct. Genomics Mtg.).
http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc
http://www.isgo.org/organization/members07/010410.html
Which states that "For X-ray data, unmerged integrated intensities (omitting
outliers but including systematically-absent axial reflections) should be 
deposited
along with the final, merged intensities and amplitudes for all wavelengths 
and/or
derivatives."

We worked the RCSB staff to refine the format of the mmCIF formatted
reflection containing multiple data loops for our depositions and this
has been used for more than 1300 JCSG depositions and the data is retrievable
from all wwPDB partner sites.


Regards,
Mitch


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn 
Symmons
Sent: Tuesday, September 17, 2013 3:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB

Sorry to contradict,

But the mmCIF data model certainly does not seem to require hkl unique
within the reflection data.

Like CIF the mmCIF formalism has been developed to allow a complete
description of a diffraction experiment and the data arising from it.
There is a full description at
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these
links to the dictionary and the papers describing its development).

Having chosen mmCIF for the archive and then not using its flexibility
seems a bit like having your cake and NOT eating it.

It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.

++Martyn


On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:

Dear all,

At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data
model will be required (at the moment, hkl must be unique within the
reflection data, which is logical for merged data but precludes
handling of unmerged data). There are other (easier to resolve) issues
to work out, e.g. having to do with file naming and distribution via
the wwPDB ftp archive.

The wwPDB partners are presently focusing all efforts on rolling out
the new joint deposition and annotation system. Once this system is
reasonably stable we will look into accepting/validating/distributing
new kinds of data. This concerns not only unmerged Is for X-ray but
also unassigned NOE peak lists for NMR. We will seek the advice of the
corresponding wwPDB VTFs (Validation Task Forces) to help define the
data items that need to be captured, how the data should be processed
by wwPDB, and what kind(s) of validation is/are required.

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk




On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:


Hi Folks,

Sorry for the non-ccp4 post.

I am trying to determine what is the best form of unmerged reflection
data
to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavo

Re: [ccp4bb] What kind of reflection data to deposit to PDB

2013-09-17 Thread Miller, Mitchell D. 
Hi Martyn,

  I too was puzzled by the statement that "unmerged data 
cannot be handled properly as part of a PDB deposition."

  We have deposited the unmerged original index intensities
for the refinement wavelength (and for additional wavelengths
used for phasing in the case of MAD) since 2005.

  This was based on recommendation #2 from the "Report of Task Force 
on Numerical Criteria in Structural Genomics" from the 2001 
Airlie meeting (2nd Intl. Struct. Genomics Mtg.). 
http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc
 
http://www.isgo.org/organization/members07/010410.html
Which states that "For X-ray data, unmerged integrated intensities (omitting 
outliers but including systematically-absent axial reflections) should be 
deposited 
along with the final, merged intensities and amplitudes for all wavelengths 
and/or 
derivatives."

We worked the RCSB staff to refine the format of the mmCIF formatted 
reflection containing multiple data loops for our depositions and this 
has been used for more than 1300 JCSG depositions and the data is retrievable
from all wwPDB partner sites. 


Regards,
Mitch


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn 
Symmons
Sent: Tuesday, September 17, 2013 3:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB

Sorry to contradict,

But the mmCIF data model certainly does not seem to require hkl unique 
within the reflection data.

Like CIF the mmCIF formalism has been developed to allow a complete 
description of a diffraction experiment and the data arising from it. 
There is a full description at 
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html
 
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these 
links to the dictionary and the papers describing its development).

Having chosen mmCIF for the archive and then not using its flexibility 
seems a bit like having your cake and NOT eating it.

It is strange to hear on a discussion board that recently considered the 
advantages of depositing complete image data, that a case will have to 
be made for allowing the deposition of full unmerged datasets.

++Martyn


On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:
> Dear all,
>
> At present, unmerged data cannot be handled properly as part of a PDB 
> deposition. One reason for this is that changes to the mmCIF/PDBx data 
> model will be required (at the moment, hkl must be unique within the 
> reflection data, which is logical for merged data but precludes 
> handling of unmerged data). There are other (easier to resolve) issues 
> to work out, e.g. having to do with file naming and distribution via 
> the wwPDB ftp archive.
>
> The wwPDB partners are presently focusing all efforts on rolling out 
> the new joint deposition and annotation system. Once this system is 
> reasonably stable we will look into accepting/validating/distributing 
> new kinds of data. This concerns not only unmerged Is for X-ray but 
> also unassigned NOE peak lists for NMR. We will seek the advice of the 
> corresponding wwPDB VTFs (Validation Task Forces) to help define the 
> data items that need to be captured, how the data should be processed 
> by wwPDB, and what kind(s) of validation is/are required.
>
> --Gerard
>
> ---
> Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
> ger...@ebi.ac.uk . pdbe.org
> Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
>
>
>
>
> On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:
>
>> Hi Folks,
>>
>> Sorry for the non-ccp4 post.
>>
>> I am trying to determine what is the best form of unmerged reflection 
>> data
>> to deposit to the PDB. I have single wavelength anomalous data for my
>> structure and I have two flavors of scaled files from the same exact 
>> set of
>> diffraction images: (1) data indexed and scaled in p1, and (2) data 
>> indexed
>> in p222, scaled in Scalepack using the "no merge original index" 
>> option and
>> converted to .mtz since the unit cell in the header of the output 
>> .sca file
>> was missing.
>>
>> The space group for the dataset is p212121.
>>
>> Please could you let me know what might be the best approach.
>>
>> Many thanks and cheers,
>> Raji
>>
>> -- 
>> Raji Edayathumangalam
>> Instructor in Neurology, Harvard Medical School
>> Research Associate, Brigham and Women's Hospital
>> Visiting Research Scholar, Brandeis University
>>
>
>
> Best wishes,
>
> --Gerard
>
> **
>Gerard J. Kleywegt
>
> http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
> **
>The opinions in this message are fictional.  Any similarity
>to actual opinions, living or dead, is purely coincidental.
> **
>Little kno

Re: [ccp4bb] 3D graphics linux compatibility question

2013-09-17 Thread Jose Duarte 

Hi Emmanuel

Here we have tried the nvidia Quadro 2000 with two different monitors 
(both with the built-in IR emitter, thus with synching through DVI): 
ASUS VG278HR and BenQ XL2420TX. The setup works perfectly well in Linux, 
both pymol and coot work without issues. Unfortunately we have no 
experience with other nvidia cards, so can't comment on that.


Hope it helps

Jose


---
Jose Duarte
Laboratory of Biomolecular Research
Paul Scherrer Institute
5232 Villigen PSI
Switzerland




On 09/17/2013 12:09 PM, Emmanuel Saridakis wrote:

Dear BB,
We are still a bit confused about compatibility of graphics cards with 
3D Coot/PyMol in Linux:
(a) In previous CCP4bb discussions, it was stated that only Quadro 
cards are compatible with Linux setups. But could someone tell me what 
the minimum standard really is: is it Quadro FX380, 2000, 3800 or 
something else ? The nVidia site lists Quadro 3700 and 3800 as the two 
lowest (cheapest) options compatible with Linux 3D. However, different 
CCP4ers have in the past mentioned the other two options as working 
"perfectly" or "with little trouble".
(b) If a monitor such as the ASUS VG278H 
 , which has 
an in-built nVidia 3D vision emitter which takes its stereo synch from 
a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ?
As you might imagine, we are on a rather tight budget. Any info would 
be greatly appreciated!

Emmanuel Saridakis

N.C.S.R. "DEMOKRITOS"
Athens 15 310 Greece
esari...@chem.demokritos.gr 
tel. +30-210-6503793

Re: [ccp4bb] What kind of reflection data to deposit to PDB

2013-09-17 Thread Martyn Symmons 

Sorry to contradict,

But the mmCIF data model certainly does not seem to require hkl unique 
within the reflection data.


Like CIF the mmCIF formalism has been developed to allow a complete 
description of a diffraction experiment and the data arising from it. 
There is a full description at 
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html 
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these 
links to the dictionary and the papers describing its development).


Having chosen mmCIF for the archive and then not using its flexibility 
seems a bit like having your cake and NOT eating it.


It is strange to hear on a discussion board that recently considered the 
advantages of depositing complete image data, that a case will have to 
be made for allowing the deposition of full unmerged datasets.


++Martyn


On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:

Dear all,

At present, unmerged data cannot be handled properly as part of a PDB 
deposition. One reason for this is that changes to the mmCIF/PDBx data 
model will be required (at the moment, hkl must be unique within the 
reflection data, which is logical for merged data but precludes 
handling of unmerged data). There are other (easier to resolve) issues 
to work out, e.g. having to do with file naming and distribution via 
the wwPDB ftp archive.


The wwPDB partners are presently focusing all efforts on rolling out 
the new joint deposition and annotation system. Once this system is 
reasonably stable we will look into accepting/validating/distributing 
new kinds of data. This concerns not only unmerged Is for X-ray but 
also unassigned NOE peak lists for NMR. We will seek the advice of the 
corresponding wwPDB VTFs (Validation Task Forces) to help define the 
data items that need to be captured, how the data should be processed 
by wwPDB, and what kind(s) of validation is/are required.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk




On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:


Hi Folks,

Sorry for the non-ccp4 post.

I am trying to determine what is the best form of unmerged reflection 
data

to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavors of scaled files from the same exact 
set of
diffraction images: (1) data indexed and scaled in p1, and (2) data 
indexed
in p222, scaled in Scalepack using the "no merge original index" 
option and
converted to .mtz since the unit cell in the header of the output 
.sca file

was missing.

The space group for the dataset is p212121.

Please could you let me know what might be the best approach.

Many thanks and cheers,
Raji

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] 3D graphics linux compatibility question

2013-09-17 Thread Sabuj Pattanayek 
> (a) In previous CCP4bb discussions, it was stated that only Quadro cards
> are compatible with Linux setups. But could someone tell me what the
> minimum standard really is: is it Quadro FX380, 2000, 3800 or something
> else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest
> (cheapest) options compatible with Linux 3D. However, different CCP4ers
> have in the past mentioned the other two options as working "perfectly" or
> "with little trouble".
>
>

Use the 3700 with the external nvidia emitters (these require the 3 pin
mini din connection from the emitter into the video card) and 120Hz LCD's
that don't have built-in nvidia emitters.



> (b) If a monitor such as the ASUS 
> VG278H ,
> which has an in-built nVidia 3D vision emitter which takes its stereo synch
> from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680
> ?
>

No, I've tried this with a GTX680. You cannot use a GeForce in Linux with
monitors such as the Asus VG278H with built in nvidia emitters and the
official nvidia drivers to get 3D. You have to have a quadro card with a
G8x GPU or better. In this case the cheapest card that would work is the
Quadro FX 370 (not a typo, this is a different card from the 3700). We use
a Quadro 600 or K600 with our Asus VG278H to get 3D.


> As you might imagine, we are on a rather tight budget. Any info would be
> greatly appreciated! which require the 3 pin mini din port on the video
> card.
>

The VG278H is not a cheap monitor. You may be able to get nvidia 3d vision
kit (make sure the model # comes with the 2.5mm vesa to 3 pin mini din
cable since some don't, esp. the ones bundled with 120Hz monitors) + quadro
3700 + regular 120Hz monitor for slightly less than the price of the VG278H
+ quadro.

[ccp4bb] 3D graphics linux compatibility question

2013-09-17 Thread Emmanuel Saridakis 
Dear BB,

We are still a bit confused about compatibility of graphics cards with 3D 
Coot/PyMol in Linux:

(a) In previous CCP4bb discussions, it was stated that only Quadro cards are 
compatible with Linux setups. But could someone tell me what the minimum 
standard really is: is it Quadro FX380, 2000, 3800 or something else ? The 
nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options 
compatible with Linux 3D. However, different CCP4ers have in the past mentioned 
the other two options as working "perfectly" or "with little trouble".

(b) If a monitor such as the ASUS VG278H , which has an in-built nVidia 3D 
vision emitter which takes its stereo synch from a DVI cable is used, can we 
even use the simpler GeForce GTX670 or 680 ?

As you might imagine, we are on a rather tight budget. Any info would be 
greatly appreciated!


Emmanuel Saridakis

N.C.S.R. "DEMOKRITOS"
Athens 15 310 Greece
esari...@chem.demokritos.gr
tel. +30-210-6503793