Re: [ccp4bb] CCP4 Update victim of own success

[Harry Powell]

Hi

I'd second NX; you can install a free server for one or two (I think - I only 
use one at a time ;-)) concurrent connections and a local client, then it's 
almost "like being there".

On 11 Apr 2013, at 22:54, Dyda wrote:

> Or nx, which works very well, although the server has to be installed at
> the remote end and client on the local.
> 
> www.nomachine.com
> 
> Fred
> ***
> Fred Dyda, Ph.D.   Phone:301-402-4496
> Laboratory of Molecular BiologyFax: 301-496-0201
> DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
> Bldg. 5. Room 303 
> Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
> Google maps coords: 39.000597, -77.102102
> http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
> ***

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

[ccp4bb] CCP4 Grant Renewal

[Martin Noble]

Dear BBer,

As I hope you are all aware CCP4 has been well supported throughout its 
existence by BBSRC grant income. This Research Council funding is vital for the 
continued success of the CCP4 collaboration and to support its software 
development, distribution, and out-reach activities. This core funding has 
underpinned CCP4's activities and enabled us to generate commercial license 
income to complement the core grant.

On the 24th April 2013, we will be submitting  our five-yearly grant-renewal 
application to the BBSRC.  This will be reviewed over the next few months, and 
will be considered in the highly competitive, responsive mode funding meeting 
of BBSRC committee D in September/October.

We are writing to ask those of you who are keen that CCP4 should continue in 
its work to help in ensuring a positive outcome to this application.  
Historically, we have been fortunate to draw on letters of support that we have 
uploaded to the BBSRC, and which have had a number and weight that has helped 
to make the case for funding indisputable.  This year, BBSRC have indicated 
that this approach presents challenges to them in respect of identifying 
independent refereeing downstream. We are therefore proposing instead to 
collect and hold letters of support from users of the suite who wish to voice 
such support, but to provide the BBSRC with a summary analysis of those letters 
rather than with the letters themselves.

To keep numbers appropriate, we would really need to receive some sort of 
letter from PIs, Reserch Fellows, and senior postdocs.  Those letters should be 
specific about the high-impact work that CCP4 sustains, and ideally should 
reference the workplan that WG1 has agreed for the current renewal. This 
relates specifically to work packages as follows

WP0: "Cloud infrastructure", facilitating mobility of data and projects from 
site to site, ( especially synchrotrons to home lab to laptop) and providing 
access to powerful compute-resources to apply challenging algorithms to 
difficult problems.  Headed up by Eugen Krissinel

WP1: Improved integration of structure-determination with data collection at 
the synchrotron.  This involves feed-forward (better data passed  from data 
analysis to structure determination) and feed-back (better informed decision 
making at the synchrotron as a result of better use of automated pipelines to 
know how useful the data are as soon as possible). Headed up by

WP2: Improved models for MR.  This is to build on AMPLE to make better models 
for molecular replacement: an exciting area that will make unsolveable 
structures solveable.  Headed by Airlie McCoy and Dan Rigden

WP3: Atom-free and reparameterized atomic refinement.  A tool to make EM-models 
and/or poor homology models into a better starting point for solving 
structures.  Not unlike the morphing from PHENIX, but significantly different 
and possibly better.  Headed by Kevin Cowtan

WP4: Extending the statistical model for refinement to confront the real-world 
issues that data is compromised (overlapped, from multiple crystals, collected 
while the crystal is being zapped by a death-star(TM) grade death beam). Headed 
by Garib Murshudov

If you are such a person, or could persuade such a person to contribute, then 
please could we ask for your help.  Letters and/or e-msils should go to Keith 
Wilson (keith.wil...@york.ac.uk) AS SOON AS 
POSSIBLE, and no later than 16th April.

Many thanks for your help and support,

Martin

Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466

Re: [ccp4bb] CCP4 Grant Renewal

[Martin Noble]

Hi Phil,

Since these will be mostly used for numbers, and supplied only if BBSRC change 
their mind about wanting to see the specific letters, I would say that people 
doing high impact research (which should include anyone who has been funded), 
might contribute their penny's worth.  We will be completely transparent about 
the process that we have gone through to gauge support, and the BBSRC can make 
of it what they will.  With that said, however, I would think that individuals 
who are named recipients of support from the grant would probably be a step too 
far. That would leave you as having to write a letter :-)

best wishes,

Martin

Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466
Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466






On 12 Apr 2013, at 11:19, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>>
 wrote:


I assume that Exec members should not write a letter? Or should we?
Phil

On 12 Apr 2013, at 10:46, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:



Dear BBer,

As I hope you are all aware CCP4 has been well supported throughout its 
existence by BBSRC grant income. This Research Council funding is vital for the 
continued success of the CCP4 collaboration and to support its software 
development, distribution, and out-reach activities. This core funding has 
underpinned CCP4's activities and enabled us to generate commercial license 
income to complement the core grant.

On the 24th April 2013, we will be submitting  our five-yearly grant-renewal 
application to the BBSRC.  This will be reviewed over the next few months, and 
will be considered in the highly competitive, responsive mode funding meeting 
of BBSRC committee D in September/October.

We are writing to ask those of you who are keen that CCP4 should continue in 
its work to help in ensuring a positive outcome to this application.  
Historically, we have been fortunate to draw on letters of support that we have 
uploaded to the BBSRC, and which have had a number and weight that has helped 
to make the case for funding indisputable.  This year, BBSRC have indicated 
that this approach presents challenges to them in respect of identifying 
independent refereeing downstream. We are therefore proposing instead to 
collect and hold letters of support from users of the suite who wish to voice 
such support, but to provide the BBSRC with a summary analysis of those letters 
rather than with the letters themselves.

To keep numbers appropriate, we would really need to receive some sort of 
letter from PIs, Reserch Fellows, and senior postdocs.  Those letters should be 
specific about the high-impact work that CCP4 sustains, and ideally should 
reference the workplan that WG1 has agreed for the current renewal. This 
relates specifically to work packages as follows

WP0: "Cloud infrastructure", facilitating mobility of data and projects from 
site to site, ( especially synchrotrons to home lab to laptop) and providing 
access to powerful compute-resources to apply challenging algorithms to 
difficult problems.  Headed up by Eugen Krissinel

WP1: Improved integration of structure-determination with data collection at 
the synchrotron.  This involves feed-forward (better data passed  from data 
analysis to structure determination) and feed-back (better informed decision 
making at the synchrotron as a result of better use of automated pipelines to 
know how useful the data are as soon as possible). Headed up by

WP2: Improved models for MR.  This is to build on AMPLE to make better models 
for molecular replacement: an exciting area that will make unsolveable 
structures solveable.  Headed by Airlie McCoy and Dan Rigden

WP3: Atom-free and reparameterized atomic refinement.  A tool to make EM-models 
and/or poor homology models into a better starting point for solving 
structures.  Not unlike the morphing from PHENIX, but significantly different 
and possibly better.  Headed by Kevin Cowtan

WP4: Extending the statistical model for refinement to confront the real-world 
issues that data is compromised (overlapped, from multiple crystals, collected 
while the crystal is being zapped by a death-star(TM) grade death beam). Headed 
by Garib Murshudov

If you are such a person, or could persuade such a person to contribute, then 
please could we ask for your help.  Letters and/or e-msils should go to Keith 
Wilson (keith.wil...@york.ac.uk) AS SOON AS 
POSSIBLE, and no later than 16th April.

Many thanks for your help and support,

Martin

Professor Martin Noble
Northern Instit

[ccp4bb] Survey on Software and Data Management Tools for Integrated Structural Biology

[Chris Morris]

Hi,

This questionnaire is designed to test the hypothesis that developments in 
Structural Biology methods are creating a need for new forms of facility 
access, processing and modelling software, and data archives:
http://www.surveymonkey.com/s/ZH565SN
We would be very grateful for your input.

Lucia Banci CERM
Antonio Rosato CERM
Chris Morris STFC

Chris Morris
chris.mor...@stfc.ac.uk
Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
Mobile: 07921-717915
Skype: chrishgmorris
http://pims.structuralbiology.eu/
http://www.citeulike.org/blog/chrishmorris
STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, 
Warrington, WA4 4AD UK


-- 
Scanned by iCritical.

Re: [ccp4bb] DNA structures superimpose

[Ed. Pozharski]

Doesn't lsqkab work? It just needs proper atom matching. 

Coot definitely does superimpose DNA.  One problem is that simple-lsq works on 
a single chain, but you can trick it by changing chain id and renumbering the 
other strand.

As for helix rotation, you can derive it from rotation reported by lsq.  But it 
is more common to look at DNA geometry directly for changes (3DNA or Curves+).

 Original message 
From: "Veerendra Kumar (Dr)"  
Date: 04/12/2013  2:18 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] DNA structures superimpose 
 
Dear CCP4 members,
Is there any program to superimpose the DNA structures? I also want to measure 
the relative domain rotation angle. I tried using DynDom but it does not work 
for me. 
Can someone suggest a program which can output the rotation angles? 

Thank you 

Best Regards

Veerendra kumar

CONFIDENTIALITY:This email is intended solely for the person(s) named and may 
be confidential and/or privileged.If you are not the intended recipient,please 
delete it,notify us and do not copy,use,or disclose its content.

Towards A Sustainable Earth:Print Only When Necessary.Thank you.

Re: [ccp4bb] DNA structures superimpose

[Gerard DVD Kleywegt]

LSQMAN aligns just about anything, incl. DNA and RNA - 
http://xray.bmc.uu.se/usf/lsqman_man.html


There's a ready-to-use macro that will do all the hard work for you - 
ftp://xray.bmc.uu.se/pub/gerard/omac/align_rna.lsqmac - there's one line that 
may need editing, it defines the name of the nominal "CA" atom and currently 
reads: & mytype C4*


--DVD



On Fri, 12 Apr 2013, Veerendra Kumar (Dr) wrote:


Dear CCP4 members,
Is there any program to superimpose the DNA structures? I also want to measure 
the relative domain rotation angle. I tried using DynDom but it does not work 
for me.
Can someone suggest a program which can output the rotation angles?

Thank you

Best Regards

Veerendra kumar


CONFIDENTIALITY:This email is intended solely for the person(s) named and may 
be confidential and/or privileged.If you are not the intended recipient,please 
delete it,notify us and do not copy,use,or disclose its content.

Towards A Sustainable Earth:Print Only When Necessary.Thank you.




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 !
**

[ccp4bb] Refmac error

[Peer Mittl]

 Dear Colleagues, 

For some reason Refmac refuses to read the file "mon_lib_list.cif" athough the 
file exists. The error message is as follows:

 Open failed: Unit:   7, File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif)

Last system error message: Illegal seek
 Refmac_5.7.0029:   Open failed: File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
   
 Refmac_5.7.0029:   Open failed: File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif 

Any advice would be welcome.

-Peer

Re: [ccp4bb] Refmac error

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Peer,

can you send the output of the command
 ls -l /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif

Best,
Tim

On 04/12/2013 04:11 PM, Peer Mittl wrote:
> Dear Colleagues,
> 
> For some reason Refmac refuses to read the file "mon_lib_list.cif"
> athough the file exists. The error message is as follows:
> 
> Open failed: Unit:   7, File:
> /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
> (logical:
> /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif) 
>  Last system error
> message: Illegal seek Refmac_5.7.0029:   Open failed: File:
> /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
>  Refmac_5.7.0029:   Open failed: File:
> /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
> 
> Any advice would be welcome.
> 
> -Peer
> 
> 

- -- 
- --
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 Mozilla - http://enigmail.mozdev.org/

iD8DBQFRaCFtUxlJ7aRr7hoRAhTcAKCU7lbVkKNjgOvsapJMD95UkQ1GjQCfQNef
oOSULaJ9q+BdRm3h2MxT4iA=
=FB76
-END PGP SIGNATURE-

[ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

Dear users,

Is it advisable to refine the occupancy of
a ligand for a 2.0Ang data by approximately
changing the values of occupancy based on
its b-factor?
After refinement, there were some negative
densities appearing in some parts of the
ligand, like at the centre of a pyrimidine
ring, so I expected that the problem is with
the occupancy. (the crystal was obtained by
co-crystallisation method).
Kindly provide some suggestions.

Thanking you
With Regards
Kavya


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

Dear Kavya

What about using occupancy refinement in refmac?
link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy 
refinement.

R


On 12 Apr 2013, at 17:12, Kavyashree Manjunath 
 wrote:

> Dear users,
> 
> Is it advisable to refine the occupancy of
> a ligand for a 2.0Ang data by approximately
> changing the values of occupancy based on
> its b-factor?
> After refinement, there were some negative
> densities appearing in some parts of the
> ligand, like at the centre of a pyrimidine
> ring, so I expected that the problem is with
> the occupancy. (the crystal was obtained by
> co-crystallisation method).
> Kindly provide some suggestions.
> 
> Thanking you
> With Regards
> Kavya
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Unexplained negative fo-fc

[Pavel Afonine]

Hi,

not knowing other details, the most naive guess is that this may be a
footprint of mask-based bulk-solvent model. Next one is that you are
contouring at too low/high level (note, sometimes, if, for instance,
solvent content is high, you need to look above/below 3sigma). Of course,
there could be gazillions of other causes.

Pavel

On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven  wrote:

> Hi everyone,
> I was recently looking at the following structure deposited in the
> PDB: 4g1m. Overall, the structure fits nicely the density, but the map
> shows large red blobs inside some of the domains (negative density
> disappears around 5 sigma). Could this be due to an excessive low R
> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a
> resolution of 2.85 A?
>

Re: [ccp4bb] Unexplained negative fo-fc

[Pavel Afonine]

P.S.: you are not alone having such R-factors

On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven  wrote:
>
>> Could this be due to an excessive low R
>> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a
>> resolution of 2.85 A?
>
>
Histogram of Rwork for models in PDB at resolution 2.75-2.95 A:
 0.134 - 0.157  : 10
 0.157 - 0.180  : 75< your model
 0.180 - 0.203  : 365
 0.203 - 0.226  : 666
 0.226 - 0.249  : 653
 0.249 - 0.272  : 247
 0.272 - 0.295  : 52
 0.295 - 0.318  : 11
 0.318 - 0.341  : 1
 0.341 - 0.364  : 1
Histogram of Rfree for models in PDB at resolution 2.75-2.95 A:
 0.191 - 0.210  : 27
 0.210 - 0.230  : 105
 0.230 - 0.249  : 271 < your model
 0.249 - 0.269  : 472
 0.269 - 0.288  : 649
 0.288 - 0.308  : 377
 0.308 - 0.328  : 129
 0.328 - 0.347  : 34
 0.347 - 0.366  : 14
 0.366 - 0.386  : 3
Histogram of Rfree-Rwork for all model in PDB at resolution 2.75-2.95 A:
 0.001 - 0.011  : 23
 0.011 - 0.021  : 87
 0.021 - 0.030  : 195
 0.030 - 0.040  : 377
 0.040 - 0.050  : 407
 0.050 - 0.060  : 408 < your model
 0.060 - 0.070  : 296
 0.070 - 0.079  : 162
 0.079 - 0.089  : 81
 0.089 - 0.099  : 45
Number of structures considered: 2081

The above histograms were obtained using command:

phenix.r_factor_statistics 2.85

Pavel

Re: [ccp4bb] DNA structures superimpose

[Barry Finzel]

Measuring Angles is another matter, but the superposition services of  
the DrugSite will align an arbitrary selection of DNA residues (the  
moving molecule) onto a target residue selection on another  
structure.  The selection can include a duplex, or even a duplex and  
some protein residues.


If you don't know which residues align, you can 'search moving PDB'  
for those that are 'like' the target geometry


Transformed structures can be downloaded in PDB format, or as a Pymol  
session, after putting them in the outbox


https://drugsite.msi.umn.edu/superimpose/superimpose


-- Barry


Barry C. Finzel
Professor
Medicinal Chemistry Department
College of Pharmacy
University of Minnesota
308 Harvard St S.E.
Minneapolis, MN 55455
Tel: (612) 626-5979
Fax: (612) 624-0139
finze...@umn.edu



On Apr 12, 2013, at 1:18 AM, Veerendra Kumar (Dr) wrote:


Dear CCP4 members,
Is there any program to superimpose the DNA structures? I also want  
to measure the relative domain rotation angle. I tried using DynDom  
but it does not work for me.

Can someone suggest a program which can output the rotation angles?

Thank you

Best Regards

Veerendra kumar

CONFIDENTIALITY:This email is intended solely for the person(s)  
named and may be confidential and/or privileged.If you are not the  
intended recipient,please delete it,notify us and do not copy,use,or  
disclose its content.


Towards A Sustainable Earth:Print Only When Necessary.Thank you.

Re: [ccp4bb] CCP4 Update victim of own success

[James Holton]

Alright, alright,

I should thank Eugene for being such a good sport.  And I should also 
apologize for all the work I just created for him!


 I fully appreciate all the years and years of effort and struggle that 
has gone into making ccp4i and other crystallographic GUIs the 
accessible tools that they are today.  I think these efforts should 
continue, and we should all send Martin Noble one of those letters he needs.


But, when it comes to GUIs, I have always found them counterproductive.  
In my humble opinion, the purpose of computers and other machines is to 
DO work for me, not create work for me, and I already have enough 
buttons to push each day.  This is why my favorite command-line programs 
are things like "xautomation", "xse" and a tcl extension called "cwind" 
that lets you send mouse clicks and keystrokes into a Windoze machine 
from a tcl script. Comes in really handy for those late-night dialog 
boxes that always seem to pop up at 4am and would otherwise generate a 
user-support call because "X" has stopped working.  Yes, I could SSH in, 
open a tunnel through my firewall to an NX server and launch a vncviewer 
within the NX session and then (eventually) click on the "OK" button.  
But I'd rather just sleep through all that.


-James Holton
MAD Scientist


On 4/11/2013 9:34 AM, Jim Pflugrath wrote:
I think James gets to 'fight' like in the old game of rogue by 
pressing the h, j, k, l keys on his keyboard (not a detachable one 
either).  While Eugene gets to use a modern game controller or a Wii.


Ooops, game is already over and James has lost.

Jim



*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Felix 
Frolow [mbfro...@post.tau.ac.il]

*Sent:* Thursday, April 11, 2013 11:25 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] CCP4 Update victim of own success

I would serve as a second in this duel, but I respect very much both 
engaged is this duel…

Drop you pistols or swords !
:-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of 
Molecular Microbiology and Biotechnology

Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

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

On Apr 11, 2013, at 18:46 , eugene.krissi...@stfc.ac.uk 
 wrote:



That's really hard. Duel?

Eugene

On 11 Apr 2013, at 16:32, James Holton wrote:



CCP4 has a GUI?

-James Holton
MAD Scientist

On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk 
 wrote:
Sorry that this was unclear. We assume that updater is used 
primarily from ccp4i, where nothing changed (and why it should be 
used from command line at all ?:)). The name was changed because it 
is reserved in Windows, which caused lots of troubles. Now it will 
stay as is.


Eugene

On 11 Apr 2013, at 05:16, James Stroud wrote:


On Apr 10, 2013, at 9:30 PM, > 
> 
wrote:


No, it got renamed to ccp4um :) That should have been written in 
update descriptions, was it not?



There was only one mention of "ccp4um" that I could find in all 
update descriptions that I found (6.3.0-020). I only figured out 
what information was trying to be communicated because of your 
message (see attachment).


James






On 11 Apr 2013, at 03:54, James Stroud wrote:

Hello All,

I downloaded a crispy new version of CCP4 and ran update until the 
update update script disappeared. Is the reason that CCP4 has 
reached its final update?


James









--
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[Nat Echols]

On Fri, Apr 12, 2013 at 10:27 AM, James Holton  wrote:

>  But, when it comes to GUIs, I have always found them counterproductive.
> In my humble opinion, the purpose of computers and other machines is to DO
> work for me, not create work for me, and I already have enough buttons to
> push each day.
>

This is a very defensible position with regards to your normal workflow (or
mine) - but beamline scientists (or software developers) are not very
representative of crystallographers as a group.  I've seen a lot of
reflexive anti-GUI mentality from users who don't fall into either
category, presumably because a senior postdoc or PI told them "real
crystallographers use the command line", when in reality they'd be better
served by figuring out on their own what workflow is most efficient for
them.

-Nat

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

Respected Sir,

I saw this option in refmac5 - 5.6.0037, (I use
refmac5-5.6.0117), but is this option present in
GUI?

Thanking you
With Regards
Kavya

> Dear Kavya
>
> What about using occupancy refinement in refmac?
> link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
> refinement.
>
> R
>
>
> On 12 Apr 2013, at 17:12, Kavyashree Manjunath 
>  wrote:
>
>> Dear users,
>>
>> Is it advisable to refine the occupancy of
>> a ligand for a 2.0Ang data by approximately
>> changing the values of occupancy based on
>> its b-factor?
>> After refinement, there were some negative
>> densities appearing in some parts of the
>> ligand, like at the centre of a pyrimidine
>> ring, so I expected that the problem is with
>> the occupancy. (the crystal was obtained by
>> co-crystallisation method).
>> Kindly provide some suggestions.
>>
>> Thanking you
>> With Regards
>> Kavya
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>
> Roberto A. Steiner
> Group Leader
> Randall Division of Cell and Molecular Biophysics
> King's College London
> roberto.stei...@kcl.ac.uk
>
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL
> London
>
> Phone 0044 20 78488216
> Fax0044 20 78486435
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] CCP4 Update victim of own success

[James Holton]

I agree with Nat.  There are good GUIs and bad GUIs, just like there are 
good command-line programs and bad command-line programs.  Bad programs 
are easy to write and good ones are hard. Conservation of "work" I think.


-James Holton
MAD Scientist

On 4/12/2013 10:38 AM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 10:27 AM, James Holton > wrote:


But, when it comes to GUIs, I have always found them
counterproductive.  In my humble opinion, the purpose of computers
and other machines is to DO work for me, not create work for me,
and I already have enough buttons to push each day.


This is a very defensible position with regards to your normal 
workflow (or mine) - but beamline scientists (or software developers) 
are not very representative of crystallographers as a group.  I've 
seen a lot of reflexive anti-GUI mentality from users who don't fall 
into either category, presumably because a senior postdoc or PI told 
them "real crystallographers use the command line", when in reality 
they'd be better served by figuring out on their own what workflow is 
most efficient for them.


-Nat

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

So there is a CCP4 GUI

Just prepare a txt file with the relevant occupancykeywords and use it in the 
GUI under 'Refmac keyword file'

Best
R

>From my iPhone

On 12 Apr 2013, at 19:50, "Kavyashree Manjunath"  wrote:

> Respected Sir,
> 
> I saw this option in refmac5 - 5.6.0037, (I use
> refmac5-5.6.0117), but is this option present in
> GUI?
> 
> Thanking you
> With Regards
> Kavya
> 
>> Dear Kavya
>> 
>> What about using occupancy refinement in refmac?
>> link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
>> refinement.
>> 
>> R
>> 
>> 
>> On 12 Apr 2013, at 17:12, Kavyashree Manjunath 
>> wrote:
>> 
>>> Dear users,
>>> 
>>> Is it advisable to refine the occupancy of
>>> a ligand for a 2.0Ang data by approximately
>>> changing the values of occupancy based on
>>> its b-factor?
>>> After refinement, there were some negative
>>> densities appearing in some parts of the
>>> ligand, like at the centre of a pyrimidine
>>> ring, so I expected that the problem is with
>>> the occupancy. (the crystal was obtained by
>>> co-crystallisation method).
>>> Kindly provide some suggestions.
>>> 
>>> Thanking you
>>> With Regards
>>> Kavya
>>> 
>>> 
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>> 
>> 
>> Roberto A. Steiner
>> Group Leader
>> Randall Division of Cell and Molecular Biophysics
>> King's College London
>> roberto.stei...@kcl.ac.uk
>> 
>> Room 3.10A
>> New Hunt's House
>> Guy's Campus
>> SE1 1UL
>> London
>> 
>> Phone 0044 20 78488216
>> Fax0044 20 78486435
>> 
>> 
>> 
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>> 
>> 
> 
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> 

Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

What, I'm afraid, people rarely realise these days, is that their desktops are, 
essentially, GUIs to various OS features, so they obviously use GUI more 
frequently than they think :) After all, this is all matter of habits and 
training, and the reality is that people get more and more GUI-oriented these 
days, like it or not. Whether to fight the reality or try to use it for benefit 
is, certainly, every developer's own choice. I still remember payroll officers 
saying that hand calculators (and even their predecessors) were much more 
convenient and robust than modern software, but do not hear this for some 15 
years already ...

Eugene


On 12 Apr 2013, at 19:09, James Holton wrote:


I agree with Nat.  There are good GUIs and bad GUIs, just like there are good 
command-line programs and bad command-line programs.  Bad programs are easy to 
write and good ones are hard.  Conservation of "work" I think.

-James Holton
MAD Scientist

On 4/12/2013 10:38 AM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 10:27 AM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
But, when it comes to GUIs, I have always found them counterproductive.  In my 
humble opinion, the purpose of computers and other machines is to DO work for 
me, not create work for me, and I already have enough buttons to push each day.

This is a very defensible position with regards to your normal workflow (or 
mine) - but beamline scientists (or software developers) are not very 
representative of crystallographers as a group.  I've seen a lot of reflexive 
anti-GUI mentality from users who don't fall into either category, presumably 
because a senior postdoc or PI told them "real crystallographers use the 
command line", when in reality they'd be better served by figuring out on their 
own what workflow is most efficient for them.

-Nat



-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update victim of own success

[James Stroud]

On Apr 12, 2013, at 12:44 PM, eugene.krissi...@stfc.ac.uk wrote:

> What, I'm afraid, people rarely realise these days, is that their desktops 
> are, essentially, GUIs to various OS features, so they obviously use GUI more 
> frequently than they think :) After all, this is all matter of habits and 
> training, and the reality is that people get more and more GUI-oriented these 
> days, like it or not. Whether to fight the reality or try to use it for 
> benefit is, certainly, every developer's own choice. I still remember payroll 
> officers saying that hand calculators (and even their predecessors) were much 
> more convenient and robust than modern software, but do not hear this for 
> some 15 years already ...
> 
> Eugene


There is nothing intrinsically wrong with a GUI. The problem, for those who 
like to take advantage of automation, is that a GUI is a bottleneck if it can't 
be automated in some way. In my opinion, the best automation is based on an API 
(in my favorite scripting language, of course).

The original unix tools were built with automation in mind, using pipes, 
redirects, and file I/O to control the flow of information. This automation 
wasn't designed because the architects couldn't conceive of a GUI, but because 
it was and is efficient.

A utility can easily lock a user into a GUI. The usual cruel method is by 
spawning a dialog box the forces the user to acknowledge whatever triviality 
the program is trying to communicate (instead of sending the information to a 
log file where it belongs). If a program locks the user into a GUI, by whatever 
means, then the program can't be automated. And if it can't be automated it 
becomes a source of inefficiency. I think this is James Holton's point.

Most of CCP4 can be automated by using the utilities from the command line, 
taking advantage of pipes, redirects, and file I/O as envisioned by the unix 
architects. CCP4 can also be run via a GUI, which I take advantage of in 
certain situations. It's a great model for user interaction. Long may it live 
(and may modal dialog boxes die a horrible and quick death).

James



> 
> On 12 Apr 2013, at 19:09, James Holton wrote:
> 
> 
> I agree with Nat.  There are good GUIs and bad GUIs, just like there are good 
> command-line programs and bad command-line programs.  Bad programs are easy 
> to write and good ones are hard.  Conservation of "work" I think.
> 
> -James Holton
> MAD Scientist
> 
> On 4/12/2013 10:38 AM, Nat Echols wrote:
> On Fri, Apr 12, 2013 at 10:27 AM, James Holton 
> mailto:jmhol...@lbl.gov>> wrote:
> But, when it comes to GUIs, I have always found them counterproductive.  In 
> my humble opinion, the purpose of computers and other machines is to DO work 
> for me, not create work for me, and I already have enough buttons to push 
> each day.
> 
> This is a very defensible position with regards to your normal workflow (or 
> mine) - but beamline scientists (or software developers) are not very 
> representative of crystallographers as a group.  I've seen a lot of reflexive 
> anti-GUI mentality from users who don't fall into either category, presumably 
> because a senior postdoc or PI told them "real crystallographers use the 
> command line", when in reality they'd be better served by figuring out on 
> their own what workflow is most efficient for them.
> 
> -Nat
> 
> 
> 
> -- 
> Scanned by iCritical.
> 

[ccp4bb] Puzzling Structure

[Michel Fodje]

Has anyone else noticed a problem with the structure  of the N-terminal capsid 
domain of HIV-2  PDB 2wlv.
Load it up to in coot and navigate to residue B118.

/Michel.

Re: [ccp4bb] Puzzling Structure

[Michel Fodje]

By the way, you will need to show symmetry atoms to see the problem.

>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>Michel Fodje
>Sent: April-12-13 1:14 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] Puzzling Structure
>
>Has anyone else noticed a problem with the structure  of the N-terminal
>capsid domain of HIV-2  PDB 2wlv.
>
>Load it up to in coot and navigate to residue B118.
>
>
>
>/Michel.

Re: [ccp4bb] Puzzling Structure

[Phoebe A. Rice]

Looks like a typo to me: if you change the CRYST space group record from 
P212121 to P21212, as the paper says it is, the packing problem goes away.

++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

773 834 1723; pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/

http://www.rsc.org/shop/books/2008/9780854042722.asp


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel Fodje 
[michel.fo...@lightsource.ca]
Sent: Friday, April 12, 2013 2:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure

By the way, you will need to show symmetry atoms to see the problem.

>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>Michel Fodje
>Sent: April-12-13 1:14 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] Puzzling Structure
>
>Has anyone else noticed a problem with the structure  of the N-terminal
>capsid domain of HIV-2  PDB 2wlv.
>
>Load it up to in coot and navigate to residue B118.
>
>
>
>/Michel.

Re: [ccp4bb] Puzzling Structure

[Eugene Osipov]

Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
placed . I think that authors (if they are reading this board ) must fix
errors.  To be honest this is not first time I see such models.
12.04.2013 23:17 пользователь "Michel Fodje" 
написал:

By the way, you will need to show symmetry atoms to see the problem.

>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>Michel Fodje
>Sent: April-12-13 1:14 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] Puzzling Structure
>
>Has anyone else noticed a problem with the structure  of the N-terminal
>capsid domain of HIV-2  PDB 2wlv.
>
>Load it up to in coot and navigate to residue B118.
>
>
>
>/Michel.

Re: [ccp4bb] Puzzling Structure

[Pavel Afonine]

This explains why I cannot reproduce published R-factors (with files from
PDB I get ~40%). If I force my favorite refinement program to use P21212
then I get R close to reported in PDB file header.
This makes it worth reminding that it's rarely a good idea to edit PDB file
out of refinement.

Pavel


On Fri, Apr 12, 2013 at 12:33 PM, Phoebe A. Rice  wrote:

> Looks like a typo to me: if you change the CRYST space group record from
> P212121 to P21212, as the paper says it is, the packing problem goes away.
>
> ++
>
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
>
> 773 834 1723; pr...@uchicago.edu
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/
>
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel
> Fodje [michel.fo...@lightsource.ca]
> Sent: Friday, April 12, 2013 2:17 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Puzzling Structure
>
> By the way, you will need to show symmetry atoms to see the problem.
>
> >-Original Message-
> >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> >Michel Fodje
> >Sent: April-12-13 1:14 PM
> >To: CCP4BB@JISCMAIL.AC.UK
> >Subject: [ccp4bb] Puzzling Structure
> >
> >Has anyone else noticed a problem with the structure  of the N-terminal
> >capsid domain of HIV-2  PDB 2wlv.
> >
> >Load it up to in coot and navigate to residue B118.
> >
> >
> >
> >/Michel.
>

Re: [ccp4bb] Puzzling Structure

[Eugene Osipov]

In my opinion pdb must perform more strict checks of structures. I can
remember at least 2 structures without OXT entry for C terminal tail . Of
course rcsb won't accept my fixes.  As graduate student I am not sure that
I can point out mistakes to unknown author
12.04.2013 23:34 пользователь "Eugene Osipov" 
написал:

> Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
> placed . I think that authors (if they are reading this board ) must fix
> errors.  To be honest this is not first time I see such models.
> 12.04.2013 23:17 пользователь "Michel Fodje" 
> написал:
>
> By the way, you will need to show symmetry atoms to see the problem.
>
> >-Original Message-
> >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> >Michel Fodje
> >Sent: April-12-13 1:14 PM
> >To: CCP4BB@JISCMAIL.AC.UK
> >Subject: [ccp4bb] Puzzling Structure
> >
> >Has anyone else noticed a problem with the structure  of the N-terminal
> >capsid domain of HIV-2  PDB 2wlv.
> >
> >Load it up to in coot and navigate to residue B118.
> >
> >
> >
> >/Michel.
>
>

Re: [ccp4bb] Puzzling Structure

[Savvas Savvides]

The CRYST1 in the pdb header is problematic.
CRYST1   95.520   47.815   88.570  90.00  90.00  90.00 P 21 21 218 
it looks like the number '1' was paired to the space group rather than the 
space grop number (i.e. nr. 18 for P21212)
Table 1 in the paper specifies P212121 as the space group.




On 12 Apr 2013, at 21:14, Michel Fodje  wrote:

> Has anyone else noticed a problem with the structure  of the N-terminal 
> capsid domain of HIV-2  PDB 2wlv.
> Load it up to in coot and navigate to residue B118.
>  
> /Michel.

Re: [ccp4bb] Puzzling Structure

[Savvas Savvides]

i meant to say P21212

On 12 Apr 2013, at 21:47, Savvas Savvides  wrote:

> The CRYST1 in the pdb header is problematic.
> CRYST1   95.520   47.815   88.570  90.00  90.00  90.00 P 21 21 218 
> it looks like the number '1' was paired to the space group rather than the 
> space grop number (i.e. nr. 18 for P21212)
> Table 1 in the paper specifies P212121 as the space group.
> 
> 
> 
> 
> On 12 Apr 2013, at 21:14, Michel Fodje  wrote:
> 
>> Has anyone else noticed a problem with the structure  of the N-terminal 
>> capsid domain of HIV-2  PDB 2wlv.
>> Load it up to in coot and navigate to residue B118.
>>  
>> /Michel.
> 

Re: [ccp4bb] Puzzling Structure

[Garib N Murshudov]

It is typo:
R factor for p212121 - 0.4 
   for p21212- around 0.18

Although water seem to have been moved around using p212121




On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:

> Looks like a typo to me: if you change the CRYST space group record from 
> P212121 to P21212, as the paper says it is, the packing problem goes away.
> 
> ++
> 
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> 
> 773 834 1723; pr...@uchicago.edu
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/
> 
> http://www.rsc.org/shop/books/2008/9780854042722.asp
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel Fodje 
> [michel.fo...@lightsource.ca]
> Sent: Friday, April 12, 2013 2:17 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Puzzling Structure
> 
> By the way, you will need to show symmetry atoms to see the problem.
> 
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Michel Fodje
>> Sent: April-12-13 1:14 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Puzzling Structure
>> 
>> Has anyone else noticed a problem with the structure  of the N-terminal
>> capsid domain of HIV-2  PDB 2wlv.
>> 
>> Load it up to in coot and navigate to residue B118.
>> 
>> 
>> 
>> /Michel.

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] Puzzling Structure

[Pavel Afonine]

In this particular case attempting to calculate R-factor using data and
model files and making sure that the R you get is not twice as large as
published one would entirely suffice -:)

Pavel


On Fri, Apr 12, 2013 at 12:42 PM, Eugene Osipov wrote:

> In my opinion pdb must perform more strict checks of structures. I can
> remember at least 2 structures without OXT entry for C terminal tail . Of
> course rcsb won't accept my fixes.  As graduate student I am not sure that
> I can point out mistakes to unknown author
> 12.04.2013 23:34 пользователь "Eugene Osipov" 
> написал:
>
> Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
>> placed . I think that authors (if they are reading this board ) must fix
>> errors.  To be honest this is not first time I see such models.
>> 12.04.2013 23:17 пользователь "Michel Fodje" 
>> написал:
>>
>> By the way, you will need to show symmetry atoms to see the problem.
>>
>> >-Original Message-
>> >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> >Michel Fodje
>> >Sent: April-12-13 1:14 PM
>> >To: CCP4BB@JISCMAIL.AC.UK
>> >Subject: [ccp4bb] Puzzling Structure
>> >
>> >Has anyone else noticed a problem with the structure  of the N-terminal
>> >capsid domain of HIV-2  PDB 2wlv.
>> >
>> >Load it up to in coot and navigate to residue B118.
>> >
>> >
>> >
>> >/Michel.
>>
>>

Re: [ccp4bb] Unexplained negative fo-fc

[Laurie Betts]

My experience is also that the bulk solvent model sometimes makes the mask
exclude internal large cavities.

Laurie Betts


On Fri, Apr 12, 2013 at 12:03 PM, Pavel Afonine  wrote:

> P.S.: you are not alone having such R-factors
>
> On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven wrote:
>>
>>> Could this be due to an excessive low R
>>> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a
>>> resolution of 2.85 A?
>>
>>
> Histogram of Rwork for models in PDB at resolution 2.75-2.95 A:
>  0.134 - 0.157  : 10
>  0.157 - 0.180  : 75< your model
>  0.180 - 0.203  : 365
>  0.203 - 0.226  : 666
>  0.226 - 0.249  : 653
>  0.249 - 0.272  : 247
>  0.272 - 0.295  : 52
>  0.295 - 0.318  : 11
>  0.318 - 0.341  : 1
>  0.341 - 0.364  : 1
> Histogram of Rfree for models in PDB at resolution 2.75-2.95 A:
>  0.191 - 0.210  : 27
>  0.210 - 0.230  : 105
>  0.230 - 0.249  : 271 < your model
>  0.249 - 0.269  : 472
>  0.269 - 0.288  : 649
>  0.288 - 0.308  : 377
>  0.308 - 0.328  : 129
>  0.328 - 0.347  : 34
>  0.347 - 0.366  : 14
>  0.366 - 0.386  : 3
> Histogram of Rfree-Rwork for all model in PDB at resolution 2.75-2.95 A:
>  0.001 - 0.011  : 23
>  0.011 - 0.021  : 87
>  0.021 - 0.030  : 195
>  0.030 - 0.040  : 377
>  0.040 - 0.050  : 407
>  0.050 - 0.060  : 408 < your model
>  0.060 - 0.070  : 296
>  0.070 - 0.079  : 162
>  0.079 - 0.089  : 81
>  0.089 - 0.099  : 45
> Number of structures considered: 2081
>
> The above histograms were obtained using command:
>
> phenix.r_factor_statistics 2.85
>
> Pavel
>
>

Re: [ccp4bb] CCP4 Update victim of own success

[Boaz Shaanan]

Hi Nat,


Whichever way the input file for the run is prepared (via GUI or command line), anybody who doesn't inspect the log file at the end of the run is doomed and bound to commit senseless errors. I was taught a long time ago that computers always do what you
 told them to do and not what you think you told them, which is why inspecting the log file helps. BTW, I find the GUI's (ccp4i or phenix) as great help in preparing the command file, certainly the skeleton which can then be modified and run via the command
 line if needed.


  Cheers,


               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 Nat Echols [nathaniel.ech...@gmail.com]
Sent: Friday, April 12, 2013 8:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update victim of own success




On Fri, Apr 12, 2013 at 10:27 AM, James Holton  wrote:




But, when it comes to GUIs, I have always found them counterproductive.  In my humble opinion, the purpose of computers and other machines is to DO work for me, not create work for me, and I already have enough buttons to push each day.





This is a very defensible position with regards to your normal workflow (or mine) - but beamline scientists (or software developers) are not very representative of crystallographers as a group.  I've seen a lot of reflexive anti-GUI mentality from users
 who don't fall into either category, presumably because a senior postdoc or PI told them "real crystallographers use the command line", when in reality they'd be better served by figuring out on their own what workflow is most efficient for them.


-Nat

Re: [ccp4bb] Puzzling Structure

[Robbie Joosten]

Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group, then the
annotation pipeline understandably messes things up. If the originally
uploaded PDB file was kept by PDBe, then the problem can be recovered quite
easily by the annotators. Perhaps the topic starter, Michel Fodje, can send
a bug report to PDBe. In my experience, the annotators are very helpful
resolving these matters.  


Hoping that the depositors solve the problem by themselves, is probably in
vain: There are many crystallographers who do not read the CCP4BB (which is
a shame, really); they didn't notice the enormous amount of water related
bumps in their final model (which is in the validation report you get after
deposition and in REMARK 500 of the PDB file you have to approve); they also
didn't notice the huge number of symmetry-related bumps; the R-factors in
the PDB file are different from (and better than) the ones in Table 1. Also
notice that the paper was submitted on April 21st 2009 and the model was
deposited on June 29th 2009. Paper accepted on July 8th 2009. But I'm sure
the referees had a chance to properly assess the quality of the structure
model ;-)


Cheers,
Robbie

P.S. It's pretty awesome that the problem was solved in less than 20 minutes
by the CCP4BB (that is, by Phoebe Rice)


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Garib N Murshudov
> Sent: Friday, April 12, 2013 21:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Puzzling Structure
> 
> It is typo:
> R factor for p212121 - 0.4
>for p21212- around 0.18
> 
> Although water seem to have been moved around using p212121
> 
> 
> 
> 
> On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:
> 
> 
>   Looks like a typo to me: if you change the CRYST space group record
> from P212121 to P21212, as the paper says it is, the packing problem goes
> away.
> 
>   ++
> 
>   Phoebe A. Rice
>   Dept. of Biochemistry & Molecular Biology
>   The University of Chicago
> 
>   773 834 1723; pr...@uchicago.edu
>   http://bmb.bsd.uchicago.edu/Faculty_and_Research/
> 
>   http://www.rsc.org/shop/books/2008/9780854042722.asp
> 
>   
>   From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> Michel Fodje [michel.fo...@lightsource.ca]
>   Sent: Friday, April 12, 2013 2:17 PM
>   To: CCP4BB@JISCMAIL.AC.UK
>   Subject: Re: [ccp4bb] Puzzling Structure
> 
>   By the way, you will need to show symmetry atoms to see the
> problem.
> 
> 
> 
>   -Original Message-
> 
> 
>   From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
> On Behalf Of
> 
> 
>   Michel Fodje
> 
> 
>   Sent: April-12-13 1:14 PM
> 
> 
>   To: CCP4BB@JISCMAIL.AC.UK
> 
> 
>   Subject: [ccp4bb] Puzzling Structure
> 
> 
> 
>   Has anyone else noticed a problem with the structure  of the
> N-terminal
> 
> 
>   capsid domain of HIV-2  PDB 2wlv.
> 
> 
> 
>   Load it up to in coot and navigate to residue B118.
> 
> 
> 
> 
> 
>   /Michel.
> 
> 
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology Francis Crick Avenue
> Cambridge Biomedical Campus Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk
> Web http://www.mrc-lmb.cam.ac.uk 
> 
> 
> 
> 
> 
> 

Re: [ccp4bb] CCP4 Update victim of own success

[Nat Echols]

On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
wrote:

>  Whichever way the input file for the run is prepared (via GUI or command
> line), anybody who doesn't inspect the log file at the end of the run is
> doomed and bound to commit senseless errors. I was taught a long time ago
> that computers always do what you told them to do and not what you think
> you told them, which is why inspecting the log file helps.
>

I agree in principle - I would not advocate that anyone (*especially*
novices) run crystallography software as a "black box".  However, whether
or not a program constitutes a black box has nothing to do whether it runs
in a GUI or not.  The one advantage a GUI has is the ability to convey
inherently graphical information (plots, etc.).  That it is still necessary
to inspect the log file(s) carefully reflects the design of the underlying
programs; ideally any and all essential feedback should also be displayed
in the GUI (if one exists).  Obviously there is still much work to be done
here.

-Nat

Re: [ccp4bb] CCP4 Update victim of own success

[Ed Pozharski]

On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan 
mailto:bshaa...@exchange.bgu.ac.il>> wrote:


Whichever way the input file for the run is prepared (via GUI or
command line), anybody who doesn't inspect the log file at the end
of the run is doomed and bound to commit senseless errors. I was
taught a long time ago that computers always do what you told them
to do and not what you think you told them, which is why
inspecting the log file helps.


I agree in principle - I would not advocate that anyone (*especially* 
novices) run crystallography software as a "black box".  However, 
whether or not a program constitutes a black box has nothing to do 
whether it runs in a GUI or not.  The one advantage a GUI has is the 
ability to convey inherently graphical information (plots, etc.).  
That it is still necessary to inspect the log file(s) carefully 
reflects the design of the underlying programs; ideally any and all 
essential feedback should also be displayed in the GUI (if one 
exists).  Obviously there is still much work to be done here.


-Nat


It is hard to blame "novices" for running crystallography software as a 
black box when the websites from which they download the said software 
use the word "automated" to describe it.  Because, at least according to 
wikipedia (another great resource that should be used with care), 
"automation is the operation of machinery without human supervision".  
Checking the log-files or messages supplied by GUI seems to fall under 
"human supervision", which "automated" programmes should not really 
require.  I am not advocating return to the stone age when naming a 
tutorial for a widely used model building software "... for morons" was 
probably considered a joke (not a good one too).  I am just saying that 
it is perhaps quite predictable that with promise of automation comes 
the expectation of, well, automation.  Whether the true automation of 
crystallographic structure determination may become available in the 
future is perhaps debatable.  Whether it is already available probably 
isn't.


On a broader question of GUI versus command line, both obviously have 
their uses.  Mastering command line gives one flexibility and perhaps 
greater insight into what programmes actually do.  Do I prefer a little 
button that opens a file chooser dialog over sam-atom-in?  Absolutely.  
But I am glad that --pdb and --auto command line options are supplied, 
because I can then write a little bash pipeline to pass 50 expected 
protein-ligand complex datasets through simple refmac-coot cycle to 
quickly see which ones are interesting.  In that regard, both ccp4 and 
phenix are doing it the right way - gui is simply a gateway to the 
command-line controlled code. I can then choose the interface that fits 
particular situation.


As for the relatively new CCP4 update feature, it is absolutely awesome.

Cheers,

Ed.



--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Kavyashree Manjunath]

Thank you Sir.

With Regards
Kavya

> So there is a CCP4 GUI
>
> Just prepare a txt file with the relevant occupancykeywords and use it in
> the GUI under 'Refmac keyword file'
>
> Best
> R
>
> From my iPhone
>
> On 12 Apr 2013, at 19:50, "Kavyashree Manjunath" 
> wrote:
>
>> Respected Sir,
>>
>> I saw this option in refmac5 - 5.6.0037, (I use
>> refmac5-5.6.0117), but is this option present in
>> GUI?
>>
>> Thanking you
>> With Regards
>> Kavya
>>
>>> Dear Kavya
>>>
>>> What about using occupancy refinement in refmac?
>>> link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
>>> refinement.
>>>
>>> R
>>>
>>>
>>> On 12 Apr 2013, at 17:12, Kavyashree Manjunath 
>>> wrote:
>>>
 Dear users,

 Is it advisable to refine the occupancy of
 a ligand for a 2.0Ang data by approximately
 changing the values of occupancy based on
 its b-factor?
 After refinement, there were some negative
 densities appearing in some parts of the
 ligand, like at the centre of a pyrimidine
 ring, so I expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.

 Thanking you
 With Regards
 Kavya


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>>>
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