[ccp4bb] PLEASE RESPOND – Request for support for the 2024-2028 CCP4 grant application for funding through the BBSRC UK

[Eugene Krissinel - STFC UKRI]

Dear All,


CCP4 asks you to support the 2024-2028 CCP4 grant application for funding 
through the BBSRC by signing on

the following web page:


https://forms.office.com/e/Abkb8fkHJx


Please express your support for the valuable resource that benefits the whole 
community.


Further details are appended below and in the attached document.


Many thanks,


Eugene Krissinel on behalf of Ivo Tews, CCP4 Chair.


Request for support for the 2024-2028 CCP4 grant application for funding 
through the BBSRC


Dear colleague,

We are writing to ask for your support for the scientific proposal we are about 
to submit to the BBSRC on behalf of CCP4 this month, that will deliver 
methodology to advance macromolecular crystallography. Collaboration partners 
in this proposal are the Universities of Liverpool, Newcastle, Southampton, 
York, the LMB Cambridge, STFC laboratories at RAL, and the Diamond Light 
Source. The core scientific support by BBSRC grants has been central to the 
success of CCP4 and has underpinned our ability to raise additional funds 
through commercial licences that support maintenance and distribution of the 
software and the user community.

Over the past year, CCP4 has collated ideas to define the current scientific 
challenges we need to address. The CCP4 Executive selected the strongest 
proposals, sharing and discussing them with the community at the Working Group 
1 meeting at the CCP4 study weekend earlier this year. Important new trends 
accelerate and enrich structural biology. The new-generation of machine 
learning computational models have a major impact – allowing us to use these 
models in our science and to solve new structures. The exponential growth of EM 
depositions complements macromolecular crystallography, providing many 
structures of membrane proteins and macromolecular complexes.

Your support underlines the central role that macromolecular crystallography 
continues to play in basic and translational bioscience, delivering the 
throughput and resolution needed for drug discovery and chemical probes, 
experimentally validating and improving computational models, and ideally 
complementing the strength of cryo-EM. The scientific objectives in the 
proposed work packages (WPs) build on the outputs of previous grants to deliver 
novel science and tools to transform the utility, throughput and accuracy of 
macromolecular crystal structure:


  *   to develop a theoretical framework to support the multi data - multi 
model nature of modern structural studies and enable joint refinement and 
description of the dynamic behaviour of macromolecules (WP1/WP2 - Diamond 
Source, the LMB Cambridge, and the Universities of Southampton and York);
  *   to generate novel tools for exploiting electron diffraction from 
macromolecular crystals (WP3 - STFC laboratories at RAL);
  *   to integrate exciting developments in AI to apply deep learning based 
predictions of contacts and distances, in particular for complexes and RNA 
targets (WP4 - Liverpool University).

We ask you to endorse our application by signing up on a form at 
https://forms.office.com/e/Abkb8fkHJx your email, your affiliation, and your 
position (PI, Technical staff, PDRA, PhD, undergraduate, or other). We will use 
the information to generate statistics that will be included with this 
application to the BBSRC (and no other purpose).

If you are a PI, we additionally ask you to send a letter of support directly 
to the CCP4 Chair (ivo.t...@soton.ac.uk). Letters of support must be received 
by the 17th of April.

With many thanks in advance for your time and support.

Ivo Tews
CCP4, Chair

The Collaborative Computing Project 4 was established in 1979 and continues to 
underpin world class macromolecular structural science in the UK. Effective use 
of data collected at synchrotron, XFEL and electron microscopy facilities is at 
the heart of the project’s mission. User communities benefiting from such 
research include academics as well as industrial users. At the interface of the 
two, CCP4 enables discoveries that underlie vaccine and therapy discovery 
(including, e.g., SARS-CoV-2) and may equally be applied to tackle modern 
challenges such as adaptation to climate change, biotechnology, or public 
health.





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CCP4_2024-28_CommunitySuppor.pdf
Description: CCP4_2024-28_CommunitySuppor.pdf

[ccp4bb] Position in CCP4 Core Group

[Eugene Krissinel - STFC UKRI]

Dear All,

A software engineer position is available in CCP4 Core group in Rutherford 
Appleton Laboratory, Oxfordshire, UK. Please see details here: 
https://careersportal.co.uk/UKRI-careers/jobs/software-engineer-computational-scientist-3024
 and let know anybody who may be interested.

Many thanks,

Eugene Krissinel.




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[ccp4bb] Alexey Vagin

[Eugene Krissinel - STFC UKRI]

Dear All,

It is with a great sadness that I share with you that Alexey Vagin passed away 
this Saturday in the Radcliffe Hospital in Oxford after suffering from a heart 
attack with subsequent complications. He was 78 years old.

Alexey made many developments in methods and software for macromolecular 
crystallography, to which he devoted his whole life. He is known for his BLANC 
Suite for structure solution done at the Moscow Institute of Crystallography in 
the 1980s, as well as for his contributions to Refmac and Monomer Library. Many 
thousands of researchers have benefited from his work on Molrep and Balbes 
software for Molecular Replacement. After his retirement in 2010, Alexey 
developed and actively maintained the MorDA software for MR, which became a 
monument to his efforts.

Alexey's work will continue to serve generations of researchers through his 
contributions to CCP4, where we will take the best care of his distinguished 
legacy.

With sympathy to everyone who knew Alexey personally and for whom this is very 
sad news,

Eugene




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Re: [ccp4bb] Structural alignment and classification

[Eugene Krissinel - STFC UKRI]

yes selecting models and chains in SSM & Gesamt is possible -- Eugene


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: 06 March 2023 14:55
To: ccp4bb 
Subject: Re: [ccp4bb] Structural alignment and classification

Does Superpose or GESAMT align multiple structures?
And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 
etc?
Eleanor

On Mon, 6 Mar 2023 at 14:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Or you could use Gesamt - also in CCP4.

Harry

> On 6 Mar 2023, at 13:15, Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> wrote:
>
> Dear Armando,
>
> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign 
> (https://zhanggroup.org/US-align/).
> In my tests, THESEUS sometimes crashed in different ways. USalign is very 
> robust; SUPERPOSE is fast.
>
> HTH,
> Kay
>
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert 
> mailto:xalb...@iqfr.csic.es>> wrote:
>
>> Dear all,
>> I want to align several structures we obtained from a fragment screening 
>> campaign and cluster them according to RMSD.
>> Is MNYFIT still running? What else can I run?
>> Thank you
>> Armando
>>
>> 
>>
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Re: [ccp4bb] Structural alignment and classification

[Eugene Krissinel - STFC UKRI]

Having indeed written Gesamt some 10-12 years ago, I had to refresh my memory 
before answering.

Gesamt definitely aligns multiple structures, just give them all on command 
line.

It should do clustering in "sheaf" mode (which assumes that chains have same 
lengths and atoms are matched one-to-one). May be Daniel (in cc) can see how to 
implement clustering in his doings.

Gesamt can also identify conformations, i.e. similar substructures with 
relative displacement or rotation in compared structures.

Run gesamt without parameters to print all command-line options.

For saying more I need specific questions.

Eugene


From: CCP4 bulletin board  on behalf of Armando Albert 

Sent: 06 March 2023 15:19
To: ccp4bb 
Subject: Re: [ccp4bb] Structural alignment and classification

Thank you all.
What about the analysis? Does any program cluster the structures according to 
their structural similarity?
Armando


> El 6 mar 2023, a las 15:58, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió:
>
> Hi Eleanor
>
> According to
>
>https://www.ccp4.ac.uk/html/gesamt.html
>
> "Gesamt aligns two or more structures…”
>
> and
>
>https://www.ccp4.ac.uk/html/superpose.html
>
> "superpose aligns and superposes two or more protein structures…”
>
> But the real expert is probably Eugene.
>
> Harry
>
>> On 6 Mar 2023, at 14:55, Eleanor Dodson  wrote:
>>
>> Does Superpose or GESAMT align multiple structures?
>> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 
>> etc?
>> Eleanor
>>
>> On Mon, 6 Mar 2023 at 14:53, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Or you could use Gesamt - also in CCP4.
>>
>> Harry
>>
>>> On 6 Mar 2023, at 13:15, Kay Diederichs  
>>> wrote:
>>>
>>> Dear Armando,
>>>
>>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign 
>>> (https://zhanggroup.org/US-align/).
>>> In my tests, THESEUS sometimes crashed in different ways. USalign is very 
>>> robust; SUPERPOSE is fast.
>>>
>>> HTH,
>>> Kay
>>>
>>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
>>> wrote:
>>>
 Dear all,
 I want to align several structures we obtained from a fragment screening 
 campaign and cluster them according to RMSD.
 Is MNYFIT still running? What else can I run?
 Thank you
 Armando

 

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This message 

[ccp4bb] Position opening in UC Davis

[Eugene Krissinel - STFC UKRI]

On behalf of Dr. Nitzan Shabek, please see below  -- Eugene Krissinel




Subject: Open postdoctoral position at University of California Davis



The Shabek lab is looking for a postdoctoral fellow with a strong background in 
structural biology to join immediately to our research group at the University 
of California, Davis (shabek-lab.ucdavis.edu/).

We use structure- function approaches to study unique signaling pathways and 
their regulation by the Ubiquitin Proteasome System. We have new funded 
projects by NSF and DOE.



Qualifications:



• Must be a recent Ph.D. in Biochemistry and/or Plant Biology and/or Structural 
Biology

• Experience in molecular biology, protein purification techniques (experience 
with baculovirus expression is preferred but not required), and 
protein-protein/molecule interactions.

• Experience in structural biology (X-ray crystallography and/or Cryo-EM).

• Strong communications skills and ability to train junior scientists



Compensation and benefits for postdocs in UC Davis are the highest in the 
country. Davis is a beautiful Californian town located near Sacramento, and 
close to San Francisco, and several National Parks. The Shabek lab has access 
to ALS beamlines in Berkeley National Labs and SSRL in Stanford, as well as 
CryoEM facilities (BioEM in Davis or Brookhaven National labs).



To apply:



Email directly to Dr. Nitzan Shabek (nsha...@ucdavis.edu) with the subject line:

Postdoc in Structural Biology Application.



Please include a cover letter that highlights your research experience & 
interests, CV, and contact information of 2-3 references.

(please use your institutional email, if possible, otherwise it may go to spam)





__

Nitzan Shabek, Ph.D.

Plant Biology Department

College of Biological Sciences

University of California, Davis

Office: (530)-752-8187

Lab: (530)-754-1580

Email: nsha...@ucdavis.edu<mailto:nsha...@ucdavis.edu>

Lab website: https://shabek-lab.ucdavis.edu/




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[ccp4bb] CCP4 Cloud news

[Eugene Krissinel - STFC UKRI]

Dear All,

In response to your feedback and requests, we have significantly increased 
default CPU quota for all CCP4 Cloud accounts and introduced automatic top-up 
of cloud storage. You should see your new quotas at next login, along with a 
notification e-mail from the system. Please notify CCP4 of any problems.

Always connect to CCP4 Cloud via icon launcher found in CCP4 setup, or directly 
at https://cloud.ccp4.ac.uk when working from a tablet device or smartphone.

Your feedback is important for future development and improvement of CCP4.

Kind regards,

Eugene Krissinel.



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Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] New vacancy at CCP4 Core Group

[Eugene Krissinel - STFC UKRI]

Dear All,

CCP4 is hiring a Computational Scientist for CCP4/EBI joint project. Please see 
details here:

https://jobs.newscientist.com/en-gb/job/1401744598/computational-scientist/?utm_campaign=google_jobs_apply_source=google_jobs_apply_medium=organic

Do not hesitate to contact me with any questions.

Eugene Krissinel.


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sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] CCP4 Cloud down -- resolved

[Eugene Krissinel - STFC UKRI]

Dear All,

CCP4 Cloud is now back to fully operational state after recent hardware 
failure. The failure did not affect user data and projects. Please report any 
malfunction to CCP4 team.

Many thanks for using CCP4 Cloud,

Eugene Krissinel

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recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] CCP4 Cloud outage

[Eugene Krissinel - STFC UKRI]

Dear All,

CCP4 Cloud was taken down abruptly due to hardware malfunction, which we try to 
rectify. All user and project data should be safe but unavailable at the 
moment. Once the problem is resolved, we will inform you with separate posting.

Apologies for the inconvenience,

Eugene Krissinel.

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recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] Research position in CCP4 Core Group

[Eugene Krissinel - STFC UKRI]

Dear All,

We are recruiting a Computational Scientist for working on a research project, 
funded by BBSRC UK, in CCP4 Core Group. Please see job advert with detailed 
description and application link here:

https://jobs.newscientist.com/en-gb/job/1401740324/computational-scientist/

Please make anybody with potential interest aware of this opportunity.

Eugene Krissinel


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recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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[ccp4bb] iUCR-25 takes place in August 2021

[Eugene Krissinel - STFC UKRI]

Dear All,

We would like to draw your attention to the recent announcement from iUCR-25 
organisers:

https://mailchi.mp/909bcb8a8cd9/iucr25-prague-call-for-abstracts?e=e7b950fa73

Last 12 months may be confidently called as the "year online", and we wonder if 
there may be fresh submissions to the "Online crystallography" Special Session 
of iUCR-25: we would gladly consider reports not only on new online tools and 
methods, but also on your experience of doing crystallographic research in 
online and hybrid mode, revealed need and ideas for new online instruments, 
approaches and all related matters. Please contribute and share your thoughts 
and findings.

Many thanks,

Eugene Krissinel
Christian Hübschle
Chairs, Special Session "Online Crystallography" iUCR-25


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the recipient may sustain due to presence of any viruses. Opinions, conclusions 
or other information in this message and attachments that are not related 
directly to UKRI business are solely those of the author and do not represent 
the views of UKRI.




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Re: [ccp4bb] Fwd: Refmac error

[Eugene Krissinel]

Dear Nadine,

Many thanks for sharing your project with me on CCP4 Cloud. The reason for
Refmac failure is absolutely clear: the previous Coot job exported PDB
file, using commas (wie im besten Deutsch) instead of periods (as we would
expect in best English) for all float-point numbers. You can see it if you
go to the previous Coot job report, scroll down to "Output Structure",
press "Display" and scroll down a bit.

This effect is known to be peculiar to WinCoot -- have you used Windows
machine to run Coot in job 179? And had you used a different machine to run
Coot in job 169, which produced output file in correct format?

The only way to cope with the situation, known to me, is to ensure that
your Windows machine uses US/English locale settings. This takes tweaking
Language settings in Windows Control Panel and rebooting the machine.
Regrettably, you will have to repeat job 179 in new locale. If it contains
particularly valuable results that are difficult to reproduce, let me know
and I will advise you of the rescue procedure.

Admittedly, you are by far not the only one who encounters this problem,
which appears in all locales with float point formats different from
US/English. Therefore, I cc WinCoot developer on this email (they are aware
anyway, and are working on the issue), as well as CCP4 BB list, where you
placed your request initially, for other CCP4 users to be aware of this
feature. And there is an obvious homework for us here at CCP4.

Once again, many thanks for your report. Please unshare this project now
(simply remove my login name where you have put it for sharing before).

Kind regards,

Eugene


On Fri, May 29, 2020 at 9:52 AM Nadine Gerlach  wrote:

> Hey Eugene,
>
> actually this happend not just for one project of mine, but I shared one
> project with you now. Scroll down to the last refmac run after model
> building with coot. I just tried it again but it is still the same result.
>
> Thanks for the help!!
>
> Nadine
>
>
> Am 28.05.2020 um 19:28 schrieb Eugene Krissinel:
>
> Dear Nadine,
>
> We would need more information on what happens. You can share your project
> with me and I can have a look at it. To share the project, open it, then
> push Main Manu button in top-left corner, choose "Share" and set my login
> name (eugene), then confirm to me by e-mail. Your data and project will be
> treated as confidential.
>
> Many thanks for writing to us (use c...@ccp4.ac.uk rather than BB list
> for this type of queries please)
>
> Eugene
>
>
> -- Forwarded message -
> From: Nadine Gerlach 
> Date: Thu, 28 May 2020 at 14:21
> Subject: Refmac error
> To: 
>
>
> Hey everybody,
>
> I am running refmac in CCP4 ccloud after Coot and I get this error message:
>
>  *** error running refmac5: Error in command.call
> Return code: 512
>
> Any held is really appreaciated!
>
> Best wishes,
> Nadine
>
> --
> Nadine Gerlach
> PhD candidate
> MPG MARUM Bridge Group Marine Glycobiology
> MARUM, University Bremen & Max Planck Institute for Marine Microbiology
> Tel: +49 421 218-65758
> Email: nger­lach@mpi-bre­men.de, ngerl...@marum.de
> MARUM Pavillon room 1110
> Leobener Straße
> 28359 Bremen, Germany
>
> This email and any attachments are intended solely for the use of the
> named recipients. If you are not the intended recipient you must not use,
> disclose, copy or distribute this email or any of its attachments and
> should notify the sender immediately and delete this email from your
> system. UK Research and Innovation (UKRI) has taken every reasonable
> precaution to minimise risk of this email or any attachments containing
> viruses or malware but the recipient should carry out its own virus and
> malware checks before opening the attachments. UKRI does not accept any
> liability for any losses or damages which the recipient may sustain due to
> presence of any viruses. Opinions, conclusions or other information in this
> message and attachments that are not related directly to UKRI business are
> solely those of the author and do not represent the views of UKRI.
>
> --
> Nadine Gerlach
> PhD candidate
> MPG MARUM Bridge Group Marine Glycobiology
> MARUM, University Bremen & Max Planck Institute for Marine Microbiology
> Tel: +49 421 218-65758
> Email: nger­lach@mpi-bre­men.de, ngerl...@marum.de
> MARUM Pavillon room 1110
> Leobener Straße
> 28359 Bremen, Germany
>
>

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has

[ccp4bb] CCP4 7.1 released

[Eugene Krissinel]

e CCP4
Cloud Client, a piece of software linking CCP4 Cloud with Coot installed
locally. Just double-click on the CCP4 Cloud Client icon (CCP4 Diamond with
a cloud and wireless sign) in order to start using CCP4 Cloud right after
installation of CCP4 7.1 (you will be required to register as CCP4 Cloud
user first time).

The CCP4 Core Group will be happy to help anyone to start using CCP4 Cloud.
Development of CCP4 Cloud was supported by BBSRC UK Grant BB/L007037/1 and
is a result of a collaborative effort of many developers and enthusiasts.
CCP4build

*Automated model builder (from Eugene Krissinel and Andrey Lebedev, CCP4
Core Group)*

CCP4build combines several applications: CParrot, CBuccaneer, Refmac, Coot
and EDStats, for the enhancement of automatic model building in CCP4.
CCP4build explores several model building scenarios in an iterative
approach with rollbacks, and adjusts automatically to building in both
experimental phases and phases obtained in the course of molecular
replacement. CCP4build is available in CCP4 Cloud.
BUSTER interface

*Interface to BUSTER software from Global Phasing Ltd.*

The interface allows a user to refine macromolecular structures with BUSTER
software from Global Phasing Ltd. The interface is available through the
CCP4 Cloud - both in your own installation as well as through the CCP4
Cloud service at RC Harwell (UK).

The latter case requires online authorisation for academic users with
Global Phasing Ltd. (which are kindly providing the software to all
academic users free of charge), which is done via an authorisation facility
found in user’s account settings. Use of the interface within your local
CCP4 Cloud installation requires a separate, local installation from
www.globalphasing.com.
Technical notes

For Mac OSX and Linux platforms, on-line setup through the CCP4 Setup
Manager is the recommended option. CCP4 Setup Manager enables you to choose
a desirable set of components, download, install and configure them
automatically.

Before installing CCP4 7.1, PLEASE MAKE SURE THAT NO CCP4 PROGRAMS ARE
RUNNING, PARTICULARLY CCP4i AND CCP4i2. The simplest way to achieve that is
to REBOOT YOUR COMPUTER BEFORE THE INSTALLATION OF CCP4.

Installation on MS Windows systems requires downloading the whole package
as an executable installer and running it on your machine. Be prepared to
see a warning message from MS Windows, suggesting that the software may be
harmful for your system – please trust CCP4 and choose “install anyway”. It
is necessary that you REBOOT YOUR WINDOWS PC AFTER INSTALLATION, before
attempting to run any of CCP4 programs.

We advise you to always include Coot in your installation package and
install it simultaneously with the rest of CCP4. If you intend to use Coot
from other sources, be prepared to link it with CCP4 after installation and
manage it separately. CCP4 cannot provide updates to Software installed
from sources other than CCP4 and cannot guarantee a flawless integration of
such software – although we will do our best in order to resolve any issues
you may encounter.

Please note that, starting from CCP4 7.1, 32-bit packages are no longer
available.
Acknowledgements

We would like to thank all of the developers who have contributed to CCP4
7.1, and all of those who have helped in testing it. The following
publication should be used to cite the use of CCP4:

M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R.
Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J.
McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R.
J. Read, A. Vagin and K. S. Wilson (2011) *Overview of the CCP4 suite and
current developments*, Acta Cryst *D67* 235-242.

Use of individual CCP4 programs should be acknowledged also by the citation
of respective publications, where required (please cf. from program
documentation). CCP4 is supported by the BBSRC UK through grant
BB/S006974/1 (CCP4 Advanced Integrated Approaches to Macromolecular
Structure Determination), as well as by our industrial users.
Final remarks

CCP4 7.1 is out now. A considerable effort has been put into developing,
compiling, bundling and testing its many new components and underlying
libraries. Despite all the effort we've made, bugs and unforeseen
“features” will most certainly be found in the Suite, which has grown
substantially in size. When bugs and errors are discovered, the best way to
deal with them is to report them to us at c...@stfc.ac.uk. We value highly
all feedback from our users, and together we will bring CCP4 yet closer to
community expectations and standards.

Many thanks for being CCP4 users,

Eugene Krissinel

on behalf of CCP4 Core Group:

Charles Ballard
Andrey Lebedev
Ronan Keegan
David Waterman
Kyle Stevenson
Ville Uski
Oleg Kovalevskiy
Tarik Drevon
Karen McIntyre



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.

[ccp4bb] CCP4 Computational Scientist

[Eugene Krissinel]

Dear All,

CCP4 is looking for computational scientist to work on a research project
in Electron Diffraction. The Project is funded by BBSRC UK, and will be
conducted in CCP4 Core Group based in Rutherford Appleton Laboratory, UK.

For full job details and direct links to online application portal, please
visit one of the following web-sites:

https://www.topcareer.jobs/Vacancy/irc250548_10011.aspx
https://findajob.dwp.gov.uk/details/3026333
https://brightrecruits.com/jobs/ccp4-computational-scientist

All informal enquires may be sent to eugene.krissi...@stfc.ac.uk

Kind regards,
Eugene Krissinel.



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] CCP4 Workshop at ECM-32

[Eugene Krissinel]

Dear All,

Please take a notice of a 1-day CCP4 Workshop, which will be run as part of
ECM-32 meeting in Vienna on 17th of August 2019. Full information may be
found here:

https://ecm2019.org/satellites/ccp4-structure-solution/

Please register if you are interested. Everybody is invited.

Kind regards,

Eugene Krissinel.



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Scientific Programmer Position at CCP4 Core Group

[Eugene Krissinel]

Dear All,

This is a reminder that today is the closing date for applications for the
Scientific Programmer position at CCP4 Core Group. Full details and
application procedure may be found in any of the following pages:


   - Topcareer: http://topcareer.jobs/Vacancy/irc247462_9019.aspx
   - Jobs.ac: https://www.jobs.ac.uk/job/BPG216/ccp4-scientific-programmer
   - New Scientist:
   
https://jobs.newscientist.com/en-gb/job/1401660392/ccp4-scientific-programmer/


Personal enquiries are welcome.

Kind regards,

Eugene Krissinel.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Scientific programmer position at CCP4 Core Group

[Eugene Krissinel]

Dear All,

CCP4 is looking for candidates interested in Scientific Programmer position
at CCP4 Core Group. Full details and application procedure may be found in
any of the following pages:


   - Topcareer: http://topcareer.jobs/Vacancy/irc247462_9019.aspx
   - Jobs.ac: https://www.jobs.ac.uk/job/BPG216/ccp4-scientific-programmer
   - New Scientist:
   
https://jobs.newscientist.com/en-gb/job/1401660392/ccp4-scientific-programmer/


Personal enquiries are welcome.

Kind regards,

Eugene Krissinel.



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] CCP4 Scientific Programmer Position at CCP4 Core Group

[Eugene Krissinel]

Dear All,

This is a repeat announcement of an opening in CCP4 core Group for the
Scientific Programmer Position. The post is for 3 years and will be
allocated in the Research Complex at Harwell, Rutherford-Appleton
Laboratory, in some 17 miles south from Oxford, United Kingdom. Job advert
and link for on-line applications follow below in this post. If this does
not apply to you, please pass this e-mail on your colleagues and friends
who may be interested in this exciting opportunity.

Many thanks,

Eugene Krissinel.


CCP4 Scientific Programmer*STFC - The Science and Technology Facilities
Council*
Location:DidcotSalary:£28,384 to £29,566 per annum plus excellent benefits
Hours:Full TimeContract Type:Contract / Temporary Placed on:12th March 2015
Closes:22nd April 2015Job Ref:IRC180113

*About Us: *The Science and Technology Facilities Council is a
world-leading multi-disciplinary science organisation, and our goal is to
deliver economic, societal, scientific and international benefits to the UK
and its people – and more broadly to the world.

CCP4 is a large and well-established project, hosted by STFC, with the aim
of developing and maintaining state of the art structure solution and
analysis software for protein crystallography. The CCP4 Software Suite is
one of the most comprehensive and most widely used in its field.

*About The Role: *Applications are invited for a CCP4 Scientific Programmer
to work in the core CCP4 team. You will assist CCP4 developer’s teams in
RAL, University of York and University of Newcastle in the roll-out of
CCP4i2, CCP4’s new graphical front end, to end users with subsequent
activities on its further development, improvement and increasing
functionality.

*This is a complex activity, which will include, but is not limited to, the
following tasks:*

   - Develop and maintain the CCP4 release branch related to CCP4i2 and the
   corresponding development environment. This includes the maintenance of BZR
   repositories; accommodation of all relevant modifications and additions to
   the Suite; builds, tests and dynamic updates required for CCP4i2
   development and releases
   - Learn CCP4i2 structure and code for being able to optimise and adopt
   it as necessary, and introduce new features
   - Work in close collaboration with CCP4 developers in both UK and
   overseas on various aspects of CCP4i2 development

You will work closely with other members of the core team and there is
frequent contact with collaborating scientists, code developers and users.
The CCP4 team contribute to several major development projects, and you may
be involved in these as appropriate.


*About You**You will have the following:*

   - Degree in numerate science subject or computer science
   - Good communication skills in English, verbal and written
   - Experience of software development in both Python and C++
   - Ability to analyse and solve problems independently
   - Ability to collaborate with colleagues at remote sites

Knowledge of protein crystallography, as well as practical experience of
both unix-based and Windows operating systems, is beneficial but not
essential, as all relevant training and introduction will be provided.
Candidates with good aesthetic taste for GUI design are particularly
welcome.

*Benefits: *An excellent index linked pension scheme, 30 days leave
allowance and flexi-time are offered. Full details of offered benefits can
be found on STFC’s careers pages https://www.stfc.ac.uk/1895.aspx

*How to apply: *Applications are handled by UK SBS; to apply please visit
our job board at http://www.topcareer.jobs/Vacancy/irc180113_5225.aspx and
submit your CV and cover letter. If you are unable to apply online please
contact us by telephone on 01793 867000.

For an informal discussion about this role please contact: Dr Eugene
Krissinel at eugene.krissi...@stfc.ac.uk

[ccp4bb] CCP4 6.5 Windows-32

[Eugene Krissinel]

Dear CCP4 Users,


CCP4 Core Group would like to estimate the demand for 32-bit Windows 
distribution of CCP4 Release 6.5.


Therefore, could you please help it by replying to this e-mail without 
changing the subject _/*if and only if*/__/*you have to use CCP4 on a 
32-bit Windows PC*/__/.

/_
Please do not put any message in as only the total number of replies 
will be counted, and please do not reply to all so that your e-mail 
does not increase traffic on CCP4 BB.



*/HOW TO IDENTIFY WHETHER YOUR WINDOWS IS 32 OR 64-BIT/*

- open Control Panel
- go to System and Security
- click System
- read System type. It should say something like XX-bit Operating 
System, YYY processor



/*WHY WE ASK YOU TO GIVE YOUR FEEDBACK*/

Although it does not scale linearly with the number of supported OSes, 
each OS requires separate manual effort to make a release and support it 
through updates. Two years ago we ran a similar query regarding 32-bit 
Mac OSX, and only a handful of users reported the use of 32-bit Mac 
hardware. We took the decision not to provide 32-bit Mac OSX binaries 
then because that was clearly uneconomical. At that point we were 
already 5 years behind Apple's own decision not to produce and support 
32-bit hardware and OSes any longer.


Today, we observe a similar situation for Linux and MS Windows. 
According to CCP4 download stats, only 10% of CCP4 Linux users have 
32-bit machines. Up to this point, we did not release 32-bit 6.5 package 
for MS Windows, and only a few users have asked for it.


In difference of Mac OSX, 32-bit versions of MS Windows and Linuxes are 
still provided by the respective vendors. Therefore, we will not drop 
32-bit CCP4 packages for these systems if actual demand proves to be 
significant.



/*PLEASE NOTE:*//*
*/
1. Using 32-bit CCP4 packages becomes increasingly disadvantageous, 
because some programs may require 64-bit memory space, depending on data 
and structure size.


2. It is highly unlikely that a 5-year old and newer computer hardware 
is not a 64-bit one. The installed OS may be, however, both 32 and 
64-bit. Please see the previous note if you are choosing between the 
systems.




Many thanks for your help,

Eugene Krissinel.

Re: [ccp4bb] RMSD of dimers

[Eugene Krissinel]

No, the question seems to be slightly different. While one can use 
either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms 
would balance RMSD between both chains and produce something optimal for 
both chains. What is required, however, is optimal superposition on one 
pair of chains (one from each dimer) but measuring RMSD on the other 
pair of chains from same dimers. Nothing impossible in principle but no 
corresponding option in general-purpose aligners (this requires 
something like masks/selections for residues to superimpose and residues 
to measure the RMSD on). If this were a common and frequent problem, we 
could have it implemented in SSM/GESAMT.


Eugene

On 26/02/2015 12:47, Eleanor Dodson wrote:
Doesnt pisa give you some of this information? It lists all likely 
homodimers and I think gives RMSD too

Eleanor

On 24 February 2015 at 22:00, Thomas Holder 
thomas.hol...@schrodinger.com mailto:thomas.hol...@schrodinger.com 
wrote:


Hi Dan,

gaps/insertions should be no problem for PyMOL's rms_cur command,
as long as chain identifiers match (and all other atomic
identifiers!).

See http://pymolwiki.org/index.php/Fit for a description of the
matchmaker argument.

Cheers,
  Thomas

On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu
mailto:dbon...@ihv.umaryland.edu wrote:

 I have a family of homodimers (denoted A1B1, A2B2, A3B3...)
which I have superimposed using Chain A. Several programs will
produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I
would like to know the RMSDs of Chain B2, B3, B4... to Chain B1
when I have superimposed the structures relative to Chain A. I
have tried using Pymol though there are gaps/insertions so
rms/rms_cur will not work. Does anyone else have any other
suggestions?

 Thanks in advance,

 Dan

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [ccp4bb] CCP4 Release 6.5

[Eugene Krissinel]

 Does this mean I need to download the installation package from the CCP4

- yes

 and is this why the update tool in 6.4.0 is not showing up the latest release?

- no, this must be something different

 Should I install into the current 6.4.0 directory or a new one?

- some CCP4 components rely on CCP4 directory name to be correct. It is 
therefore advisable to keep it as suggested by CCP4 installer/tarball, which is 
‘ccp4-6.5’ for this release

 Will my existing data folders etc. be retained?

- you should be able to see all your data and projects in ccp4i after upgrade; 
I do not remember reports on lost data due to CCP4 upgrade from users :)

Best regards,

Eugene



 
 Thanks.
 Mohamed
 
 On 18/12/2014 21:54, Eugene Krissinel wrote:
 Dear CCP4 Users,
 
 
 
 The CCP4 Core Group is very pleased to announce the release of the latest 
 version of the CCP4 Software Suite. Version 6.5 (Hellifield) is now 
 available from the CCP4 download website:
 
 
 
 http://www.ccp4.ac.uk/download.php
 
 
 
 The release is available for Linux, Mac OSX and Windows platforms. This 
 release mostly consolidates updates in CCP4 6.4.0 update series, but also 
 introduces a number of technical improvements and new features.
 
 
 
 The whys and wherefores:
 
 
 
 Why is it necessary to switch to CCP4 6.5 now?
 
 a)  Because it brings new features and updates
 
 b)  Because the update line of 6.4.0 is now discontinued
 
 c)  Because support for 6.4.0, as well as for all earlier versions of CCP4, 
 is now stopped.
 
 
 
 Why did CCP4 make a new release rather than keeping on updating the current 
 one?
 
 Because over the last year, the difference between the release and the 
 development (trunk) branches of CCP4 has reached a point where merging them 
 takes a considerable effort and makes updates unfeasible.
 
 
 
 Why 6.5 and not 6.5.0?
 
 Because the last numeral will be now defined by the last CCP4 update applied 
 (not to worry, updates will not change the CCP4 directory name, which will 
 remain ‘ccp4-6.5’ for the lifetime of the release). The full version number 
 (including updates) will be printed on top of all the log files.
 
 
 
 
 
 1. New Components and Updates
 
 
 
 Below is a selected list of updates and new components; for more details 
 please see the individual program documentation.
 
 
 
 New:
 
 
 
 Privateer-validate: validation of carbohydrate structures from Jon Agirre 
 (The University of York)
 
 -   Calculates the conformation of pyranoses and furanoses using the 
 Cremer-Pople algorithm.
 
 -   Compares the detected conformation to the minimal-energy conformation of 
 the sugar.
 
 -   Performs basic stereochemistry and geometry checks.
 
 -   Computes a real space correlation coefficient against a positive omit 
 density. Outputs 2mFo-DFc, mFo-DFc and omit mFo-DFc maps.
 
 -   Describes N- and O-glycan structures.
 
 
 
 Feckless: combination of multilattice files from Mosflm for Pointless  
 Aimless, from Phil Evans (MRC/LMB).
 
 
 
 Acedrg v90 and LibG: chemoinformatics support for Refmac (geometry and 
 restraint generator), from Garib Murshudov’s team at MRC/LMB.
 
 
 
 Blend v0.5.10: optimum selection of multi-crystal datasets for merging from 
 James Foadi, MPL, Harwell, UK
 
 -   suggests favourable or desirable combinations of datasets
 
 -   provides tools for easy management of multi-crystal operations
 
 -   reads in integrated data from MOSFLM or XDS
 
 -   outputs scaled data and associated statistics using POINTLESS and AIMLESS
 
 
 
 Crank-2: conceptually redesigned and considerably improved Crank pipeline 
 for automatic experimental phasing from Navraj Pannu and Pavol Skubak, 
 University of Leiden, The Netherlands.
 
 
 
 
 
 Updated:
 
 
 
 Aimless v0.5.1 (Scaling multiple observations of reflections)
 
 -   some options for XFEL data (SAMPLESD, Rsplit, batch rejection)
 
 -   use estimated scale parameter errors in sigma(I); improved SDcorrection
 
 -   CC(1/2) maximum resolution from curve fit
 
 -   matrix of run-run correlations
 
 
 
 Pointless v1.9.23 (Laue group determination)
 
 -   bug fixes
 
 
 
 Prosmart v0.845 (Macromolecular restraints generator)
 
 -   Enabled structural comparison and restraint generation functionalities 
 with DNA/RNA chains
 
 -   Ability to calculate and display screw axis-angle representation 
 corresponding to rigid-body transformations
 
 -   Support for UCSF Chimera
 
 -   Various technical enhancements and changes to default 
 parameters/behaviour
 
 
 
 Buccaneer v1.6.0 (Model autobuilding)
 
 -   new modes for building after molecular replacement, with facilities for 
 differing levels of data quality and model agreement
 
 
 
 CCP4 MG v2.10.0 (Molecular graphics)
 
 -   Visualization of multiple bonds and aromatic rings
 
 -   Load molecules from SMILES string
 
 -   Load molecules from ccp4srs database
 
 -   Better hydrogen bond calculation parameters and base pair sticks
 
 -   Many bug fixes.
 
 
 
 Xia2 v0.3.8.0  (Automated data

[ccp4bb] CCP4 Release 6.5

[Eugene Krissinel]

 of industrial users.







Last remarks



CCP4 6.5 is out now. Although we think of it as our best ever release, most 
certainly, we have overlooked some bugs or inadvertently made mistakes here and 
there. CCP4 is quite a large software suite, and difficult to test 
comprehensively. When bugs and errors are discovered, the best way to deal with 
them is to report straight to us at c...@stfc.ac.ukmailto:c...@stfc.ac.uk. We 
value feedback of our users extremely high, and together we will bring CCP4 yet 
closer to community expectations and standards.





Many thanks for being CCP4 users,



Eugene Krissinel



on behalf of CCP4 Core Team:



Marcin Wojdyr

Charles Ballard

Andrey Lebedev

Ville Uski

Ronan Keegan

David Waterman.

Re: [ccp4bb] asymmetric homotrimer in the asu

[Eugene Krissinel]

It is in fact possible that different solution conditions favor different 
oligomeric assemblies. For example, perhaps your protein, which in one set of 
solution conditions prefers the monomer, prefers some other assembly under the 
crystallization conditions (we've seen this in our own work). Perhaps the 
higher (or lower) salt concentration, the presence (or absence) of the 
precipitation reagent, etc. pushes any oligomer equilibrium that exists for 
your protein.

- this all is very true; in addition, oligomeric state does depend on protein 
concentration, too. jsPISA at CCP4 (http://www.ccp4.ac.uk/pisa) calculates 
concentration profiles for probable macromolecular assemblies, which may be 
useful to check with. The effect of salt/precipitators/pH is not there, though.

Eugene


Regardless of what our final conclusion would be for this case, we became 
rather generally interested to find other similar cases of homomeric assemblies 
related only by non crystallographic translation symmetry (or as Engin Qzka 
pointed out improper NCS is the conventional terminology). So to rephrase our 
question we are interested to learn about additional structures of homomoeric 
improper ncs assemblies.

An interesting case of heterologous interfaces engaged is that of the VP40 
protein. A recent publication from the Saphire group (PMID 
23953110http://www.ncbi.nlm.nih.gov/pubmed/23953110) may present an 
instructive situation, though I don't know the details of the NCS observed. 
Here an octameric assembly (PDB 4LDM, ASU=monomer) and a hexameric assembly 
(PDB 4LDD, ASU=dimer) of the same protein engage different interfaces on the 
protomers. In forming the oligomer, the protomers are aligned with alternating 
interfaces.

Emily.


I truly appreciate ANY open-minded or skeptic thought, profound or trivial that 
we get here! They all, definitely those made by Mark Garavito, contribute to 
shaping our mind around this riddle.
Thanks for commenting on the skepticism, I brought it up as part of the 
discussion but a glitch of my own coffee time haziness might have slipped in. 
Perhaps I should try some o-cha instead .. :)

cheers,
Hay


On Dec 12, 2014, at 3:05 AM, Jeremy Tame wrote:

Dear Hay

I suggest that you use analytical ultracentrifugation to determine the 
oligomeric state of the protein in solution.
Mass spectrometry and light scattering are also useful, but there are so many 
examples of gel filtration proving
erroneous it has questionable value as an analytical technique. For an example 
of a dimer interface predicted by
PISA to be real you could look at Yoshida et al, JMB 423, 351 (2012). The 
protein is in fact a monomer in solution.
PISA is a fantastic tool, but interfaces in crystals do not always reflect the 
solution state. My guess (with the
information I have) is that your protein is probably a monomer too.

With regard to Michael Garavito's reply requesting more information, I would 
like to comment that scepticism
is indeed an important god in the pantheon of science, but that that minor 
deity open-mindedness also deserves the
occasional nod. 10-fold crystal symmetry is one example, but the list of 
impossible things now become mainstream
is a long one (continental drift, Earth 100,000 years old, quantum 
mechanicsand so on). Bayes theorem cannot
help you discover the truth if you have set its prior probability to zero. But 
I haven't my morning o-cha yet either.

good luck
Jeremy


On Dec 11, 2014, at 9:27 PM, Hay Dvir wrote:

Dear all,


We have a structure of a rather tightly packed homotrimer protein in the ASU 
with no apparent crystallographic or non-crystallographic rotational symmetry 
between monomers.
Attempting to establish the biological assembly, we are very interested to hear 
about additional similar cases you might know of.

Thanks in advance,
Hay


---
Hay Dvir Ph. D.
Head Technion Center for Structural Biology
Technion Haifa 323, Israel
Tel: +(972)-77-887-1901tel:%2B%28972%29-77-887-1901
Fax: +(972)-77-887-1935tel:%2B%28972%29-77-887-1935
E-mail hd...@technion.ac.ilmailto:hd...@technion.ac.il
Website http://tcsb.technion.ac.ilhttp://tcsb.technion.ac.il/

Re: [ccp4bb] superpose bug?

[Eugene Krissinel]

Correct syntax is

superpose A.pdb B.pdb -o C.pdb

Doing

superpose A.pdb B.pdb C.pdb

will result in *multiple* structure alignment of all three structures (i.e. 
C.pdb ought to be an input, rather than output, file here). In general,

superpose XYZ1.pdb XYZ2.pdb XYZ3.pdb . XYZN.pdb

will do multiple aligment of all N structures.

Run superpose without parameters in order to get description of all 
command-prompt options.

Hope this helps,

Eugene



From: Lijun Liu [lijunli...@gmail.com]
Sent: Wednesday, November 19, 2014 12:17 AM
To: ccp4bb
Subject: [ccp4bb] superpose bug?

Hi:

I have a bunch of pdb files and would like to superpose them to one of
them based on secondary structure matching.  I would like to get a
script to do so (not a one-by-one job by hand).

I tried superpose but it seemed to have some problems with output
option.  Assuming C.pdb is the output pdb, and A.pdb and B.pdb are
inputs.


superpose A.pdb B.pdb   (this works, without output)
superpose A.pdb B.pdb C.pdb  (* ERROR #15 READ:)
Adding -s option get same errors (without output pdb it works).

When running within ccp4i with output C.pdb, it does work.


I tried to generate an input script from ccp4i running. Unfortunately,
running with the particular superpose using S-S-M option did not
generate an input card (other options OK, what a bad luck).

I appreciate a working script (ccp46.4.0) or a debugged source code
for compilation.  Thanks.

Lijun Liu

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Re: [ccp4bb] superpose bug?

[Eugene Krissinel]

Yes, certainly, guilty as sin :)

Thanks,
Eugene


From: Tim Gruene [t...@shelx.uni-ac.gwdg.de]
Sent: Wednesday, November 19, 2014 11:22 AM
To: Krissinel, Eugene (STFC,RAL,SC); ccp4bb
Subject: Re: [ccp4bb] superpose bug?

Hi Eugene,

would you update the documentation?
A canonical 'man superpose' produces

 superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ]

where [-s CID1/2] are optional selection strings in [1]MMDB convention,
and [foo_out.pdb] is an optional output file.

i.e. the syntax Lijun Liu used.

Cheers,
Tim


On 11/19/2014 10:33 AM, Eugene Krissinel wrote:
 Correct syntax is

 superpose A.pdb B.pdb -o C.pdb

 Doing

 superpose A.pdb B.pdb C.pdb

 will result in *multiple* structure alignment of all three structures (i.e. 
 C.pdb ought to be an input, rather than output, file here). In general,

 superpose XYZ1.pdb XYZ2.pdb XYZ3.pdb . XYZN.pdb

 will do multiple aligment of all N structures.

 Run superpose without parameters in order to get description of all 
 command-prompt options.

 Hope this helps,

 Eugene


 
 From: Lijun Liu [lijunli...@gmail.com]
 Sent: Wednesday, November 19, 2014 12:17 AM
 To: ccp4bb
 Subject: [ccp4bb] superpose bug?

 Hi:

 I have a bunch of pdb files and would like to superpose them to one of
 them based on secondary structure matching.  I would like to get a
 script to do so (not a one-by-one job by hand).

 I tried superpose but it seemed to have some problems with output
 option.  Assuming C.pdb is the output pdb, and A.pdb and B.pdb are
 inputs.

 
 superpose A.pdb B.pdb   (this works, without output)
 superpose A.pdb B.pdb C.pdb  (* ERROR #15 READ:)
 Adding -s option get same errors (without output pdb it works).

 When running within ccp4i with output C.pdb, it does work.
 

 I tried to generate an input script from ccp4i running. Unfortunately,
 running with the particular superpose using S-S-M option did not
 generate an input card (other options OK, what a bad luck).

 I appreciate a working script (ccp46.4.0) or a debugged source code
 for compilation.  Thanks.

 Lijun Liu


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

GPG Key ID = A46BEE1A


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Re: [ccp4bb] SSM followed by all atom RMS calculation?

[Eugene Krissinel]

This problem cannot have an ultimate solution unless your chains are of the 
same length and you postulate that residues should be corresponded one-to one. 
But if this is the case, LSQKAB is the tool.

If correspondence between C-alphas is ambiguous, you need to align structures 
in order to find the best set of corresponding atoms. This is what SSM (or 
GESAMT) does and it cannot be guaranteed that a an atom in one chain will have 
a match in another chain. Note that alignment != best rms superposition.

Eugene

On 12 Sep 2014, at 14:45, KAUSHIK H.S. wrote:

Hi,

I want to calculate main-chain and side-chain deviations between sets of 
identical proteins modeled into different 3D structures.  While SSM superposes 
well, it calculates RMS only for the residues considered for superposing.  
Though LSQKAB program calculates RMS for all positions, fails when the topology 
is not closely related.

For now, I do SSM superpose, identify the residues, explicitly mention them in 
LSQKAB program and then calculate RMS for each position.

However, is there a way we can make SSM calculate RMS for all positions?
Or,
Is there a program which will give all atom RMS for a previously superposed 
protein structure ensemble?


Thanks,
Kaushik,
Molecular Biophysics Unit,
IISc, India



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Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix

[Eugene Krissinel]

This is just a petty function in CCP4's MMDB library -- Eugene

On 4 Sep 2014, at 20:52, Chen Zhao wrote:

 Hi all,
 
 I am just curious whether there are some tools extracting the Euler angles 
 from a fractional coordinate matrix. I have no luck searching it online. 
 
 Alternatively, I found the analytical solution for the Euler angles from an 
 orthogonal coordinate matrix. So in the worst case, my problem reduces to 
 calculating the transformation matrix between the fractional and orthogonal 
 coordinate system. I feel a little bit at a loss because it is 6 years since 
 I last studied linear algebra. How can I calculate this for a specific unit 
 cell?
 
 Thanks a lot in advance!
 
 Sincerely,
 Chen


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Re: [ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins

[Eugene Krissinel]

It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather than 
PISA -- Eugene

On 13 Aug 2014, at 12:33, Eleanor Dodson wrote:

I think PISA does this for you - it overlaps structural features and gives an 
RMSD on those parts that fit and a useful list of matching residues.
You can run it from CCP4I or at PDBe.

If you ant more than CA RMSD then you will need to select out the spans to fit 
and use the LSQKAB overlap procedure
FIT MAIN RESi n n+m CHAIN A
MATCH RESI b b+m CHAIN C

FIT ….

etc

for example - you can do that in the GUI

Eleanor


On 13 August 2014 02:48, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:
Dear Sreetama,

I use an ancient superposition program which rejects all atom pairs deviating 
more than 3 sigma and repeats this procedure until convergence. It then reports 
the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find 
this an excellent method to separate the core from variable loop regions. It 
also ensures a robust superposition of the cores, ignoring variable loops.

Best,
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
sreetama das
Gesendet: Mittwoch, 13. August 2014 08:12
An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] RMSD between structures of homologous proteins

Dear all,
   When calculating the RMSD between structures of homologous proteins, 
where there are large changes in the loop region(s), which RMSD should be 
reported - an overall value which may be inflated due to the deviations in the 
loops, or separate values for the core and loop regions?
What is the best way to calculate the RMSD for superposition of the cores - 
should I prepare a separate PDB file by removing the coordinates of the loop 
residues and then superpose?

Thanks in advance,
Sreetama das,
PhD student,
Physics, IISc



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[ccp4bb] PISA server @ CCP4

[Eugene Krissinel]

Dear All,

CCP4 releases new PISA web-server at the following URL:  
http://www.ccp4.ac.uk/pisa . As always, constructive criticism, bug reports and 
feature requests are welcome.

Enjoy!

Eugene Krissinel.


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Re: [ccp4bb] CCP4-6.4.0 Update 018

[Eugene Krissinel]

CCP4 server was barely accessible to me for some 2 hours yesterday evening, 
this should be the most plausible explanation of the effect. However, let us 
know if problem reappears.

Eugene

On 14 Jun 2014, at 10:55, Mark van Raaij wrote:

same happened to me yesterday evening, but when I retried this morning, the 
update installed fine.
Did not change anything in between.

On 14 Jun 2014, at 11:21, Felix Frolow wrote:

CCP4BB list,
Today I tried to install update 018, however I have lost the ability to do it 
from the GUI. Menu for checking available installation have disappeared 
mysteriously.
Any clue not related to something I probably did between previous installation 
and this one will be welcomed. I do brute force reinstallation right now and 
hope it will work.

FF

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

On Jun 13, 2014, at 23:07 , Andrey Lebedev 
andrey.lebe...@stfc.ac.ukmailto:andrey.lebe...@stfc.ac.uk wrote:

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

• refmac5 (all platforms):
 – Fixed restraints for M- and P-peptides
 – Fixed SAD scaling issue

• monomers (all):
 – Fixed description for M- and P-peptides and some other entries

• pointless (all):
 – Update to 1.9.10 fixing a long-standing bug in reindexing files with 
different (permuted) unit cells

• aimless (all):
 – Fix to explicit run definitioin

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team



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Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



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Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

I take this chance to to confirm once more, as publicly as possible, that file 
paths with spaces are discouraged in today's CCP4. This inconvenience 
originates from ancient times in computing when good half of CCP4 was written 
and when spaces were disallowed on file system nodes.

Please take a notice of this fact as CCP4 core still receives (albeit 
infrequent) bug reports, where surprising behaviour is due to using file paths 
with white spaces.

Fixing this has proved to be a hard problem, purely because of technical 
choices made quite a number of years ago. But good news are that this 
limitation will be removed in new CCP4 Gui under development.

Eugene

On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:

 This also occurred to me once where the file path had a space,(/Google 
 Drive/), when I moved the file somewhere else it worked. I was using baverage 
 from the CCP4i GUI.
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 09:20, Tim Gruene wrote:
 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me No tables were fund in 
 this file. Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?
 
 Thanks!
 
 Bing
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 


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Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

Dear Felix,

I, too, do not use spaces and file names in Russian :) However, these things 
are coming nearly for free and automatic with today's development tools, so 
little effort, if any, is required to adopt them, while the benefits in terms 
of user friendliness and convenience are not exactly negligible. Many thanks 
for understanding our situation

-- Eugene

On 3 Jun 2014, at 12:58, Felix Frolow wrote:

Possibility to have file names with the spaces is a curse put on the community 
by Microsoft, and it will be a big mistake to introduce this to CCP4 (my 
opinion).
I guess there are much more important things new CCP4 GUI should deal with. If 
CCP4 GUI will start to go this way,
file names with spaces will become file names with spaces and multilingual, in 
some these languages writing is going in the different direction.
In my introduction to UNIX, I teach in the beginning of practical protein 
crystallography my first demand from student is to forget about spaces in the 
fie names and the life will be much easier.
No fix is needed for that, concentrate on more important problems :-)
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.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jun 3, 2014, at 14:47 , Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk wrote:

I take this chance to to confirm once more, as publicly as possible, that file 
paths with spaces are discouraged in today's CCP4. This inconvenience 
originates from ancient times in computing when good half of CCP4 was written 
and when spaces were disallowed on file system nodes.

Please take a notice of this fact as CCP4 core still receives (albeit 
infrequent) bug reports, where surprising behaviour is due to using file paths 
with white spaces.

Fixing this has proved to be a hard problem, purely because of technical 
choices made quite a number of years ago. But good news are that this 
limitation will be removed in new CCP4 Gui under development.

Eugene

On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:

This also occurred to me once where the file path had a space,(/Google Drive/), 
when I moved the file somewhere else it worked. I was using baverage from the 
CCP4i GUI.

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 09:20, Tim Gruene wrote:

Dear Bing,

can you post the exact command you were using, please? Also please check
with a different PDB file. In case you are using baverage from the
command line, can you make sure you are actually using the program from
ccp4 by typing 'which baverage' at the command prompt?

Regards.
Tim

On 06/02/2014 10:16 PM, Wang, Bing wrote:

Hi CCP4,

Recently when I input my pdb file and run the baverage in the ccp4 suit to 
check the temperature factor, it always tell me No tables were fund in this 
file. Could you tell me how to fix this problem? Or is there another software 
instead of baverage I could use to check the temperature factor?

Thanks!

Bing


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

GPG Key ID = A46BEE1A



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Re: [ccp4bb] lsqkab problem to be reported to developer

[Eugene Krissinel]

Charlie,

Most probably this indicates a problem with your PDB file, either a format or 
things like misplaced or absent residue name etc. If you can send me your files 
and exact command that you run, I can have a look into this.

In future, if you see a message like report to developer please send it to 
CCP4 group rather than BB, this will help to deal with it faster.

Many thanks,

Eugene


On 30 May 2014, at 22:54, Carter, Charlie wrote:

 This is a bizarre problem. I'm trying to superimpose multiple conformations 
 of the same protein using segments I expect not to change. LSQKAB bails with 
 this error each time:
 
 *** RWBROOK error: point code unitfunction
 ***1 -1022MMDB_F_Atom
 *** file   : 4ARC_rot.pdb
 *** reason : internal error #2 -- report to developer
 *** Execution stopped.
 
 It also appears very likely that the superposition is wrong. I expect an RMSD 
 for the superimposed atoms (main chain only) of less than 2 Å, yet the 
 program reports that the RMSD is 7 Å.
 
 Thanks to anyone for a diagnosis and prescription.
 
 Charlie


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Re: [ccp4bb] Superpose

[Eugene Krissinel]

My guess is that only atom pairs that are superposed to some measure of 
distance between them, are output. Can't say that I checked lsqkab code this 
weekend, but documentation does not suggest anything like that.

Is this a problem for you? note that you can use other aligners/superposers in 
CCP4, ssm or Gesamt which will output all coordinates.

Eugene

On 10 May 2014, at 21:00, hbo...@pasteur.edu.uy
 wrote:

 Hi Eugene, thanks for your response.
 
 Yes, the program is LSQKAB. No aligment is pursued, the aim is just to 
 superpose models and get all the information as tables. Looking at old jobs 
 (CCP4 6.2: LSQKAB version 6.2 : 13/03/09), it seems it always did the same, 
 the results on xyz and B rms just a subset of the atoms (most) being 
 superposed are written to the log file. This is independent on the specific 
 PDB files in use (I have tested a few only)can this be confirmed by 
 you/circumvented by the user (i.e. by changing the com file) or eventualy 
 solved?
 
 Thanks again!
 
 H
 
 
 Quoting Eugene Krissinel eugene.krissi...@stfc.ac.uk:
 
 I would say the guess is a wrong one. SS superposition is used only  as a 
 seed for further refinement. SSM (superpose) outputs all  residues (not all 
 atoms) and marks those which get aligned. Then,  superposition is done using 
 aligned residues. Alignment !=  superposition.
 
 As to LSQKAB, it's pure superposition, not alignment AFAIK.  Alignment 
 should be given to LSQKAB in form of atom pairs that  should be used for 
 superposition.
 
 No idea what is wrong in this example though.
 
 Eugene
 
 On 9 May 2014, at 23:33, Tim Gruene wrote:
 
 Dear H,
 
 you are referring to superpose, but your logfile lists the output from
 LSQKAB, which are two different programs. According to the man-page of
 superpose, it uses secondary structure elements for superposition, so
 maybe the missing atoms are those not part of a helix and not part of a
 strand. Just a guess.
 
 Best,
 Tim
 
 On 05/09/2014 08:05 PM, Horacio Botti wrote:
 Dear all,
 
 Why does (if it is suppossed to do so) Superpose output results for a
 subset of atoms only? See a summary of log file below (just the top
 lines, data on atoms, and final data and message). In the example,
 results for residues 69-76 are absent, other atoms are absent as well,
 but the number of atoms that were skipped in the analysis is 0 (NUMBER
 OF ATOMS EXCLUDED BY RADCHK IS 0). Of course, the atoms for these
 residues are present in the pdb files and no alternative conformations
 are being modeled. If you display a table from the log graph window, you
 find xyz RMS for all atoms including the missed atoms. I also need info
 on B RMS, which are not displayed in log graph.
 
 What can I do to get a complete log file?
 
 Thanks in advance!
 
 H
 
 #CCP4I VERSION CCP4Interface 2.2.0
 #CCP4I SCRIPT LOG superpose
 #CCP4I DATE 09 May 2014  09:21:04
 #CCP4I USER hbotti
 #CCP4I PROJECT ..
 #CCP4I JOB_ID 30
 #CCP4I SCRATCH /tmp/hbotti
 #CCP4I HOSTNAME pxf8.ipmont.lan
 #CCP4I PID 8268
 
 
 
 
 
 
 
 
 
 
 
 ###
 ###
 ###
 ### CCP4 6.3: LSQKAB   version 6.3 : 13/03/09##
 ###
 User: hbotti  Run date:  9/ 5/2014 Run time: 09:21:04
 
 
 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst.
 D50, 760-763.
 as well as any specific reference in the program write-up.
 
 
 Data line--- title ..
 Data line--- fit res MAIN 66 to 544 chain B
 Data line--- match 66 to 544 chain C
 Data line--- output xyz rms deltas
 Data line--- end
 
 
 
 LSQKAB RUN
 ..
 
 
 
 OPEN FILES AS REQUESTED
 Opening coordinate file of model to be moved
 
 Logical name: XYZIN2  File name: ...
 PDB file is being opened on unit 1 for INPUT.
 
 MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
 
 
RF  RO
 
   0.010  -0.000   0.002   0.000   96.790   0.000 -19.210  -0.000
  -0.000   0.008  -0.000  -0.0000.000 133.030   0.000   0.000
   0.000  -0.000   0.009  -0.0000.000   0.000 106.024  -0.000
  -0.000   0.000  -0.000   1.000   -0.000   0.000  -0.000   1.000
 
 
 Logical name: XYZOUT  File name: ..
 
 Opening coordinate file of fixed model.
 
 Logical name: XYZIN1  File name: ...
 PDB file is being opened on unit 3 for INPUT.
 
 MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
 
 
RF  RO
 
   0.010  -0.000   0.002   0.000   96.610   0.000 -18.928  -0.000
  -0.000   0.008  -0.000  -0.0000.000 132.960   0.000   0.000
   0.000  -0.000   0.009  -0.0000.000   0.000

Re: [ccp4bb] Superpose

[Eugene Krissinel]

I would say the guess is a wrong one. SS superposition is used only as a seed 
for further refinement. SSM (superpose) outputs all residues (not all atoms) 
and marks those which get aligned. Then, superposition is done using aligned 
residues. Alignment != superposition.

As to LSQKAB, it's pure superposition, not alignment AFAIK. Alignment should be 
given to LSQKAB in form of atom pairs that should be used for superposition.

No idea what is wrong in this example though.

Eugene

On 9 May 2014, at 23:33, Tim Gruene wrote:

 Dear H,
 
 you are referring to superpose, but your logfile lists the output from
 LSQKAB, which are two different programs. According to the man-page of
 superpose, it uses secondary structure elements for superposition, so
 maybe the missing atoms are those not part of a helix and not part of a
 strand. Just a guess.
 
 Best,
 Tim
 
 On 05/09/2014 08:05 PM, Horacio Botti wrote:
 Dear all,
 
 Why does (if it is suppossed to do so) Superpose output results for a
 subset of atoms only? See a summary of log file below (just the top
 lines, data on atoms, and final data and message). In the example,
 results for residues 69-76 are absent, other atoms are absent as well,
 but the number of atoms that were skipped in the analysis is 0 (NUMBER
 OF ATOMS EXCLUDED BY RADCHK IS 0). Of course, the atoms for these
 residues are present in the pdb files and no alternative conformations
 are being modeled. If you display a table from the log graph window, you
 find xyz RMS for all atoms including the missed atoms. I also need info
 on B RMS, which are not displayed in log graph.
 
 What can I do to get a complete log file?
 
 Thanks in advance!
 
 H
 
 #CCP4I VERSION CCP4Interface 2.2.0
 #CCP4I SCRIPT LOG superpose
 #CCP4I DATE 09 May 2014  09:21:04
 #CCP4I USER hbotti
 #CCP4I PROJECT ..
 #CCP4I JOB_ID 30
 #CCP4I SCRATCH /tmp/hbotti
 #CCP4I HOSTNAME pxf8.ipmont.lan
 #CCP4I PID 8268
 
 
 
 
 
 
 
 
 
 
 
 ###
 ###
 ###
 ### CCP4 6.3: LSQKAB   version 6.3 : 13/03/09##
 ###
 User: hbotti  Run date:  9/ 5/2014 Run time: 09:21:04
 
 
 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst.
 D50, 760-763.
 as well as any specific reference in the program write-up.
 
 
 Data line--- title ..
 Data line--- fit res MAIN 66 to 544 chain B
 Data line--- match 66 to 544 chain C
 Data line--- output xyz rms deltas
 Data line--- end
 
 
 
 LSQKAB RUN
  ..
 
 
 
  OPEN FILES AS REQUESTED
  Opening coordinate file of model to be moved
 
  Logical name: XYZIN2  File name: ...
  PDB file is being opened on unit 1 for INPUT.
 
  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
 
 
 RF  RO
 
0.010  -0.000   0.002   0.000   96.790   0.000 -19.210  -0.000
   -0.000   0.008  -0.000  -0.0000.000 133.030   0.000   0.000
0.000  -0.000   0.009  -0.0000.000   0.000 106.024  -0.000
   -0.000   0.000  -0.000   1.000   -0.000   0.000  -0.000   1.000
 
 
  Logical name: XYZOUT  File name: ..
 
  Opening coordinate file of fixed model.
 
  Logical name: XYZIN1  File name: ...
  PDB file is being opened on unit 3 for INPUT.
 
  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
 
 
 RF  RO
 
0.010  -0.000   0.002   0.000   96.610   0.000 -18.928  -0.000
   -0.000   0.008  -0.000  -0.0000.000 132.960   0.000   0.000
0.000  -0.000   0.009  -0.0000.000   0.000 106.156  -0.000
   -0.000   0.000  -0.000   1.000   -0.000   0.000  -0.000   1.000
 
 
 FORMATTED  UNKNOWN file opened on unit   7
 
 Logical name: RMSTAB, Filename: .
 
 
 
 FORMATTED  UNKNOWN file opened on unit   8
 
 Logical name: DELTAS, Filename: ..
 
 
   - NO MATCH FOR WORKCD ATOM -  142CA  B  IN REFRCD FILE
 
  **  ZERO OCCUPANCIES IN WORKING   SET **  0.0
  **  ZERO OCCUPANCIES IN REFERENCE SET **  0.0
 LSFIT
  ATOMS IN WORKING MOLECULE(1915 TO BE REFINED)
  ATOMS IN REFERENCE MOLECULE
 CENTROID OF WORKING MOLECULE  :   10.597 -61.757  22.304
 CENTROID OF WORKING MOLECULE  :(fractional)0.151  -0.464   0.210
 CENTROID OF REFERENCE MOLECULE:   13.208 -36.008  70.253
 CENTROID OF REFERENCE MOLECULE:(fractional)0.266  -0.271   0.662
 Distance between CENTROIDS  :   54.488
 Direction cosines of vector between CENTROIDS:  -0.048  -0.473  -0.880
 
 
  NUMBER OF ATOMS EXCLUDED BY RADCHK IS 0
 
  RMS   B 

Re: [ccp4bb] PyMol and Schrodinger

[Eugene Krissinel]

Thank you Piotr, this is very useful to know.

Cheers,

Eugene

On 24 Apr 2014, at 22:18, Piotr Sliz wrote:

 Eugene,
 
 SBGrid Consortium supports certain paid programs such as Pymol, Schrodinger, 
 and Geneious, and academic laboratories have access to a limited pool of 
 tokens. For more serious computations it might be easier to get an individual 
 license, yet for starters the SBGrid shared-token library is certainly a 
 viable option. 
 
 Access to the commercial tokens is included in SBGrid membership, though 
 limited depending on your geographic location and affiliation. Please email 
 h...@sbgrid.org for a more detailed description of this program.
 
 Kind Regards,
 
 Piotr
 


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Re: [ccp4bb] PyMol and Schrodinger

[Eugene Krissinel]

 SBGrid is a also good option if you can afford it. It comes with PyMOL 
 licenses.

- it would be helpful if SBGrid people can comment on this. AFAIK, nothing in 
SBGrid comes with paid licenses, and SBGrid fees are just for installing and 
maintaining the software. Individual program licenses are to be acquired in 
addition -- unless I am grossly wrong or PyMOL is an exception here.

Eugene


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Re: [ccp4bb] Coot error

[Eugene Krissinel]

If you are using a standalone Coot package, you may want to try one from 
regular CCP4 distribution instead. Coot is integrated in CCP4 6.4.0, and 
installation of CCP4 is fully automated so that no manual tweaking should be 
required.

Eugene

On 15 Apr 2014, at 13:24, Monica Mittal wrote:

 Hi all 
 I am facing a problem while installing coot in CentOS. After configuring its 
 showing No package'glib-2.0' found. Either it asks me to adjust 
 PKG_CONFIG_PATH env variable if i installed in non standard prefix or i can 
 set set env variables GLIB_CFLAGS and GLIB_LIBS to avoid need to call 
 pkg-config.
 
 But how to do any of the above. I dont  have idea. So guidance on this will 
 be highly appreciated.
 
 Thanx
 Monica


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Re: [ccp4bb] superposing multiple structural segments between two PDBs

[Eugene Krissinel]

Dear Sreetama,

For this, Gesamt from ccp4 should do the work. Run gesamt without parameters to 
get instructions, they are basically the same as for ccp4's superpose.

HTH,

Eugene


On 19 Mar 2014, at 07:34, sreetama das wrote:

Dear All,
 Is there a way to superpose multiple, discontinuous stretches of 
residues between two protein chains ?

Dali output shows that there are discontinuous stretches between the PDBs that 
are being aligned. But I can not find any option to download the superposed 
PDB. The output generated from PDBefold (which gives link to the transformed 
PDB) is different.

regards,
sreetama


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Re: [ccp4bb] CPRODRG segfault on Mac OS X 10.9,

[Eugene Krissinel]

Dear All,

CCP4 Core Group is aware of the issue and is looking into it. Once fixed, new 
cprodrg will be put into update.

Thank you,

Eugene Krissinel

On 25 Nov 2013, at 13:46, Oliver Clarke wrote:

 Hi all,
 
 I have recently been trying to use the LIDIA ligand-viewer of Coot, which 
 calls cprodrg.
 
 I am running CCP4 6.4.0 with all the latest updates on a Macbook Air 
 (mid-2012 model) with OS X 10.9 installed and the latest nightly build of 
 coot (r4833).
 
 Unfortunately, when I run cprodrg either via coot or from the command line, 
 it crashes with what appears to be a segmentation violation (stderr 
 reproduced below). Does anyone have any thoughts as to what may be causing 
 this or how to fix it?
 
 Many thanks,
 Oliver
 
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 html !-- CCP4 HTML LOGFILE --
 hr
 !--SUMMARY_END--/FONT/B
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 pre
 
 ###
 ###
 ###
 ### CCP4 6.4: PRODRGversion 2.5-AA0717 : ##
 ###
 User: olibclarke  Run date: 25/11/2013 Run time: 08:34:44
 
 
 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 
 760-763.
 as well as any specific reference in the program write-up.
 
 !--SUMMARY_END--/FONT/B
 forrtl: severe (180): SIGBUS, bus error occurred
 Image  PCRoutineLineSource
 cprodrg000113FC  Unknown   Unknown  Unknown
 cprodrg000111AC  Unknown   Unknown  Unknown
 cprodrg00011164  Unknown   Unknown  Unknown


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[ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Eugene Krissinel]

Dear CCP4 Users,

CCP4 Core Team would like to apologise for temporary withdrawal of update 
6.4.0-002, announced earlier this week. The withdrawal is due to a technical 
fault in the update mechanism, which will be rectified soon. Currently, the 
update is put on hold and is not visible for client installations.

A few users reported problems with starting ccp4i immediately after 
installation of the update. Should you have experienced the same, please start 
ccp4um from terminal:

sudo /path-to/ccp4-6.4.0/bin/ccp4um

and uninstall update 6.4.0-002 by unchecking the corresponding box and pressing 
Apply (use 'sudo' *only* if your ccp4 is installed in write-protected area). 
After that, everything should be back normal.

Windows users, as well as those who are able to run ccp4i after 2nd update, 
need do nothing.

I would like to acknowledge prompt bug reports from responsible users on this 
occasion, which helped us to minimise the negative effect of the bug on all 
others. CCP4 as a project depends on the feedback from user community, and Core 
Team is grateful for all the help and feedback we receive.

Please refrain from update attempts until further announcement or until new 
updates are reported available by your ccp4i.

Many thanks,

Eugene Krissinel



Begin forwarded message:

From: Andrey Lebedev 
andrey.lebe...@stfc.ac.ukmailto:andrey.lebe...@stfc.ac.uk
Date: 6 November 2013 12:52:31 GMT
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Reply-To: andrey.lebe...@stfc.ac.ukmailto:andrey.lebe...@stfc.ac.uk

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released. This is the first 
update for both CCP4 and ARP/wARP in tandem.

The ARP/wARP component of this update will be available to those Mac and Linux 
users who have previously installed both packages via the CCP4 Package manager 
or from the joint bundle downloaded from CCP4 web-site. A standalone ARP/wARP 
package including the current update can be downloaded from the EMBL-Hamburg 
site at www.arp-warp.orghttp://www.arp-warp.org/.

The following changes will be applied to the ARP/wARP installation:

• The use of non-crystallographic symmetry for protein chain tracing has been 
enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes 
and now works well.
• The routine for ligand identification has been made faster and some small 
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific 
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.

The following changes will be applied to the CCP4-6.4.0 installation:

• MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and bug 
fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check in 
ccp4i.

Andrey Lebedev


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Re: [ccp4bb] Comparison of Water Positions across PDBs

[Eugene Krissinel]

This is to be answered by PDB people, who definitely read BB :)

Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts 
this out

Eugene

On 30 Oct 2013, at 12:09, Andreas Förster wrote:

 Dear all,
 
 this water discussion is flowing increasingly towards a place where I feel a 
 bit out of my depth.
 
 What is the convention for numbering water molecules?  Is there preference 
 for:
 
 - putting waters into a separate chain (W for water or S for solvent)?
 - splitting waters according to the peptide chains in the structure?
 - appending all waters to chain A?
 
 
 Thanks.
 
 
 Andreas
 
 
 
 
 On 30/10/2013 11:57, MARTYN SYMMONS wrote:
 At deposition the PDB runs a script that renumbers authors'  waters
 according to a scheme based on the residue they are nearest from N to C
 terminus along each chain. This renumbering started  when waters were
 assigned to macromolecular chains rather than getting a chain id of
 their own.  I have failed to find the rationale explained in any PDB
 documents - but it could be motivated by this sort of consideration when
 waters from different chains or entries are to be compared. Having said
 that I do not know if there are any cases where this approach has
 successfully matched waters. ..
 
 However an associated step which is certainly a help is that, in the
 case of multiple chains, the crystal symmetry is applied to replace
 waters with their symmetry equivalent position if it is closer to a
 different chain.
 
 I believe a freely available program implementing a similar approach is
 WATERTIDY in CCP4 which might be a good place to start.  It gives a
 pretty complete output, detailing residues actually H-bonded to the
 waters, and you could parse that for further analysis and comparisons.
 
 Best wishes.
   Martyn
 
 -- 
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London


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Re: [ccp4bb] Conflicting Qt on OS X 10.6

[Eugene Krissinel]

Yes, this is a result of some imperfectness in shared build (6.3.0 was static). 
The bug should have been fixed in updated release bundles, and also in the 
recent update.

Eugene

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dmitry Rodionov 
[d.rodio...@gmail.com]
Sent: Monday, October 28, 2013 5:40 PM
To: ccp4bb
Subject: Re: [ccp4bb] Conflicting Qt on OS X 10.6

Thanks for the suggestions!
I just opened a new terminal window, and it appears that problem had 
disappeared (by itself?).
Sorry for the false alarm- I'll go see a mental health professional.

Best regards,
Dmitry

On 2013-10-28, at 12:49 PM, William Scott wrote:

 It looks like it should be doing the right thing, i.e.,


 zsh-% otool -L qtrview
 qtrview:
   @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit 
 (compatibility version 4.9.0, current version 4.9.3)
   
 @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns
  (compatibility version 4.8.0, current version 4.8.4)
   @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui 
 (compatibility version 4.8.0, current version 4.8.4)
   @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml 
 (compatibility version 4.8.0, current version 4.8.4)
   @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork 
 (compatibility version 4.8.0, current version 4.8.4)
   @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore 
 (compatibility version 4.8.0, current version 4.8.4)

 If you have $DYLID_LIBRARY_PATH set, try unsetting it.



 On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote:

 Good day!

 I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after 
 spitting out a screenful of messages like

 objc[2975]: Class QCocoaMenu is implemented in both 
 /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui 
 and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two 
 will be used. Which one is undefined.

 Just like the message says, I have Qt 4 installed in the standard location. 
 It seems like the global Qt it is being used instead of the one supplied 
 with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the 
 problem.
 Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions.

 Is there a way to make qtrview use CCP4's Qt and ignore other versions?

 Thanks!

 Best regards,
  Dmitry




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[ccp4bb] CCP4 Release 6.4.0 follow-up

[Eugene Krissinel]

Dear CCP4 users,

It has been reported to us shortly after 6.4.0 release last week, that the 
software was dysfunctional for some users. The reason was found to be the clash 
between Qt framework distributed with CCP4 6.4.0 and the one installed locally. 
This problem is now fixed, and new CCP4 distribution packages are available 
from our web-site:

http://www.ccp4.ac.uk/download/

In order to identify whether your CCP4 setup is affected by the bug, please 
check if any of the symptoms below applies:

- ccp4i shows permanently Network off? in low-right corner
- greyed, dysfunctional Manage Updates button in ccp4i
- even if Manage Updates button is functional, CCP4 updater does not start
- QtRView result viewer does not start
- other Qt-based applications, such as qtpisa and viewhkl, do not start or do 
not work properly

If you find your setup affected by the bug, or have any doubts, we advise you 
to re-install 6.4.0 now.

CCP4 setups with working updater will be synchronised with today's changes 
through the corresponding update soon. 

CCP4 Core Group apologises for any inconvenience and would like to encourage 
all users to report any problems with CCP4 software that they have encountered.

Sincerely yours,

Eugene Krissinel


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Re: [ccp4bb] CCP4 Setup manager

[Eugene Krissinel]

This is most probably because of last-minute changes for CCP4 release, you just 
got us in a *very* wrong moment, we are moving files on the server. Please come 
back in 2 hours or so.

Eugene.

On 10 Oct 2013, at 17:55, Swastik Phulera wrote:

 Dear All,
 I am currently setting up a system running UBUNTU-12.04.3 (64 bit version),
 When I try to install CCP4 software suite by using the software suite, it 
 kinda gets hung with the message Now communicating with CCP4 server, please 
 wait.. for ever
 Any help would be usefull.
 Regards
 Swastik


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[ccp4bb] CCP4 Release 6.4.0 out

[Eugene Krissinel]

Dear CCP4 Users,


The CCP4 Core Group is very pleased to announce the release of the latest 
version of the CCP4 Software Suite. Version 6.4.0 (Long Preston) is now 
available from the CCP4 download website:

http://www.ccp4.ac.uk/download.phphttp://www.ccp4.ac.uk/download/

The release is available for Linux, Mac OSX and Windows platforms. The release 
mostly consolidates updates in the CCP4 6.3.0 update series, but also 
introduces a number of technical improvements and new features.


1. New Components and Updates (please see list of new features in individual 
programs documentation)

New:
 QtRView (Generic graphical result viewer)
 ccp4um  (Integrated CCP4 updater)
 QtPISA  (Graphical front-end to PISA software)

Updated:
 Phaserv2.5.5(Molecular Replacement and Experimental
  Phasing)
 Refmacv5.8.0048 (Macromolecular refinement)
 CTruncate v1.13.0   (Intensity to amplitude conversion and
  reflection data statistics)
 Aimless   v0.2.1(Scaling multiple observations of
  reflections)
 Pointless v1.8.4(Laue group determination)
 Xia2  v0.3.6.1  (Automated data processing)
 Dimplev1.2  (Automated difference map calculations)
 Libcheck  v5.2.01   (Monomer library management program)
 Superpose v1.0.3(Now includes multiple structure
  alignment)
 Ample stable(ab initio molecular replacement)
 CCP4mgv2.7.3(CCP4 Molecular Graphics, much improved
  on features and stability)
 Coot  v0.7.2(Interactive model building; v0.7.1 on
  Windows)
 Arp/wArp  v7.4  (Model building suite from EMBL-
  Hamburg)

CCP4 Graphical User Interface:

  *   multiple bug fixes
  *   incremental changes to accommodate new programs and program updates
  *   import from imosflm quickscale
  *   crossec interface for estimation on anomalous scattering



2. Important technical changes

CCP4 6.4.0 is released on the back of significant changes in CCP4 repositories, 
build and distribution mechanisms. On the user side, these changes are 
reflected in the following:

2.1 Coot is now integrated with CCP4 core on Linux and Mac OSX. This means, 
that for the first time, we distribute portable Coot, which is expected to work 
on all Linuxes. This also means that Coot updates through CCP4 update mechanism 
are now possible. Coot may be launched by typing ‘coot’ in CCP4-sourced 
environment in OS terminal, or, if CCP4 Setup Manager was used for 
installation, by clicking ‘Coot’ icon on your desktop. On Mac OSX, Coot icon is 
placed within the ccp4-6.4.0 directory.

2.2 CCP4 Update manager, ccp4um, is now integrated with the Suite and does not 
require a separate installation as an add-on feature. Updates are now possible 
for all CCP4 ‘external’ components (including Coot, CCP4 MG and Arp/wArp), 
provided that they have been installed in the same master root as CCP4. To 
ensure that, users are advised to use CCP4 Setup Manager for the installation 
of CCP4 on Linux and Mac OSX. Using CCP4 Setup Manager also ensures that the 
latest updates are applied at time of installation. Next, CCP4 Update Manager 
can be now run in the command-prompt (non-graphical) mode, in order to ease the 
life of system administrators. The corresponding command is ‘ccp4um -auto’.

2.3 Source code distribution of the suite has undergone considerable changes. 
For Release 6.4.0, CCP4 offers 3 ways to build the Suite from source code:

a) the “old style” source tarball, which is conceptually
   identical to what it was before, i.e., one does
   ‘configure’, then ‘make’ and finally ‘make install’.
   Note that CCP4 Updates cannot be applied to thus compiled
   CCP4 setups. We distribute the old style tarball for the
   very last time, considering 6.4.0 Release as transient
   in this sense

b)   the “new style” source tarball, which contains both
   source codes and a system to update compiled setups
   directly from CCP4 repositories. The “new style”
   compilation and building is different from the one in
   “old style” tarballs, but not overly complex. Please see
   full set of instructions at
   http://devtools.fg.oisin.rc-harwell.ac.uk/src-readme.html.
   The updates will be done from the release branch of CCP4
   repositories, from which all CCP4 updates are generated.

c) CCP4-JHBuild. This is a comprehensive build system, used
   by CCP4 in-house. It builds the latest, untested,
   unreleased versions of CCP4 libraries and programs and
   is intended primarily for CCP4 developers. Instructions
   are given at 
http://devtools.fg.oisin.rc-harwell.ac.ukhttp://devtools.fg.oisin.rc-harwell.ac.uk//.

Finally, please note that CCP4 Core Group supports a number of nightly builds 
on various platforms, which are accessible through CCP4 Developers Page at 
http://www.ccp4.ac.uk/dev/main.php.


3. ARP/wARP 7.4 co-distribution

ARP/wARP 

Re: [ccp4bb] CCP4 Release 6.4.0 out

[Eugene Krissinel]

Dear Felix,

No, it does not come through updates. 6.3.0 update line will terminate tomorrow 
or soon after.

This must be a fresh install.

It can co-exist with 6.3.0 on Linux platforms and Mac OSX platforms, except for 
QtMG on Mac OSX, which will be superseded (but it is advisable to supersede it 
anyway). If you install through package manager, do not choose to delete 
previous installations when prompted.

Many thanks,

Eugene


On 10 Oct 2013, at 20:46, Felix Frolow wrote:

 Will it be installed through 6.3.0 update system?
 Should it be a fresh install?
 What will happened in this case to 6.3.0?
 
 Wills it  coexist?
 
 
 
 FF
 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 Oct 10, 2013, at 22:31 , Eugene Krissinel eugene.krissi...@stfc.ac.uk 
 wrote:
 
 Dear CCP4 Users,
 
 
 The CCP4 Core Group is very pleased to announce the release of the latest 
 version of the CCP4 Software Suite. Version 6.4.0 (Long Preston) is now 
 available from the CCP4 download website:
 
 http://www.ccp4.ac.uk/download.phphttp://www.ccp4.ac.uk/download/
 
 The release is available for Linux, Mac OSX and Windows platforms. The 
 release mostly consolidates updates in the CCP4 6.3.0 update series, but 
 also introduces a number of technical improvements and new features.
 
 
 1. New Components and Updates (please see list of new features in individual 
 programs documentation)
 
 New:
 QtRView (Generic graphical result viewer)
 ccp4um  (Integrated CCP4 updater)
 QtPISA  (Graphical front-end to PISA software)
 
 Updated:
 Phaserv2.5.5(Molecular Replacement and Experimental
 Phasing)
 Refmacv5.8.0048 (Macromolecular refinement)
 CTruncate v1.13.0   (Intensity to amplitude conversion and
 reflection data statistics)
 Aimless   v0.2.1(Scaling multiple observations of
 reflections)
 Pointless v1.8.4(Laue group determination)
 Xia2  v0.3.6.1  (Automated data processing)
 Dimplev1.2  (Automated difference map calculations)
 Libcheck  v5.2.01   (Monomer library management program)
 Superpose v1.0.3(Now includes multiple structure
 alignment)
 Ample stable(ab initio molecular replacement)
 CCP4mgv2.7.3(CCP4 Molecular Graphics, much improved
 on features and stability)
 Coot  v0.7.2(Interactive model building; v0.7.1 on
 Windows)
 Arp/wArp  v7.4  (Model building suite from EMBL-
 Hamburg)
 
 CCP4 Graphical User Interface:
 
 *   multiple bug fixes
 *   incremental changes to accommodate new programs and program updates
 *   import from imosflm quickscale
 *   crossec interface for estimation on anomalous scattering
 
 
 
 2. Important technical changes
 
 CCP4 6.4.0 is released on the back of significant changes in CCP4 
 repositories, build and distribution mechanisms. On the user side, these 
 changes are reflected in the following:
 
 2.1 Coot is now integrated with CCP4 core on Linux and Mac OSX. This means, 
 that for the first time, we distribute portable Coot, which is expected to 
 work on all Linuxes. This also means that Coot updates through CCP4 update 
 mechanism are now possible. Coot may be launched by typing ‘coot’ in 
 CCP4-sourced environment in OS terminal, or, if CCP4 Setup Manager was used 
 for installation, by clicking ‘Coot’ icon on your desktop. On Mac OSX, Coot 
 icon is placed within the ccp4-6.4.0 directory.
 
 2.2 CCP4 Update manager, ccp4um, is now integrated with the Suite and does 
 not require a separate installation as an add-on feature. Updates are now 
 possible for all CCP4 ‘external’ components (including Coot, CCP4 MG and 
 Arp/wArp), provided that they have been installed in the same master root as 
 CCP4. To ensure that, users are advised to use CCP4 Setup Manager for the 
 installation of CCP4 on Linux and Mac OSX. Using CCP4 Setup Manager also 
 ensures that the latest updates are applied at time of installation. Next, 
 CCP4 Update Manager can be now run in the command-prompt (non-graphical) 
 mode, in order to ease the life of system administrators. The corresponding 
 command is ‘ccp4um -auto’.
 
 2.3 Source code distribution of the suite has undergone considerable 
 changes. For Release 6.4.0, CCP4 offers 3 ways to build the Suite from 
 source code:
 
 a) the “old style” source tarball, which is conceptually
  identical to what it was before, i.e., one does
  ‘configure’, then ‘make’ and finally ‘make install’.
  Note that CCP4 Updates cannot be applied to thus compiled
  CCP4 setups. We distribute the old style tarball for the
  very last time, considering 6.4.0 Release as transient

Re: [ccp4bb] CCP4 Release 6.4.0 out

[Eugene Krissinel]

Dear Felix,

It is probably poor formatting in my e-mail, apologies. The download page is

http://www.ccp4.ac.uk/download/

and yes it shows 6.4.0 for me. You may be seeing cached page. If so, press down 
and hold 'Shift' on your keyboard and click 'Reload' control button in your 
browser (it may be in the end of url prompt, or a designated button in the 
toolbar depending on your browser).

Many thanks for trying

Eugene


On 10 Oct 2013, at 20:48, Felix Frolow wrote:

http://www.ccp4.ac.uk/download.phphttp://www.ccp4.ac.uk/download/http://www.ccp4.ac.uk/download.php%3Chttp://www.ccp4.ac.uk/download/%3E
leads nowhere
there is still no 6.4.0 on the official download site
Am i trigger happy? Too fast ?
FF

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

On Oct 10, 2013, at 22:31 , Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk wrote:

Dear CCP4 Users,


The CCP4 Core Group is very pleased to announce the release of the latest 
version of the CCP4 Software Suite. Version 6.4.0 (Long Preston) is now 
available from the CCP4 download website:

http://www.ccp4.ac.uk/download.phphttp://www.ccp4.ac.uk/download/http://www.ccp4.ac.uk/download.php%3Chttp://www.ccp4.ac.uk/download/%3E

The release is available for Linux, Mac OSX and Windows platforms. The release 
mostly consolidates updates in the CCP4 6.3.0 update series, but also 
introduces a number of technical improvements and new features.


1. New Components and Updates (please see list of new features in individual 
programs documentation)

New:
QtRView (Generic graphical result viewer)
ccp4um  (Integrated CCP4 updater)
QtPISA  (Graphical front-end to PISA software)

Updated:
Phaserv2.5.5(Molecular Replacement and Experimental
 Phasing)
Refmacv5.8.0048 (Macromolecular refinement)
CTruncate v1.13.0   (Intensity to amplitude conversion and
 reflection data statistics)
Aimless   v0.2.1(Scaling multiple observations of
 reflections)
Pointless v1.8.4(Laue group determination)
Xia2  v0.3.6.1  (Automated data processing)
Dimplev1.2  (Automated difference map calculations)
Libcheck  v5.2.01   (Monomer library management program)
Superpose v1.0.3(Now includes multiple structure
 alignment)
Ample stable(ab initio molecular replacement)
CCP4mgv2.7.3(CCP4 Molecular Graphics, much improved
 on features and stability)
Coot  v0.7.2(Interactive model building; v0.7.1 on
 Windows)
Arp/wArp  v7.4  (Model building suite from EMBL-
 Hamburg)

CCP4 Graphical User Interface:

 *   multiple bug fixes
 *   incremental changes to accommodate new programs and program updates
 *   import from imosflm quickscale
 *   crossec interface for estimation on anomalous scattering



2. Important technical changes

CCP4 6.4.0 is released on the back of significant changes in CCP4 repositories, 
build and distribution mechanisms. On the user side, these changes are 
reflected in the following:

2.1 Coot is now integrated with CCP4 core on Linux and Mac OSX. This means, 
that for the first time, we distribute portable Coot, which is expected to work 
on all Linuxes. This also means that Coot updates through CCP4 update mechanism 
are now possible. Coot may be launched by typing ‘coot’ in CCP4-sourced 
environment in OS terminal, or, if CCP4 Setup Manager was used for 
installation, by clicking ‘Coot’ icon on your desktop. On Mac OSX, Coot icon is 
placed within the ccp4-6.4.0 directory.

2.2 CCP4 Update manager, ccp4um, is now integrated with the Suite and does not 
require a separate installation as an add-on feature. Updates are now possible 
for all CCP4 ‘external’ components (including Coot, CCP4 MG and Arp/wArp), 
provided that they have been installed in the same master root as CCP4. To 
ensure that, users are advised to use CCP4 Setup Manager for the installation 
of CCP4 on Linux and Mac OSX. Using CCP4 Setup Manager also ensures that the 
latest updates are applied at time of installation. Next, CCP4 Update Manager 
can be now run in the command-prompt (non-graphical) mode, in order to ease the 
life of system administrators. The corresponding command is ‘ccp4um -auto’.

2.3 Source code distribution of the suite has undergone considerable changes. 
For Release 6.4.0, CCP4 offers 3 ways to build the Suite from source code:

a) the “old style” source tarball, which is conceptually
  identical to what it was before, i.e., one does
  ‘configure’, then ‘make’ and finally ‘make install’.
  Note that CCP4 Updates cannot be applied to thus compiled
  CCP4

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

[Eugene Krissinel]

Completely agree. Perhaps there could be a distinction between working and 
deposition formats. They are for different purposes and, therefore, could 
differ from each other -- Eugene

On 19 Sep 2013, at 10:45, Phil Evans wrote:

 Do you really want to read the whole of a long reflection loop into memory 
 rather than parsing it one line at a time (which should be possible once you 
 have worked out what is in the file)? That would end up with storing the 
 reflection list twice, the memory copy of the input file and the internal 
 representation for the program. I do get complaints from people trying to run 
 e.g. Pointless with large datasets on 32-bit machines, crashing because it 
 runs out of memory
 
 If you imagine someone corresponding to the XDS INTEGRATE.HKL file with 120 
 characters/reflection, then a dataset with 10^7 reflections (not outrageously 
 large these days) occupies 1.2e9 bytes, over 1GB, which seems a lot to add 
 gratuitously to memory demands even on today's computers 
 
 Of course (in my opinion) a working format (as opposed to an archive format) 
 should be binary for size, accuracy (FP dynamic range) and speed. 
 A quick comparison (using Pointless)
 
 Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB, 15 secs
 Read equivalent binary MTZ file, 262MB, 2.6 secs
 
 Phil
 
 On 18 Sep 2013, at 15:58, yayahjb yaya...@gmail.com wrote:
 
 Dear Colleagues,
 
 There are two major issues that tend to trip up CIF programmers:
 
  1.  Dealing with the order independence of CIF.  Unlike PDB format, tags in 
 CIF can validly
 be presented in any order.  This means you cannot simply scan a CIF for a 
 tag you want and
 start processing from that point forward as you do with a PDB file.  In 
 general to read
 a CIF properly, you need to read all of it into memory before you can do 
 anything with it.
 A common mistake is to assume that just because many CIFs have been written 
 with tags in
 a given order, the next CIF you encounter will also have the tags in that 
 order.
 
 2.  Doing the lexical scan (the tokenizing) correctly.  CIF uses a context 
 sensitive grammar,
 so lexers based on simple BNF tend to make mistakes, and most reliable CIF 
 lexers are
 hand-written rather than being generated from a grammar.  The advice to use 
 a pre-written
 and tested lexer is sensible.
 
 The bottom line is that, while it is relatively easy to write a valid CIF, 
 reading CIFs reliably
 can be a very challenging programming task, because you need to write code 
 that will handle
 the very complex general case, rather than just specific examples.  
 Fortunately there are
 software packages to help you do this.
 
 Herbert J. Bernstein
 
 On 9/18/13 10:41 AM, Peter Keller wrote:
 Hi Phil,
 
 I agree that the issue that you raise (about the need to define the data 
 items and categories propery) is an important one that needs proper 
 consideration. However, your mail could be read to suggest that correct 
 parsing of CIF-format data is a secondary issue that doesn't deserve the 
 same attention from developers.
 
 I hope that this isn't quite what you meant  There are already 
 mutually-incompatible CIF dialects out there that have been created by 
 developers coding to their own understanding and interpretations of the 
 CIF/STAR format. I am sure that you would not want to be the creator of yet 
 another one :-) Correct tokenising is a necessary (but not sufficient) 
 condition for preventing the problem getting worse.
 
 In practice, the code and applications that I have seen, and the 
 discussions about this that I have had, all suggest that developers find it 
 more difficult to write code that tokenises CIF/STAR-format data correctly 
 than code that handles other text formats that they have to deal with in 
 this field. My experience suggests that this is an important practical 
 issue with real-world ramifications, and it is worthwhile devoting some 
 effort to it.
 
 Regards,
 Peter.
 
 On Wed, 18 Sep 2013, Phil Evans wrote:
 
 Date: Wed, 18 Sep 2013 13:38:07 +0100
 From: Phil Evans p...@mrc-lmb.cam.ac.uk
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.
 
 As a novice looking at mmCIF from a developers point of view, for 
 reflection data, the complication is not so much tokenising (parsing), but 
 what items to write or to expect to read. For example as far as I can see 
 an observed intensity may be encoded in a reflection loop (merged or 
 unmerged) as any one of the following, and there seem to be similar 
 choices for other items:-
 
 
 _refln_intensity_meas
 _refln.F_squared_meas
 _refln.pdbx_I_plus, _refln.pdbx_I_minus
 
 _diffrn_refln.counts_net
 _diffrn_refln.intensity_net
 
 If I'm writing a file, which should I use, and if I'm reading one which 
 ones should I expect? And is there a distinction between merged and 
 unmerged data?
 
 confused (easily)
 Phil
 
 
 
 On 17 Sep 2013, at 15:30, Peter Keller 

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

[Eugene Krissinel]

I doubt that memory mapping will help the problem in any way. At best, it will 
translate lack of RAM into overhead of data exchange between disk and RAM, 
although seamlessly for programmer. However, modern OSes do this anyway for 
excessive heap allocations. Phil's comment was specifically about 32-bit, 
rather than RAM, limitations.

Do you like it or not, but handling large data is a problem for sparse formats 
like mmCIF, which are not optimised for that, the format was created with 
different ideas in mind

Eugene


On 19 Sep 2013, at 12:12, Peter Keller wrote:

 On Thu, 2013-09-19 at 10:45 +0100, Phil Evans wrote:
 Do you really want to read the whole of a long reflection loop into
 memory rather than parsing it one line at a time (which should be
 possible once you have worked out what is in the file)? That would end
 up with storing the reflection list twice, the memory copy of the
 input file and the internal representation for the program. I do get
 complaints from people trying to run e.g. Pointless with large
 datasets on 32-bit machines, crashing because it runs out of memory
 
 This is a good question. My take on Herb's comment is that you need to
 look at the whole CIF to work out what is in it before starting to
 process any of it. However, that doesn't necessarily involve reading the
 whole file into memory: you can in effect index the contents in an
 initial pass and then look up and process the parts that you are
 interested in.
 
 At a technical level, I would suggest considering the use of
 memory-mapping for this, which makes it look to the application like the
 file has been read into memory, but avoids the overhead of actually
 assigning heap memory and copying into it. (Virtual memory is still
 needed of course, but the limitation there is on the range of memory
 addresses that a process can handle, not the amount of physical RAM
 available to it.) For read-only access this is a simple and efficient
 way of getting the data that you want out of a CIF and into your own
 internal representation. Unmapping the file when you have finished will
 also be much more efficient than freeing heap memory (which can take a
 lot of CPU). There can be problems in certain contexts with addressing
 in a file that is longer than 2GB, but that will still get us a long
 way. Note that you can memory-map regions of a file: you don't have to
 map the whole thing.
 
 Many people on this list will know this already, but just for
 completeness In a C/C++ context, use the function mmap for memory
 mapping. Python has a module called mmap. In Java, use a
 java.nio.MappedByteBuffer (I provide an option to do it this way in the
 code that I released in my first message in this thread, so any Java
 programmer who is unclear about how to set about this could download it
 and have a look). 
 
 This link: http://perldoc.perl.org/PerlIO.html suggests that it is
 possible in Perl as well, but I have never looked into it so I'll leave
 that to someone else.
 
 One final point on this: line-by-line processing needs to allow for the
 fact that there is no requirement at the format specification level for
 reflection data to be one reflection per line, and that the CIF may
 contain multi-line text data (unlikely in categories containing
 reflection data, but quite possible elsewhere in the same file). I am
 sure that 99.99% of reflection CIF's will be one reflection per line,
 but that is a convention (aka dialect). When someone hits a case where
 it isn't things will go wrong with applications that don't take account
 of this.
 
 If you imagine someone corresponding to the XDS INTEGRATE.HKL file
 with 120 characters/reflection, then a dataset with 10^7 reflections
 (not outrageously large these days) occupies 1.2e9 bytes, over 1GB,
 which seems a lot to add gratuitously to memory demands even on
 today's computers 
 
 Of course (in my opinion) a working format (as opposed to an archive
 format) should be binary for size, accuracy (FP dynamic range) and
 speed. 
 
 Yes: this is also a good point, particularly for large amounts of
 tabular data that is easy to define, like reflection data. MTZ has
 served us well for a long time, and other binary formats like HDF5 have
 been designed partly with this consideration in mind. OTOH, a format
 like mmCIF is well suited to a working format for chemical
 restraint/geometry dictionaries (provided of course that dialects don't
 proliferate, and that developers use data names that are defined in a
 dictionary that is available to other developers, rather than just
 making them up). Coordinate data is somewhere in the middle, but that is
 another discussion..
 
 Regards,
 Peter.
 
 A quick comparison (using Pointless)
 
 Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB, 15 
 secs
 Read equivalent binary MTZ file, 262MB, 2.6 secs
 
 Phil
 
 On 18 Sep 2013, at 15:58, yayahjb yaya...@gmail.com wrote:
 
 Dear Colleagues,
 
 There are two major issues that 

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

[Eugene Krissinel]

Inevitably, there is a trade-off between generality and efficiency. Nothing is 
offered for free, and containers do mean a price tag for complexity and 
performance (and sometimes maintenance and support) as well. What happens, one 
always considers all this against development cost, which is normally much 
lower for established generic frameworks, so this is, in essence, a balance 
between the cost of development today and cumulative effect of inefficiency 
through (potentially many) years ahead. Without time machine at hand, it 
usually takes a very good expert to minimise chances of having inappropriate 
choice for future :)

Eugene

On 19 Sep 2013, at 12:51, Phil Evans wrote:

 There's definitely a case for working formats, but as we think about improved 
 working binary formats following on from MTZ (maybe based on HDF5 
 containers), particularly for unmerged data  (for example in the DIALS 
 project), it makes sense to use [mm]/[image]/cif definitions where 
 appropriate, for ease of conversion and to reduce confusion. However not all 
 data items that are needed (or are desirable) are currently defined, so there 
 will need to be some extensions. There is a particular problem with multiple 
 lattices (e.g. non-merohedral twins) where a single observation (intensity) 
 may have multiple indices hkl attached to it, and this doesn't fit neatly 
 into a rectangular array without padding.
 
 Phil
 
 On 19 Sep 2013, at 12:11, Eugene Krissinel eugene.krissi...@stfc.ac.uk 
 wrote:
 
 Completely agree. Perhaps there could be a distinction between working and 
 deposition formats. They are for different purposes and, therefore, could 
 differ from each other -- Eugene
 
 On 19 Sep 2013, at 10:45, Phil Evans wrote:
 
 Do you really want to read the whole of a long reflection loop into memory 
 rather than parsing it one line at a time (which should be possible once 
 you have worked out what is in the file)? That would end up with storing 
 the reflection list twice, the memory copy of the input file and the 
 internal representation for the program. I do get complaints from people 
 trying to run e.g. Pointless with large datasets on 32-bit machines, 
 crashing because it runs out of memory
 
 If you imagine someone corresponding to the XDS INTEGRATE.HKL file with 120 
 characters/reflection, then a dataset with 10^7 reflections (not 
 outrageously large these days) occupies 1.2e9 bytes, over 1GB, which seems 
 a lot to add gratuitously to memory demands even on today's computers 
 
 Of course (in my opinion) a working format (as opposed to an archive 
 format) should be binary for size, accuracy (FP dynamic range) and speed. 
 A quick comparison (using Pointless)
 
 Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB, 15 
 secs
 Read equivalent binary MTZ file, 262MB, 2.6 secs
 
 Phil
 
 On 18 Sep 2013, at 15:58, yayahjb yaya...@gmail.com wrote:
 
 Dear Colleagues,
 
 There are two major issues that tend to trip up CIF programmers:
 
 1.  Dealing with the order independence of CIF.  Unlike PDB format, tags 
 in CIF can validly
 be presented in any order.  This means you cannot simply scan a CIF for a 
 tag you want and
 start processing from that point forward as you do with a PDB file.  In 
 general to read
 a CIF properly, you need to read all of it into memory before you can do 
 anything with it.
 A common mistake is to assume that just because many CIFs have been 
 written with tags in
 a given order, the next CIF you encounter will also have the tags in that 
 order.
 
 2.  Doing the lexical scan (the tokenizing) correctly.  CIF uses a context 
 sensitive grammar,
 so lexers based on simple BNF tend to make mistakes, and most reliable CIF 
 lexers are
 hand-written rather than being generated from a grammar.  The advice to 
 use a pre-written
 and tested lexer is sensible.
 
 The bottom line is that, while it is relatively easy to write a valid CIF, 
 reading CIFs reliably
 can be a very challenging programming task, because you need to write code 
 that will handle
 the very complex general case, rather than just specific examples.  
 Fortunately there are
 software packages to help you do this.
 
 Herbert J. Bernstein
 
 On 9/18/13 10:41 AM, Peter Keller wrote:
 Hi Phil,
 
 I agree that the issue that you raise (about the need to define the data 
 items and categories propery) is an important one that needs proper 
 consideration. However, your mail could be read to suggest that correct 
 parsing of CIF-format data is a secondary issue that doesn't deserve the 
 same attention from developers.
 
 I hope that this isn't quite what you meant  There are already 
 mutually-incompatible CIF dialects out there that have been created by 
 developers coding to their own understanding and interpretations of the 
 CIF/STAR format. I am sure that you would not want to be the creator of 
 yet another one :-) Correct tokenising is a necessary (but not 
 sufficient) condition for preventing

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

[Eugene Krissinel]

It is highly advisable to start doing such structures in mmCIF, because soon 
this is likely to be the only way to go

Eugene

On 2 Sep 2013, at 09:37, Dirk Kostrewa wrote:

Dear Martyn, Pavel and other interested,

I think, an official extension by the PDB to two characters for the chain names 
and 5 digits for residues would really help. I'm currently working on a 
structure with 6x15 chains (through NCS) - it is huge and only a few programs 
can handle this by extending the PDB format.
The last PDB format revision 
3.3http://www.wwpdb.org/documentation/format33/sect9.html#ATOM still only 
allows one character for the chain name and four digits for the residue number.
More bigger structures will be published in the future and an official 
human-readable extended PDB format would really help.

Cheers,

Dirk.


Am 30.08.13 18:14, schrieb MARTYN SYMMONS:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or numbers for chains. But we could 
easily agree to switch to double letters. And long chains can be a sequence of 
letter number permutations such as A1, A2, A3 etc (actually I notice single 
numbers are allowed for the PDB - although are deprecated until all the letters 
have been used).
We could allow the first character to be a number as well - so 11 12 13 as a 
valid sequence.for a single polymer.
Conversely we could expand the atom identifier to include letters as is the 
case with most computing identifiers - however not many programs seem to pay 
attention to the atom 'numbers' in any case.

Cheers
  Martyn

Martyn Symmons (not Winn)
Cambridge


From: Dirk Kostrewa 
kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 30 August 2013, 15:36
Subject: Re: [ccp4bb] Fractional coordinate shift with two-character chain 
names?

Hi Martyn,

excellent - this worked!

Many thanks!

Cheers,

Dirk.

Am 30.08.13 16:04, schrieb Martyn Winn:
 IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There 
 may be something specific in pdbset which interferes. You can try pdbcur as 
 an alternative. Something like:

 pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb eof
 translate * frac 0 0.2 0
 end
 eof

 I just tried it on a little example, and it works for me.

 Cheers
 Martyn

 -Original Message-
 From: CCP4 bulletin board 
 [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Dirk Kostrewa
 Sent: 30 August 2013 14:41
 To: ccp4bb
 Subject: [ccp4bb] Fractional coordinate shift with two-character chain
 names?

 Dear CCP4ers,

 I want to apply a fractional coordinate shift along a polar b-axis with
 coordinates that have non-standard two-character chain names, such as
 AA, AB, and so forth. Unfortunately, neither the old USF moleman2
 nor the actual CCP4 pdbset can handle these chain names. To my
 knowledge, only COOT and PHENIX can cope with them.
 Before I start writing my own little jiffy, is there a quick way to use
 COOT or PHENIX to apply a fractional coordinate shift, or could you
 tell me, which other program I can use in this special case?

 Best regards,

 Dirk.

 --

 ***
 Dirk Kostrewa
 Gene Center Munich
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone: +49-89-2180-76845
 Fax: +49-89-2180-76999
 E-mail:kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
 WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/
 ***

--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail:kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/
***




--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/
***



-- 
Scanned by iCritical.

Re: [ccp4bb] mmCIF as working format?

[Eugene Krissinel]

This is to confirm very publicly that CCP4 libraries (of which APIs is one 
example) are open source and free to use. There are no plans to change this 
and, on contrary, there is a common consensus that it should stay as is.

Eugene


On 7 Aug 2013, at 19:16, Jeffrey, Philip D. wrote:

 Are all the APIs open source ?  I was under the impression that CCP4 had 
 moved away from that, which might justifiably reduce interest in any 
 limited-availability API.
 
 Phil Jeffrey
 Princeton
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Stroud 
 [xtald...@gmail.com]
 Sent: Wednesday, August 07, 2013 1:51 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] mmCIF as working format?
 
 On Aug 5, 2013, at 4:33 AM, Eugene Krissinel wrote:
 I just hope that one day we all will be discussing a sort of universal API 
 to read/write structural information instead of referencing to raw formats, 
 and routines to query MX data, which would be more appropriate than grep 
 (would many SB students/postdocs use grep these days? but many if them would 
 need to inspect files somehow). This, in essence, is similar to discussing 
 read/write primitives in C/C++/Fortran rather than I/O functions of BIOS and 
 HDD/BUS commands that they drive.
 
 I just want to reinforce this point by quoting it verbatim and also emphasize 
 that it was not lost on some of us.
 
 In the long term, the MM structure community should perhaps get its 
 inspiration from SQL, which focuses on the scope of data and the semantics 
 its manipulation, rather than how the data is encoded beneath the surface.
 
 James


-- 
Scanned by iCritical.

Re: [ccp4bb] mmCIF as working format?

[Eugene Krissinel]

Dear All,

The following post is on behalf of Kim Henrick, where I add some editing and 
thoughts of my own with his permission, so I refer to both of us in the text.

As Herbert notices quite rightly, we need to respect each other working 
preferences and needs. I should think that much of effort going from CCP4, PDB, 
Phenix and other players on this ground is devoted to exactly that. Here, 
providing a suitable format is an extremely important and challenging 
endeavour, which will have a significant impact on the field. It may look like 
a distraction from doing science right here, right now, but in fact, it is 
aimed at preventing a far greater distraction, which would emerge if the issue 
remains unattended and various format solutions appear here and there in 
uncontrollable manner. I hope that it may be agreed that maintaining one 
format, albeit not 100% suitable for just everyone, is preferable to 
maintaining N formats, each one 100% suitable for 1 out of N groups of 
crystallographers, with N(N-1) converters between them.

But in reality, where such a dissatisfaction with mmCIF originates from?


1) I CANNOT GREP IT

- this is not correct. By a special agreement, atom site loop in mmCIF look 
essentially the same as in PDB, or wPDB. Left-most columns are predetermined, 
compliant with PDB and made mandatory, while optional (custom or meta-data) 
columns are shifted to the right. In fact, all existing grep scripts should 
work on mmCIF already today without any modification or after a minimal 
modification.


2) I CANNOT READ IT WITH MY EYE, HATE IT

- again, coordinate data in mmCIF is just as readable as in the PDB, because it 
is arranged in exactly the same way, line-wise with keywords. Admittedly, this 
is done by agreement, rather than enforced by the format, in order to minimise 
distraction for all those reading PDB files from their screens, and those keen 
on greping them. What else many people do read? Yes, REMARKs are more readable 
in the PDB, but they are much more difficult to parse, and they are not 
suitable for keeping metadata with relational links. If one is so keen to 
human-reading REMARKS from PDB files, I suggest that this is done more 
conveniently using PDB web-pages, which are designed specially for that and 
offer many other useful options.


3) I CANNOT CHANGE A CHAIN ID IN IT USING MY FAVOURITE EDITOR

- not correct. You CAN do that in the same way as in the PDB. You CAN change 
anything in the file -- of course, if you know what you do. Because atom data 
in mmCIF is formatted in the same way as in PDB, I do not need to give you any 
instructions. By doing this, you will probably break meta data in other parts 
of mmCIF file, but this cannot be helped. Did you always care about metadata 
when changing chain ID by hand in a PDB file? I only can add that hacking into 
data is the last thing that can be advisable or that I would consider to be a 
honour to teach to students. Admittedly, we may lack tools to edit files in a 
safe way at the moment, but a constructive approach here is to raise an issue 
and suggest specifications for such tools, if not to offer your own one(s).


4) MY OWN PROGRAMS READ/WRITE ONLY PDB FORMAT AND I DON'T HAVE TIME TO REWRITE 
THEM

- all CCP4, Phenix and the PDB provide format converters. It takes only a 
superficial python wrap-up around your code to teach it mmCIF, which involves 
only extra file operations, quite cheap these days. In fact, this is what CCP4 
will do to its own codes that are considered not suitable for rewriting to 
mmCIF, so we are all in the same boat here. Certainly, this solution will 
remain applicable only where your program was applicable before. If your code 
cannot cope with new extended data, e.g., 100 protein chains, this is not a 
format issue.


5) MMCIF IS NOT SUPPORTED BY MOLECULAR VIEWERS

- this is not correct. PDB has consulted major viewer vendors and the agreement 
has been reached. All viewers coming from CCP4, Phenix and the PDB will be 
mmCIF-compatible. In fact, this is so right now, just try Coot or CCP4mg on 
mmCIF files, and if something does not work :), please report to us.


6) MMCIF IS NOTORIOUSLY DIFFICULT FOR READING AND WRITING IN APPLICATIONS

- not if you are using an API from one of CCP4, Phenix or the PDB. Really, 
there is no honour or achievement in writing a yet another parser, 
reader/writer. We work hard to provide you with tools for doing something 
better than primitive coding. Do you code from scratch when reading JPG or PNG, 
or when printing into PDF? What about MTZ, still a low-level reading, too?


7) I DO NOT LIKE YOUR APIs

- APIs are expandable and much more flexible than formats. It takes only 
collaboration spirit and effort to improve them. They can be always kept 
backward-compatible.


8) YOU HAVE DONE EVERYTHING WITHOUT ASKING ME, AGAIN

- this has nothing to do with advantages or disadvantages of mmCIF. It took 
almost 20 years of discussions around mmCIF, so 

Re: [ccp4bb] mmCIF as working format?

[Eugene Krissinel]

I just hope that one day we all will be discussing a sort of universal API to 
read/write structural information instead of referencing to raw formats, and 
routines to query MX data, which would be more appropriate than grep (would 
many SB students/postdocs use grep these days? but many if them would need to 
inspect files somehow). This, in essence, is similar to discussing read/write 
primitives in C/C++/Fortran rather than I/O functions of BIOS and HDD/BUS 
commands that they drive.

No format can suite everybody, especially given the complexity of 
macromolecular data. In contrary to the conspiracy theory of Tim, transition to 
mmCIF is actually driven by scientists, rather than programmers. PDB has 
limitations (e.g. limits on the number of atoms, residues and chains), which 
make it not suitable in many cases today and definitely not for future. This 
has been discussed many times, and one has to take measures one day; seems like 
that day is coming.

But I would really like to accentuate that working with raw format, whether 
through grep or otherwise, should increasingly become more and more unnecessary 
habit, to say the least. Formats will evolve whatever happens, and the only 
proper way to cope with it as a moving target is to use a maintained API.

Eugene

On 5 Aug 2013, at 11:10, kaiser wrote:

Tim,
  Having not read Gerard Kleywegt's announcement, and not considering myself a 
programmer, I have to disagree with the majority of your statement. Yes, using 
grep on mmcif files is awkward (but petfectly possible); awk on the other 
hand works much better. It's actually more of a pain to use it on pdb files. 
And perl, well perl can handle anything and it will always look nice while you 
write it and never look nice when you look back at it...

Just my 2 cents,

Jens

Sent from my T-Mobile 4G LTE Device



 Original message 
From: Tim Gruene t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de
Date: 2013/08/05 01:03 (GMT-08:00)
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mmCIF as working format?


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

having read Gerard Kleywegt's latest announcement on the wwPDB Workshop
(1st August) made me wonder whether it is planned to introduce mmCIF as
working format to users in addition to using it at e.g. the PDB, because
I think that would make life unnecessarily complicated.

The example mmCIF file for GroEL is about 7.5 times bigger than its PDB
file.
I know that disk space is 'cheap' nowadays, but that does not make it fast.

And personally I find mmCIF very awkward to work with, since it is not
line-oriented. 'grep', 'awk', 'perl' etc. do not work well on XML-like
files.
Instead of using mmCIF, one could, e.g. introduce a free format PDB
format, with space holders for non-assigned entities, and maybe a line
continuation character.

If mmCIF is not going to be the working format for MX (refinement)
programs I would be happy for a reassurance, and otherwise I would
appreciate some comments about the benefits of an XML file format over a
line-oriented free format for the scientists that work with structural data.
I my opinion, using XML (or mmCIF) for structural information is an
attempt of programmers to make themselves more indespensable to
scientists, rather than scientifically needed.

Best,
Tim

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.14 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFR/1xbUxlJ7aRr7hoRAkLNAKClH9RpAA7NJsH3YFOTguOo9kjwoQCZAf/m
JF1oyJNuq+8b+VsywDupElo=
=bvb3
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[ccp4bb] CCP4 Support 32 bit OSX - request for feedback

[Eugene Krissinel]

PPS So far we have received a VERY limited response to this call. Please see a 
nice hint from Bill Scott if you are in doubt whether your Mac is capable of 
running 64-bit applications:

Hi Eugene:

If there are many people who think they need 32-bit support, you might want to 
request they issue the command

  % sysctl hw |grep 64bit

If it comes back with a 1, i.e.,

   hw.cpu64bit_capable: 1

then they can still run the 64-bit binaries even if they are running a 32-bit 
kernel (eg: on 10.6.8).

The very old white iMac and the first-generation white and black macbooks are 
the only ones I am aware.

Bill

Begin forwarded message:

Date: 12 July 2013 14:09:25 GMT+01:00
To: CCP4BB ccp4bb@jiscmail.ac.ukmailto:ccp4bb@jiscmail.ac.uk
Subject: Fwd: [ccp4bb] CCP4 Support 32 bit OSX - request for feedback

PS Please consult http://support.apple.com/kb/ht3696 for how to determine your 
CPU type. Many thanks -- Eugene

Begin forwarded message:

From: Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
Date: 12 July 2013 12:47:26 GMT+01:00
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 Support 32 bit OSX - request for feedback
Reply-To: Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk

Dear CCP4 Users,

CCP4 Core Team is in final stages for 6.4.0 Release. Every release and 
subsequent support takes a considerable effort, which scales linearly with the 
number of supported platforms. This makes us to periodically revise the scope 
of support we can offer to community.

Since at least 4 years ago, Apple stopped manufacturing and support of 32-bit 
architectures, both on hardware and software side. This means that further 
support of 32-bit Macs by CCP4 will be completely unjustified in some future, 
and may be uneconomical already today.

Yet, before taking any radical actions, we would like to estimate the number of 
actual 32-bit Mac OSX users of CCP4. I therefore solicit a feedback from 
everybody who:

a) has a 32-bit Mac machine running CCP4 AND
b) uses this machine for CCP4ing routinely  AND
c) has no plans to acquire a 64-bit equivalent in 6 months time.

It would help us greatly to estimate the demand, if all such users send 
content-less e-mails to

mail-to:eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
Subject:   32-bit Mac:  YES  [system]

where [system] is your Mac OSX release, such as 10.4, 10.5 or 10.6.

PLEASE DO NOT CC THIS TO THE WHOLE CCP4BB BY MERE REPLYING TO THIS E-MAIL!

I appreciate your time and willingness to help.

Many thanks,

Eugene Krissinel.


Begin forwarded message:

Date: 10 July 2013 16:35:44 GMT+01:00
To: hari jayaram hari...@gmail.commailto:hari...@gmail.com
Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 package manager not available for 32 bit OSX?

Sadly not, we are dropping support for 32-bit Macs. You can still install 
32-bit CCP4 6.3.0 from dmg.

Sorry -- Eugene

On 10 Jul 2013, at 16:04, hari jayaram wrote:

Hi ,
I am trying to use the CCP4 package manager on my 32 bit OSX 10.6.8 running 
laptop and it complains

/bin/sh: Volume/setup/.pm/Setup.app/Contents/MacOS/Setup: Bad CPU type in 
executable.

Is there a 32 bit package manager available...
Thanks
Hari

Screen shot 2013-07-10 at 10.57.53 AM.png




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[ccp4bb] CCP4 Support 32 bit OSX - request for feedback

[Eugene Krissinel]

Dear CCP4 Users,

CCP4 Core Team is in final stages for 6.4.0 Release. Every release and 
subsequent support takes a considerable effort, which scales linearly with the 
number of supported platforms. This makes us to periodically revise the scope 
of support we can offer to community.

Since at least 4 years ago, Apple stopped manufacturing and support of 32-bit 
architectures, both on hardware and software side. This means that further 
support of 32-bit Macs by CCP4 will be completely unjustified in some future, 
and may be uneconomical already today.

Yet, before taking any radical actions, we would like to estimate the number of 
actual 32-bit Mac OSX users of CCP4. I therefore solicit a feedback from 
everybody who:

a) has a 32-bit Mac machine running CCP4 AND
b) uses this machine for CCP4ing routinely  AND
c) has no plans to acquire a 64-bit equivalent in 6 months time.

It would help us greatly to estimate the demand, if all such users send 
content-less e-mails to

mail-to:eugene.krissi...@stfc.ac.uk
Subject:   32-bit Mac:  YES  [system]

where [system] is your Mac OSX release, such as 10.4, 10.5 or 10.6.

PLEASE DO NOT CC THIS TO THE WHOLE CCP4BB BY MERE REPLYING TO THIS E-MAIL!

I appreciate your time and willingness to help.

Many thanks,

Eugene Krissinel.


Begin forwarded message:

 Date: 10 July 2013 16:35:44 GMT+01:00
 To: hari jayaram hari...@gmail.com
 Cc: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] CCP4 package manager not available for 32 bit OSX?
 
 Sadly not, we are dropping support for 32-bit Macs. You can still install 
 32-bit CCP4 6.3.0 from dmg.
 
 Sorry -- Eugene
 
 On 10 Jul 2013, at 16:04, hari jayaram wrote:
 
 Hi ,
 I am trying to use the CCP4 package manager on my 32 bit OSX 10.6.8 running 
 laptop and it complains
 
 /bin/sh: Volume/setup/.pm/Setup.app/Contents/MacOS/Setup: Bad CPU type in 
 executable.
 
 Is there a 32 bit package manager available...
 Thanks
 Hari
 
 Screen shot 2013-07-10 at 10.57.53 AM.png
 


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[ccp4bb] Fwd: [ccp4bb] CCP4 Support 32 bit OSX - request for feedback

[Eugene Krissinel]

PS Please consult http://support.apple.com/kb/ht3696 for how to determine your 
CPU type. Many thanks -- Eugene

Begin forwarded message:

From: Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
Date: 12 July 2013 12:47:26 GMT+01:00
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 Support 32 bit OSX - request for feedback
Reply-To: Eugene Krissinel 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk

Dear CCP4 Users,

CCP4 Core Team is in final stages for 6.4.0 Release. Every release and 
subsequent support takes a considerable effort, which scales linearly with the 
number of supported platforms. This makes us to periodically revise the scope 
of support we can offer to community.

Since at least 4 years ago, Apple stopped manufacturing and support of 32-bit 
architectures, both on hardware and software side. This means that further 
support of 32-bit Macs by CCP4 will be completely unjustified in some future, 
and may be uneconomical already today.

Yet, before taking any radical actions, we would like to estimate the number of 
actual 32-bit Mac OSX users of CCP4. I therefore solicit a feedback from 
everybody who:

a) has a 32-bit Mac machine running CCP4 AND
b) uses this machine for CCP4ing routinely  AND
c) has no plans to acquire a 64-bit equivalent in 6 months time.

It would help us greatly to estimate the demand, if all such users send 
content-less e-mails to

mail-to:eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
Subject:   32-bit Mac:  YES  [system]

where [system] is your Mac OSX release, such as 10.4, 10.5 or 10.6.

PLEASE DO NOT CC THIS TO THE WHOLE CCP4BB BY MERE REPLYING TO THIS E-MAIL!

I appreciate your time and willingness to help.

Many thanks,

Eugene Krissinel.


Begin forwarded message:

Date: 10 July 2013 16:35:44 GMT+01:00
To: hari jayaram hari...@gmail.commailto:hari...@gmail.com
Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 package manager not available for 32 bit OSX?

Sadly not, we are dropping support for 32-bit Macs. You can still install 
32-bit CCP4 6.3.0 from dmg.

Sorry -- Eugene

On 10 Jul 2013, at 16:04, hari jayaram wrote:

Hi ,
I am trying to use the CCP4 package manager on my 32 bit OSX 10.6.8 running 
laptop and it complains

/bin/sh: Volume/setup/.pm/Setup.app/Contents/MacOS/Setup: Bad CPU type in 
executable.

Is there a 32 bit package manager available...
Thanks
Hari

Screen shot 2013-07-10 at 10.57.53 AM.png




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-- 
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Re: [ccp4bb] CCP4 package manager not available for 32 bit OSX?

[Eugene Krissinel]

Sadly not, we are dropping support for 32-bit Macs. You can still install 
32-bit CCP4 6.3.0 from dmg.

Sorry -- Eugene

On 10 Jul 2013, at 16:04, hari jayaram wrote:

 Hi ,
 I am trying to use the CCP4 package manager on my 32 bit OSX 10.6.8 running 
 laptop and it complains
 
 /bin/sh: Volume/setup/.pm/Setup.app/Contents/MacOS/Setup: Bad CPU type in 
 executable.
 
 Is there a 32 bit package manager available...
 Thanks
 Hari
 
 Screen shot 2013-07-10 at 10.57.53 AM.png


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Re: [ccp4bb] PISA and ligands with non-natural amino acids

[Eugene Krissinel]

Dear Herman,

I am looking at protein complexes with ligands containing non-natural amino 
acids. When I run PISA, I get the total area of the ligand, as well as the area 
of the ligand-protein interface, but hydrogen bonds and salt links are not 
recognized. I therefore do not think the calculated DeltaG values can be 
trusted. Is there a way to specify non-natural ligands for PISA, or does it 
only work for amino acids which have been calibrated with help of a large 
number pdb structures?

- this is exactly the case at the moment.

Eugene



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Re: [ccp4bb] visualizing protein-protein interface

[eugene . krissinel]

This is the kind of things MG was designed to do -- Eugene

On 4 Jun 2013, at 15:18, Tobias Beck wrote:

Dear all,

I would like to visualize the interface of a protein-protein complex. The 
complex formation is modulated by a ligand that upon binding alters the overall 
structure of one protein, which then in turn forms the complex with the second 
protein (structure of the complex is known). Ligand binding does not seem to 
induce a discrete conformational switch, rather a subtle alteration of the 
contact interface. The isolated structure of the first protein without the 
ligand is known as well.

In addition to depicting the structural difference in conventional ways I was 
thinking to draw some kind of stretched out topology map of the surface that is 
interacting - first the surface from the isolated protein, then the surface as 
it is found in the complex and then maybe some kind of difference map...

Does anybody have some suggestions how to do this? I would prefer to do some 
kind of stretched out surface (basically a rectangle of the region of interest) 
and show mountains and valleys and their change, but not sure if this is 
feasible.

Thanks for any advice!

Best wishes,

Tobias.

--
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web:  http://www.protein.ethz.ch/people/tobias
___


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Re: [ccp4bb] How to generate a complete viirus PDB

[eugene . krissinel]

Would PISA not do this? -- Eugene

On 25 Apr 2013, at 09:20, abhimanyu singh wrote:

Hi Hong,

In your PDB file if the BIOMT transformation matrix (under remark 350) is 
provided, you can use this script to generate the biological assembly :
http://watcut.uwaterloo.ca/cgi-bin/makemultimer/


Greetings,
Abhi

On Thu, Apr 25, 2013 at 9:31 AM, sujata halder 
halder.suj...@gmail.commailto:halder.suj...@gmail.com wrote:
Hi,

In continuation to the previous suggestion about using the 'Oligomer Generator' 
in viperdb. To use viperdb, your pdb needs to be in the viper format. So 
download any pdb (example this one 
:http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then 
superpose your monomer onto this reference viper format pdband then upload 
your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T 
number and the option for 60mer, 30mer etc.
If this is an already published pdb then just input the id in the homepage and 
then the next page will have options for you to download a whole capsid or half 
capsid.

-Tina


On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney 
bmkea...@ncsu.edumailto:bmkea...@ncsu.edu wrote:
Hi Hong,

I would recommend that you check out the services at the VIPERdb website 
http://viperdb.scripps.eduhttp://viperdb.scripps.edu/. It looks like the 
oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful 
for what you want to do. They have many of the virus structures from the PDB 
already processed for you, or you could upload your own PDB coordinate file.

Brad

---
Bradley Kearney, Research Associate
The Scripps Research Institute
Department of Integrative Structural and Computational Biology
Jack Johnson Laboratory


From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guan 
Hong Hsiang
Sent: Wednesday, April 24, 2013 11:19 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to generate a complete viirus PDB

Dear all:
 I have one subunit PDB of one virus with a NCS record. Which program 
should I use to generate a complete virus PDB using the NCS?


Thank you   Hong Hsiang




--
Abhimanyu Kumar Singh
Ph.D. Student
Department of Macromolecular Structures
National Center for Biotechnology (CNB-CSIC)
C/ Darwin 3, Campus de Cantoblanco,
28049 Madrid, Spain.
E-Mail: abhimanyu.si...@cnb.csic.esmailto:abhimanyu.si...@cnb.csic.es



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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 
jmhol...@lbl.govmailto: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



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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 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


um-what.png



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




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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 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
 
 
 um-what.png
 
 
 
 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
 
 
 
 
 


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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

Dear Dale,

From next CCP4 release (due soon), ccp4um will be runnable from command line 
in automatic, non-graphical mode, fully cronable. I hope that that will give 
you what you want.  --check-silent is a special option for ccp4i, it only 
checks for new updates but do not install them.

Best regards,

Eugene


On 11 Apr 2013, at 18:10, Dale Tronrud wrote:

 FYI
 
   I have a small herd of computers here and find it cumbersome to ssh
 to each and fire up ccp4i just to update the systems.  ccp4i takes a
 while to draw all those boxes (particularly over ssh) and leaves files
 behind in my disk areas on computers that I'm not likely to, personally,
 run crystallographic computations.  I much prefer to simply run ccp4um
 from the command line.
 
   In fact, I would rather put it in cron and forget about it -- and
 I expect that is what --check-silent is for.  The usage statement,
 however, doesn't explicitly say that this installs the new updates it
 finds.  I'll have to experiment a bit.
 
 Dale Tronrud
 
 On 04/11/2013 05:17 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, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 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
 
 
 um-what.png
 
 
 
 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
 
 
 
 


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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

In promise for next release.

On 11 Apr 2013, at 18:16, James Stroud wrote:


On Apr 11, 2013, at 6:17 AM, 
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
eugene.krissi...@stfc.ac.ukmailto: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 ?:)).

Scriptability.


On Apr 11, 2013, at 10:34 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 [Holton] has lost.


But he wrote the game.

James



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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

In cases like this, a request at c...@stfc.ac.uk should be the way to go. CCP4 
is a community resource and we are to listen and to do what's doable. We may 
not do everything at once, but knowing what is required is vital for the 
project.

Cheers,

Eugene


On 11 Apr 2013, at 18:22, Antony Oliver wrote:

 Eugene - that's great. I too run a small suite of Macs (12) and was trying to 
 find a practical way of updating all those machines remotely. The command 
 line version of CCP4um will be very useful. 
 
 Many thanks. 
 
 Tony. 
 
 Sent from my iPhone
 
 On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.uk wrote:
 
 Dear Dale,
 
 From next CCP4 release (due soon), ccp4um will be runnable from command line 
 in automatic, non-graphical mode, fully cronable. I hope that that will give 
 you what you want.  --check-silent is a special option for ccp4i, it only 
 checks for new updates but do not install them.
 
 Best regards,
 
 Eugene
 
 
 On 11 Apr 2013, at 18:10, Dale Tronrud wrote:
 
 FYI
 
 I have a small herd of computers here and find it cumbersome to ssh
 to each and fire up ccp4i just to update the systems.  ccp4i takes a
 while to draw all those boxes (particularly over ssh) and leaves files
 behind in my disk areas on computers that I'm not likely to, personally,
 run crystallographic computations.  I much prefer to simply run ccp4um
 from the command line.
 
 In fact, I would rather put it in cron and forget about it -- and
 I expect that is what --check-silent is for.  The usage statement,
 however, doesn't explicitly say that this installs the new updates it
 finds.  I'll have to experiment a bit.
 
 Dale Tronrud
 
 On 04/11/2013 05:17 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, 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 
 eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk 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
 
 
 um-what.png
 
 
 
 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.
 


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Re: [ccp4bb] CCP4 Update victim of own success

[eugene . krissinel]

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

Eugene

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


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Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

Spasibo Andrey,

Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne 
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'

Eugene

On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:

 Dear CCP4 Users
 
 A CCP4 update has just been released, consisting of the following changes.
 
 * Aimless: Task interface fixed in part of input customisation section
 * Molrep: Improvements to scoring system and bug fixes
 * Logview: Command-prompt routine for viewing individual log files with 
 QtRView
Simply call it with path to the log file as the only parameter
 * QtRView: Cosmetic improvements and changes for Logview
 * Gesamt: Now prints superposition matrices also in fractional coordinates
 * Superpose: Now prints superposition matrices also in fractional coordinates
 
 If you do not currently receive updates, consider re-installing your
 CCP4 setup using the latest binary packages, which now have the CCP4 Update 
 Manager (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 Many thanks for using CCP4
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.
 


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[ccp4bb] Fwd: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

Apologies for everybody, the previous message was sent to BB by mistake, please 
disregard.

Eugene Krissinel

Begin forwarded message:

Date: 16 March 2013 11:25:08 GMT
To: andrey.lebe...@stfc.ac.ukmailto:andrey.lebe...@stfc.ac.uk
Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 Update 019

Spasibo Andrey,

Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne 
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'

Eugene

On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* Aimless: Task interface fixed in part of input customisation section
* Molrep: Improvements to scoring system and bug fixes
* Logview: Command-prompt routine for viewing individual log files with QtRView
  Simply call it with path to the log file as the only parameter
* QtRView: Cosmetic improvements and changes for Logview
* Gesamt: Now prints superposition matrices also in fractional coordinates
* Superpose: Now prints superposition matrices also in fractional coordinates

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


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Re: [ccp4bb] RNA 3D structure alignment

[eugene . krissinel]

superpose and gesamt in ccp4

On 14 Mar 2013, at 20:53, Chen Zhao wrote:

 Dear all,
 
 I am now struggling to align two 3D RNA structures. I know there are a bunch 
 of web servers, but they either just generated a pdb file with a single 
 aligned structure, or they left the ligand out.
 
 Does any of you have some recommendations? 
 
 Alternatively, is there some software that can calculate the transformation 
 matrix between the coordinates in 2 pdb files? Then I could add the ligand 
 back by myself. I suspect that Matlab is able to do this, but I would save it 
 as the last resort.
 
 Thank you so much!
 
 Best,
 Chen


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Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

[eugene . krissinel]

Two months ago, CCP4 deployed a new viewer for annotated result reports (plots 
etc), which does not depend on browsers and java, exactly for reasons that you 
write about. Do you use 6.3.0 with updates, and if yes, does your question mean 
that the new viewer does not work for you? The viewer (QtRView) was released in 
6.3.0-010 already integrated with ccp4i.

Eugene


On 8 Mar 2013, at 12:56, vellieux wrote:

 Hello,
 
 I think the Subject line tells it all.
 
 Former Linux box, Java was installed within a couple of browsers and I could 
 view the (nice and useful) plots within ccp4i.
 
 New Linux box, Java {plugin / extension / whatever} is deactivated to start 
 with (this Java plugin seems rather difficult to install, whatever I have 
 tried has failed so far) with a message indicating that Java is a security 
 risk.
 
 Hence I was wondering if there is an alternative to view these nice plots on 
 a Linux box nowadays. Something that would not be seen as a security threat 
 and be deactivated.
 
 Thanks in advance,
 
 Fred.
 
 -- 
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 ouvrier de la recherche
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494


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Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

[eugene . krissinel]

 Indeed there is a new viewer and it usually works.

it would be nice to have specific feedback where it does not, against previous, 
browser-based, system 

 But I also have pre 6.3.0 results that I need to view and somehow the ccp4i 
 qtRviewer does not manage to load the results...

I would think that they should be viewable with QtRView as long as you use 
6.3.0 ... we have this tested, but certainly something may have been 
overlooked. This assumes, of course, that your pre-6.3.0 projects are now in 
6.3.0

 So I was wondering if there was a Java-free alternative, I do have the log 
 files.

Like using old Linuxes to work with old projects? :) If you can give a specific 
example where QtRView fails on log files in projects imported into 6.3.0 from 
pre-6.3.0 projects, we can have a look into that.

Eugene


 
 Fred.
 
 On 08/03/13 14:04, eugene.krissi...@stfc.ac.uk wrote:
 Two months ago, CCP4 deployed a new viewer for annotated result reports 
 (plots etc), which does not depend on browsers and java, exactly for reasons 
 that you write about. Do you use 6.3.0 with updates, and if yes, does your 
 question mean that the new viewer does not work for you? The viewer 
 (QtRView) was released in 6.3.0-010 already integrated with ccp4i.
 
 Eugene
 
 
 On 8 Mar 2013, at 12:56, vellieux wrote:
 
 Hello,
 
 I think the Subject line tells it all.
 
 Former Linux box, Java was installed within a couple of browsers and I 
 could view the (nice and useful) plots within ccp4i.
 
 New Linux box, Java {plugin / extension / whatever} is deactivated to start 
 with (this Java plugin seems rather difficult to install, whatever I have 
 tried has failed so far) with a message indicating that Java is a security 
 risk.
 
 Hence I was wondering if there is an alternative to view these nice plots 
 on a Linux box nowadays. Something that would not be seen as a security 
 threat and be deactivated.
 
 Thanks in advance,
 
 Fred.
 
 -- 
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 ouvrier de la recherche
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494
 
 
 
 -- 
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 ouvrier de la recherche
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494
 


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[ccp4bb] CCP4 Update 017

[eugene . krissinel]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes:


  *   Aimless Bug fixing in task interface
  *   ccp4i Fixed long-standing issue on Linux and Mac: system Python was used 
instead of the one distributed with CCP4
  *   QtPISA Added output of monomer, interface and assembly details in plain 
text; eliminated Qt widget flashing

If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have the CCP4 Update Manager 
(ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Eugene Krissinel


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Re: [ccp4bb] Qt PISA text copy?

[eugene . krissinel]

Dear Engin,

QtPISA outputs the same textual information as the previous command-prompt 
routine, check File/Export plain text. What is probably confusing is that it 
does not export everything in one go, but rather precisely the portion that is 
currently displayed in the right-hand side of the window. E.g., if you'd like 
to export all tables for 1st stable assembly, navigate to that assembly in the 
result tree on the left (that means, open Assemblies/Stable and highlight 1st 
assembly), and then choose File/Export plain text from windows' menu.

I hope that this helps,

Eugene


On 4 Mar 2013, at 07:13, Engin Özkan wrote:

 Hi everybody,
 
 I was just trying out the new QT PISA interface in CCP4 6.3.0 (updated to 
 -017). I realized none of the beautiful tables produced can be easily 
 extracted/copied/captured into a human readable form. There are many output 
 options, including PDB files, a binary-formatted .pisa file, XMLs, and a very 
 short summary text file. I can copy the tables line by line by command-C (on 
 Mac 10.6), but any means of selecting and copying all rows have failed. I had 
 to resort to running pisa command-line, and thankfully got the tables there.
 
 This can also be accomplished simply by a copy and paste from a browser when 
 using the webserver. I must clearly be missing something using the new and 
 beautiful Qt interface (otherwise why produce these tables?). Could someone 
 please direct me to how to do this?
 
 Cheers,
 Engin
 
 -- 
 Engin Özkan
 Post-doctoral Scholar
 Laboratory of K. Christopher Garcia
 Howard Hughes Medical Institute
 Dept of Molecular and Cellular Physiology
 279 Campus Drive, Beckman Center B173
 Stanford School of Medicine
 Stanford, CA 94305
 w ph: (650)-498-7111
 cell: (650)-862-8563


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Re: [ccp4bb] Qt PISA text copy?

[eugene . krissinel]

Apologies, I'd like to retract my post, it is indeed that only general lists of 
interfaces and assemblies are exported in plain text.
We will try to fix this as soon as feasible.

Eugene


On 4 Mar 2013, at 11:13, eugene.krissi...@stfc.ac.uk
 eugene.krissi...@stfc.ac.uk wrote:

 Dear Engin,
 
 QtPISA outputs the same textual information as the previous command-prompt 
 routine, check File/Export plain text. What is probably confusing is that 
 it does not export everything in one go, but rather precisely the portion 
 that is currently displayed in the right-hand side of the window. E.g., if 
 you'd like to export all tables for 1st stable assembly, navigate to that 
 assembly in the result tree on the left (that means, open Assemblies/Stable 
 and highlight 1st assembly), and then choose File/Export plain text from 
 windows' menu.
 
 I hope that this helps,
 
 Eugene
 
 
 On 4 Mar 2013, at 07:13, Engin Özkan wrote:
 
 Hi everybody,
 
 I was just trying out the new QT PISA interface in CCP4 6.3.0 (updated to 
 -017). I realized none of the beautiful tables produced can be easily 
 extracted/copied/captured into a human readable form. There are many output 
 options, including PDB files, a binary-formatted .pisa file, XMLs, and a 
 very short summary text file. I can copy the tables line by line by 
 command-C (on Mac 10.6), but any means of selecting and copying all rows 
 have failed. I had to resort to running pisa command-line, and thankfully 
 got the tables there.
 
 This can also be accomplished simply by a copy and paste from a browser when 
 using the webserver. I must clearly be missing something using the new and 
 beautiful Qt interface (otherwise why produce these tables?). Could someone 
 please direct me to how to do this?
 
 Cheers,
 Engin
 
 -- 
 Engin Özkan
 Post-doctoral Scholar
 Laboratory of K. Christopher Garcia
 Howard Hughes Medical Institute
 Dept of Molecular and Cellular Physiology
 279 Campus Drive, Beckman Center B173
 Stanford School of Medicine
 Stanford, CA 94305
 w ph: (650)-498-7111
 cell: (650)-862-8563
 
 
 -- 
 Scanned by iCritical.
 


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Re: [ccp4bb] protein dodecamer

[eugene . krissinel]

Check with PISA@EBI, it has database searches where you can fetch all 
dodecamers in the PDB

Eugene

On 20 Feb 2013, at 06:29, Hui Wang wrote:

Dear all,

I am looking for proteins that form a dodecameric ring structure  (Not two 
rings of hexamer Nor tetrahedral distribution of subunit trimers). I found some 
phage portal proteins after a quick search in PDB, but I need more.  Does 
anyone know more protein dodecamers that has C12 symmetry?

Thanks,

Hui


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Re: [ccp4bb] Thanks for the new graphical CCP4 installer

[eugene . krissinel]

Thank you Francois

for positive feedback.

Eugene

On 15 Feb 2013, at 05:40, Francois Berenger wrote:

 It is easy to use and even nice looking.
 
 Regards,
 F.


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Re: [ccp4bb] Thx...

[eugene . krissinel]

Thank you very much Bernhard. Feedbacks like yours have enormous encouraging 
effect on developers.

Eugene.

On 1 Feb 2013, at 00:02, Bernhard Rupp (Hofkristallrat a.D.) wrote:

 Hi Fellows from the programming department(s),
 
 I just had the pleasure to work with the new update mechanism and Win CCP4
 6.3 GUI. That you can get from the summary page directly to Coot (which also
 automatically updates) and that everything works as advertised is very
 impressive and I perhaps even necessary for CCP4 to keep its market share
 with the push-button crowd. I think it is awesome progress and thanks to all
 the friendly coders for their efforts. The collective time savings are
 enormous.
 
 Best regards, BR
 -
 Bernhard Rupp
 001 (925) 209-7429
 +43 (676) 571-0536
 b...@ruppweb.org
 hofkristall...@gmail.com
 http://www.ruppweb.org/
 ---
 The road to scientific serfdom is paved with Nature papers
 ---


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Re: [ccp4bb] CCP4 Update 015

[eugene . krissinel]

Dear Boaz,

If that was not done, it's an oversight. Surely this is possible, will have a 
look into.

Thanks for reporting (but please use c...@stfc.ac.uk for future bug reports 
please),

Eugene



On 26 Jan 2013, at 14:00, Boaz Shaanan wrote:

 Dear Developers,
 
 As part of the wonderful work you're doing with development and upgrades, 
 would it be possible to also update the INDEX.html in the $CCP4/html 
 directory whenever a new program html is entered into this directory (e.g. 
 the latest aimless.html)? 
 
  Thanks,
 
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 Ville Uski 
 [ville.u...@stfc.ac.uk]
 Sent: Saturday, January 26, 2013 1:21 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] CCP4 Update 015
 
 Dear CCP4 Users
 
 A CCP4 update has just been released, consisting of the following
 changes.
 
 *   Ctruncate: Memory leak fixed.
 *   Aimless, Pointless, Ctruncate: Documentation updated following
previous changes.
 
 If you do not currently receive updates, consider re-installing your
 CCP4 setup using the latest binary packages, which now have the CCP4
 Update Manager (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0,
 therefore upgrade if necessary. Please report any bugs to
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 Many thanks for using CCP4.
 
 Ville Uski
 --
 Scanned by iCritical.


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Re: [ccp4bb] CCP4 Update 014

[eugene . krissinel]

Dear Kay,

Many thanks for nice words! We appreciate feedback from all our users.

Indeed, we expect that the update system will result in a lower frequency of 
releases. Yet, full-scale releases will be needed. A good analogy here are the 
update vs upgrade procedures in operating systems. An upgrade is needed 
whenever we face the need for structural changes in the Suite, which cannot be 
easily accommodated by a mere update due to a considerable number of various 
dependencies to be followed.

At present, we still need full releases because:

1) currently we are doing a considerable work under the hood of the CCP4 
Suite, which is not reflected in what a general user would see. Some elements 
of that include better organised source repositories, synced with updates, 
completely new build mechanism, which would allow one to update installations 
compiled from sources, new test system and some others. From time to time, this 
results in structural changes in the backyard of CCP4 suite, which cannot be 
accommodated by update mechanism

2) sometimes we have new contributions which change really a lot. For example, 
when new GUI comes to release, it will change about everything

3) sometimes, new versions of various components result in changes far beyond 
their own scope. Usually (but not always), this relates to new versions of 
phaser, cctbx, refmac and some other programs 

4) incremental updates make the Suite asynchronous on component versions. For 
example, recent phaser update resulted in duplication of cctbx, which was 
necessary in order to keep other cctbx-related components running. With time, 
this results in higher complexity and lower manageability of the suite.

I am sure that this list is far from complete, hence one more reason

5) unpredictable things happen, when updater cannot manage something.

I hope that these reflections give some insight into maters and you will be 
less disappointed by having to upgrade to 6.3.1 fairly soon :)


Best regards,

Eugene



On 20 Jan 2013, at 11:32, Kay Diederichs wrote:

 Hi Andrey, Eugene and others -
 
 it is time to say that this new system is extremely useful, and so easy to 
 use at the same time! Gone are the times when one had to worry about manually 
 updating parts of CCP4. 
 I just wonder why there should ever be a need for a CCP4 6.4.0 release; a 
 rolling update seems just adequate to me - but that's just a user's 
 perspective, and probably this has been discussed somewhere although I'm not 
 aware of it.
 
 thanks for making this available, and the hard work to make it so perfect!
 
 Kay
 
 On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev 
 andrey.lebe...@stfc.ac.uk wrote:
 
 Dear CCP4 Users
 
 A CCP4 update has just been released, consisting of the following changes.
 
 All systems:
 
 *   Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on 
 request, or when have tNCS or twinning
 *   Othercell: Various bug fixes
 *   PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex 
 situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
 empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper
 
 Linux and Mac only: *)
 
 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)
 
 *)  Corresponding changes for Windows have been already included in update 
 No 13
 
 Windows only:
 
 *   Phaser.ensembler: Corrected path to syminfo.lib
 
 
 If you do not currently receive updates, consider re-installing your CCP4 
 setup using the latest binary packages, which now have CCP4 Update manager 
 (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 
 Many thanks for using CCP4.
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.


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[ccp4bb] ccp4 update

[eugene . krissinel]

Dear Andreas,

Sorry for late response to your post and confusion with the updater. For 
technical reasons (Windows does not like names containing update :)), the 
updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin.

I hope this helps,

Eugene


Dear CCP4 maintainers,

I've come to appreciate the CCP4 update functionality, which, in our
multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update.

Update 012 removed that script with no immediately obvious replacement.
  Was that on purpose?  Is there a way of updating CCP4 from the command
line without calling CCP4i?

Thanks


Andreas


(from update.log:

[Thu Jan 3 2013 11:00:21]
Ready to make changes

  --- applying update 6.3.0-012
  --- update header read
  --- creating restore package, please wait ...
  --- done
... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed
... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed
... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed
... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed


some more blah blah)


--
 Andreas Förster, Research Associate
 Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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Re: [ccp4bb] CCP4 package and update managers: relocating installations

[eugene . krissinel]

Dear Chris,

Indeed, you cannot use Package Manager on Mac OSX for installing CCP4 in custom 
location, which is due to petty technicalities and pragmatism. However, CCP4 
can be installed in non-standard locations with raw *.dmg's downloadable from 
our web site, which is supposed to be as easy as with the PM.

In difference of Package Manager, the updater is immune to the location and can 
be used in non-standard setups.

Does this help?

Regards,

Eugene


On 16 Jan 2013, at 15:27, Chris Richardson wrote:

 Dear CCP4,
 
 While we're talking about the package and update managers, I have a question.
 
 Is there any way to install the CCP4 suite in a non-standard location under 
 OS X and still use the package manager and update facilities?  With a large 
 number of Macs it's much easier for me to have CCP4 living in a single, 
 network-mounted directory than on each machine.
 
 Under Linux, the package manager and updater allow me to put things where I 
 like.  Under OS X the package manager wants to put things in /Applications 
 and I can't edit that, despite it being in a GUI element that looks like an 
 input field.
 
 Regards,
 
 Chris
 --
 Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
 
 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
 Limited by Guarantee, Registered in England under Company No. 534147 with its 
 Registered Office at 123 Old Brompton Road, London SW7 3RP.
 
 This e-mail message is confidential and for use by the addressee only.  If 
 the message is received by anyone other than the addressee, please return the 
 message to the sender by replying to it and then delete the message from your 
 computer and network.


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[ccp4bb] CCP4 Update 013

[eugene . krissinel]

Dear CCP4 Users,


A CCP4 update has just been released, consisting of the following changes:

All systems:

  *   molrep: Significantly more accurate packing function implemented
  *   pisa: Now reports on monomeric properties ina no-complex situations
  *   JLigand: Compounds derived from smile strings are now automatically 
regularised
  *   QtRView: Improved performance on large log files, added inverse 
resolution scale in graphs, coot and ccp4mg configuration is now optionally 
imported from ccp4i settings

Linux only:

  *   Ensembler and Sculptor: Fixed file permissions in order to enable users 
other than root to use these applications

Windows only:

  *   Crank: Fix for preventing terminal windows from popping up
  *   CProdrg: HETATM notations synchronized with Refmac
  *   Pointless and Aimless: Now able to handle twice bigger datasets
  *   Scala: Corrections to plot titles
  *   Phaser: Added missing cctbx library files


If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have CCP4 Update manager (ccp4um) 
integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk


Many thanks for using CCP4.

Eugene Krissinel


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Re: [ccp4bb] Difference set of contacts

[eugene . krissinel]

CCP4 now has QtPISA, where the output is prettier than at the EBI :)

Eugene

On 6 Jan 2013, at 12:42, Eleanor Dodson wrote:

 pisa at the ebi will do this very nicely.
 
 Upload your pdb files.
 
 PISA is part of the CCP4 distribution too, but the EBI output is prettier
 Eleanor
 
 On 4 Jan 2013, at 22:11, Brad Bennett wrote:
 
 Hi all-
 I have 2 PDB files of the same protein (in slightly different states) and I 
 want to output a table of interactions (preferably hydrogen bonds, salt 
 bridges) that are unique to a structure i.e. Ser22 OG forms a hydrogen bond 
 to Lys25 NZ in structure 1 but not in structure 2. In other words, I'd like 
 to generate a difference set of contacts. Is there a way I can run NCONT or 
 CONTACT or other software (or nifty scripting) to do this?
 
 Thanks and have a nice weekend-
 Brad


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[ccp4bb] CCP4 6.3.0 update 012

[eugene . krissinel]

Dear CCP4 Users,


A CCP4 update, the last one in 2012, has just been released, consisting of the 
following changes:

* QtRView: Stability fixes and improved user experience of dynamically changing 
report pages
* CCP4 Update: Technical modifications to ccp4-6.3.0 in order to complete the 
changes introduced in update No 11
* Crank: Bug fixes in module mapro.exe (Windows only)

If you do not currently receive updates, consider re-installing your CCP4 setup 
using latest binary packages, which now have CCP4 Update manager (ccp4um) 
integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.


CCP4 Core Team wishes you a very Merry Christmas and Happy New Year 2013!


[cid:BC01B0FF-48A9-4F73-B598-537FAD429F22@rc-harwell.ac.uk]


Eugene Krissinel  Andrey Lebedev



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[ccp4bb] New CCP4-6.3.0 bundles

[eugene . krissinel]

Dear All,


CCP4 Core Team would like to inform you that ccp4-6.3.0 binary bundles, 
downloadable from CCP4 web-site, now have CCP4 Update Manager integrated. This 
means that it does not need to be installed separately any longer.

What does this mean for you?

- if you have CCP4 Update Manager installed and it works for you, you do not 
need to do anything

Otherwise,

- re-install CCP4 6.3.0 by downloading the appropriate package from our 
web-site, or by using CCP4 Package Manager

- on Linux and Mac OSX platforms, apply all available updates after 
installation using Manage Updates button in ccp4i

- on Windows platforms, updates 1 to 11 are already integrated with the bundle.


Notice for Windows users:

Starting from update 11, CCP4 Update Manager should function properly with any 
level of User Account Control settings (previously, it required the lowest 
level settings). In addition, the update contains fixes specific to Windows 8, 
therefore, the latest CCP4 6.3.0 bundle is installable on that system, too.


Many thanks for using CCP4,

Eugene Krissinel.


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Re: [ccp4bb] Error in installation of CCP4-6.3.0

[eugene . krissinel]

Dear Masaki,

I have just checked installation of CCP4-6.3.0 32 bit with Package Manager, and 
found no problems with it.

Two suggestions:

1) there are residual files from previous CCP4 installation in your temporary 
directory, which you gave to the Package Manager. Please make sure that that 
directory is empty and retry
2) you experienced an accidental data corruption during download. Please just 
retry

If, after doing (1) and (2), you still have the same problem, please contact me.

Best regards,

Eugene Krissinel.


On 17 Dec 2012, at 10:38, Masaki UNNO wrote:

Hi all

I installed Ubuntu 12.10 on my PC, today. Then I tried installing CCP4-6.3.0 on 
my system using Package Manager (32 bit) downloaded from CCP4 HP, but I failed.
On the CCP4 setup, step 5 out of 5, I received the error message as follows;
~~~
Ready to install
Selected package: Ubuntu 12.10 32-bit
===
Remove /home/X/programs/CCP4/ccp4-6.3.0
---
Decompressing CCP4 Program Suite v6.3.0, please wait ...
gzip: /home/X/programs/tmp/core2.ah.gz: invalid compressed data--crc error
~
How can I solve the problem?
Any help will be greatly appreciated.

Best regards.


~
Masaki UNNO, Ph.D.

Frotier Research Center for Applied Atomic Sciences,
Ibaraki University

Ibaraki Quantum Beam Research Center
162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
Tel: 029-352-3239, Fax: 029-287-7872
E-mail: unn...@mx.ibaraki.ac.jpmailto:unn...@mx.ibaraki.ac.jp
HP: http://www.fas.ibaraki.ac.jp/?page_id=961

~


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[ccp4bb] CCP4 6.3.0 update 010

[eugene . krissinel]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

* QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and 
ViewHKL
* Nautilus: Added a missing template pdb-file
* Hgen: Bug fix in task interface
* Acorn: Bug fix in task interface
* Crank: Bug fix in ctruncate plugin
* Monomer Library: Several entries manually curated

The easiest way to obtain the update is to install the CCP4 update client, if 
you have not done so already. Details on how to install the CCP4 Update Manager 
are available from:

http://www.ccp4.ac.uk/download/update_manual.html

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4,

Eugene Krissinel  Andrey Lebedev



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Re: [ccp4bb] fragment searching

[eugene . krissinel]

CCP4's gesamt should help you here. It can search a collection of PDB/mmCIF 
files for a structural match, any mainchain fragment with C-alphas would do.

For searching through an archive, you need to use it off-line, from a terminal 
window. Run $CCP4/bin/gesamt without parameters, it will print usage 
instructions, you need 2nd or 3rd command line template depending on how you'd 
like to specify your query fragment.

Beware that SSM/Superpose is not the best choice here and may not work at all. 
Gesamt should be reasonably fast on short fragments, I'd expect that execution 
time will be that required for opening/reading all files in the PDB :)

Hope this helps,

Eugene


On 31 Oct 2012, at 15:31, rui wrote:

Does anyone know a good way to search for a fragment matches(~16 residue long 
helix or loop) from pdb?I have a fragment of pdb and want to pull out all the 
similar structures from the pdb, any easy way to do that? Thanks a lot.



On Tue, Oct 30, 2012 at 9:34 AM, David Briggs 
drdavidcbri...@gmail.commailto:drdavidcbri...@gmail.com wrote:
Hello Adrian,

I use Research Gate and there are a few occasions where I have found
it useful, particularly the questions feature.

HTH,

Dave

David C. Briggs PhD
http://about.me/david_briggs


On 30 October 2012 16:13, Adrian Goldman 
adrian.gold...@helsinki.fimailto:adrian.gold...@helsinki.fi wrote:
 Hi,

 At the risk of starting another series of rants, and somewhat off-topic, is
 anyone actively using ResearchGate?  It is bombarding me with email
 messages, but I am uncertain as to whether people are really using it or
 whether it is just scientific spam.

 Adrian Goldman


 Adrian Goldman

 Institute of Biotechnology, University of Helsinki, Finland








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Re: [ccp4bb] CCP4superpose_only superpose interesting residues

[eugene . krissinel]

Ccp4's Gesamt (new algorithm, interfaced jointly with SSM in ccp4i) should do 
what you want -- Eugene

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zhijie Li 
[zhijie...@utoronto.ca]
Sent: Thursday, October 25, 2012 12:45 AM
To: ccp4bb
Subject: Re: [ccp4bb] CCP4superpose_only superpose interesting residues

Hi Wenhe,

Superpose allows you to specify residue (as well as Ca/main chain/side chain) 
ranges. Also in COOT you can select the range of residues used in the LSQ 
superpose calculation.

For superposing parts of the proteins only, a little trick is to cut the 
interested fragments from the original PDBs and make PDB files that contain the 
fragments only (simplest way is to edit the PDB files in a text editor) and 
superpose the fragments. If the whole proteins need to be superposed too, then 
superpose the proteins to their respective fragments. This is especially useful 
when the program does not give you options on residue ranges (for example, COOT 
SSM superpose).

Zhijie

From: WENHE ZHONGmailto:wenhezhong.xmu@gmail.com
Sent: Wednesday, October 24, 2012 6:59 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4superpose_only superpose interesting residues

Dear members,

I have one difficult task on hand and would like to ask for your advice.

I want to superpose two enzyme structures just based on several residues (e.g. 
5 residues) which we are interested in. But these two structures do not have 
similarity for overall structures. In this case, I can not really use CCP4 
Superpose to do it. May I ask do you have any idea managing to do it? Thank you.

King regards,
Wenhe

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Re: [ccp4bb] CCP4 update 6.3.0 006

[eugene . krissinel]

Dear Bill,

You have not missed anything, we do not have a mechanism for delivering source 
code *updates* in automatic fashion as yet. Our statistics shows that source 
code distributions make only 2-3% of binary downloads, therefore, I hope that 
you would understand that we have to prioritise our efforts. CCP4 is currently 
in transitional state regarding its repository system and build mechanism, so 
that not everything is in due shape, and I apologise for any inconvenience this 
is causing to you.

Current source codes are available from FusionForge at

http://fg.oisin.rc-harwell.ac.uk

just choose Project-Project List-Project Name (e.g. sfcheck) - SCM and a 
checkout command will be on the screen. These are our new repositories, but we 
have not finished migration to them yet. Codes that you do not see on 
FusionForge, are still available from CVS:

http://www.ccp4.ac.uk/cvs

We do realise that checking out sources and building them on client's side may 
be a non-trivial task to do. In order to help that, we are developing a 
completely new build system, which allows one to automatically check out CCP4 
components and build them individually or all at once with a single command. 
This is meant to be our build system for next release (hopefully), and, in 
fact, Windows part of 6.3.0 was actually built with it. I would like to 
encourage you to have a look at

http://devtools.fg.oisin.rc-harwell.ac.uk

which is a not-so-long instruction on how to use the new system. It can be used 
right away to build current source codes, so that you do not have to browse the 
repositories.

We would be highly appreciative if you give it a try and communicate your 
feedback to us. As I mentioned, things are currently being shaped, and we are 
prepared to have any suggestions. Please do not put it away if it does not work 
for you for any reason, and speak to us instead.


Responsible people, who are to be contacted for feedback/clarification/help:

New build system: Marcin Wojdyr at  marcin.woj...@stfc.ac.uk

New repositories: Charles Ballard at charles.ball...@stfc.ac.uk and/or
 Ville Uski at ville.u...@stfc.ac.uk

I hope that this clarifies the issue, but let me know if it does not.

Best regards,

Eugene




On 9 Oct 2012, at 15:09, William G. Scott wrote:

 Dear Ronan et al:
 
 I apologize if I have missed it, but is there a simple way to obtain the 
 corresponding changes in the source code for those of us who compile ccp4 
 ourselves?
 
 I looked on the web site and the ftp site but can't seem to find it.
 
 Many thanks in advance.
 
 Bill
 
 
 
 On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote:
 
 Dear CCP4 Users,
 
 A CCP4 update has just been released, consisting of the following changes:
 
 *MrBUMP: model building options added
 *PISA: new QT interface
 *AMPLE: bug fixes and expanded interface (Linux and MAC only)
 *tlsextract: correction of output format which broke parsing of output
 *DiffractionImage: corrections to reading of pilatus mini-cbf
 *ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
 launcher and bug fixes 
 *crank: bug fix (Windows only)
 
 The easiest way to obtain the update is to install the CCP4 update client, 
 if you have not done so already. Note that auto-updates will work correctly 
 only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to 
 c...@stfc.ac.uk.
 
 Many thanks for using CCP4,
 
 -- Ronan Keegan
 
 
 
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Re: [ccp4bb] residues forming the surface of a cavity

[eugene . krissinel]

Try PISA

 -- Eugene

On 4 Oct 2012, at 08:09, sreetama das wrote:

Dear all,
  Is there any CCP4 module/ other software/ web server which can 
determine which particular residues form the surface of a pocket/ binding-site 
in a protein?

Thanks in advance,
sreetama


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Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

[eugene . krissinel]

Thanks for nice question.

Currently, CCP4 update is applicable only to what is distributed as CCP4 
core, which guarantees a definite location in $CCP4 directory. Also, updates 
are not supposed to deliver releases (upgrades), but rather smallish changes 
between them.

Coot is not part of CCP4 core, and in fact, is distributed in many different 
ways, therefore, CCP4 update mechanism cannot be applied to Coot 
straightforwardly, and it is unlikely to be applicable to Coot upgrades (e.g., 
0.7 to 08).

However, the updater may be made a part of Coot package, which is something 
completely doable in principle, in which case it can deliver fixes for current 
release.

Eugene


On 1 Oct 2012, at 09:46, Dirk Kostrewa wrote:

Dear CCP4 developers,

this question might be interesting for many CCP4/Coot users:

will the Coot release 0.7 and future releases be made available to CCP4 users 
via the CCP4 software update?

Best regards,

Dirk.


 Original-Nachricht 
Betreff:[COOT] Release 0.7
Datum:  Sat, 29 Sep 2012 10:49:45 +0100
Von:Paul Emsley 
paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk
Antwort an: Paul Emsley 
paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk
An: c...@jiscmail.ac.ukmailto:c...@jiscmail.ac.uk



Hi Coot-users,

We are pleased to announce Release 0.7 of Coot.

Source:

http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz

Binaries:

http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/

Mac 10.8:

http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip


Now stick a fork in me (as they say)...

Paul.


A few notes:

  o FEATURE: RCrane [RNA builder]

  o FEATURE: Cootaneer [RNA builder]

  o FEATURE: Het-groups are now represented with bond orders.

  o FEATURE: Ligand Builder - working in conjunction with cprodrg.

  o FEATURE: JLigand interface.

  o CHANGE: symmetry operator number are no longer zero indexed. Add
trans component to symmetry file names.

  o CHANGE: Dotted surfaces now are coloured by atom type and are at
atomic radii rather than 1A.

  o CHANGE: map transformation no longer has symmetry overwrite
problems.



--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/
***





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Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

[eugene . krissinel]

We are thinking of including MG into core in one of future releases, probably 
by next summer. As to Coot, it will probably stay autonomous.

Eugene

On 1 Oct 2012, at 13:14, Dirk Kostrewa wrote:

 Dear Eugene,
 
 thank you for your kind reply and your explanation!
 
 Since the CCP4 download site offers Coot either as a stand-alone-package or 
 via the new package manager, I was hoping that new Coot releases could also 
 be handled by the wonderful CCP4 software update.
 
 A software update mechanism for Coot, be it part of CCP4 or part of Coot, 
 would help the software administrator :-).
 
 A related question just crossed my mind: when will Coot and CCP4mg become 
 part of the CCP4 core packages?
 
 Best regards,
 
 Dirk.
 
 P.S.: I've sent Paul Emsley a CC of this little conversation.
 
 
 Am 01.10.12 13:13, schrieb eugene.krissi...@stfc.ac.uk:
 Thanks for nice question.
 
 Currently, CCP4 update is applicable only to what is distributed as CCP4 
 core, which guarantees a definite location in $CCP4 directory. Also, 
 updates are not supposed to deliver releases (upgrades), but rather 
 smallish changes between them.
 
 Coot is not part of CCP4 core, and in fact, is distributed in many different 
 ways, therefore, CCP4 update mechanism cannot be applied to Coot 
 straightforwardly, and it is unlikely to be applicable to Coot upgrades 
 (e.g., 0.7 to 08).
 
 However, the updater may be made a part of Coot package, which is something 
 completely doable in principle, in which case it can deliver fixes for 
 current release.
 
 Eugene
 
 
 On 1 Oct 2012, at 09:46, Dirk Kostrewa wrote:
 
 Dear CCP4 developers,
 
 this question might be interesting for many CCP4/Coot users:
 
 will the Coot release 0.7 and future releases be made available to CCP4 
 users via the CCP4 software update?
 
 Best regards,
 
 Dirk.
 
 
  Original-Nachricht 
 Betreff:[COOT] Release 0.7
 Datum:  Sat, 29 Sep 2012 10:49:45 +0100
 Von:Paul Emsley 
 paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk
 Antwort an: Paul Emsley 
 paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk
 An: c...@jiscmail.ac.ukmailto:c...@jiscmail.ac.uk
 
 
 
 Hi Coot-users,
 
 We are pleased to announce Release 0.7 of Coot.
 
 Source:
 
 http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz
 
 Binaries:
 
 http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/
 
 Mac 10.8:
 
 http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip
 
 
 Now stick a fork in me (as they say)...
 
 Paul.
 
 
 A few notes:
 
   o FEATURE: RCrane [RNA builder]
 
   o FEATURE: Cootaneer [RNA builder]
 
   o FEATURE: Het-groups are now represented with bond orders.
 
   o FEATURE: Ligand Builder - working in conjunction with cprodrg.
 
   o FEATURE: JLigand interface.
 
   o CHANGE: symmetry operator number are no longer zero indexed. Add
 trans component to symmetry file names.
 
   o CHANGE: Dotted surfaces now are coloured by atom type and are at
 atomic radii rather than 1A.
 
   o CHANGE: map transformation no longer has symmetry overwrite
 problems.
 
 
 
 --
 
 ***
 Dirk Kostrewa
 Gene Center Munich
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone:  +49-89-2180-76845
 Fax:+49-89-2180-76999
 E-mail: kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de
 WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/
 ***
 
 
 
 
 
 
 -- 
 
 ***
 Dirk Kostrewa
 Gene Center Munich
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone:+49-89-2180-76845
 Fax:  +49-89-2180-76999
 E-mail:   kostr...@genzentrum.lmu.de
 WWW:  www.genzentrum.lmu.de
 ***
 
 


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[ccp4bb] Joint EMBL-CCP4 training course in macromolecular crystallography

[eugene . krissinel]

Dear All,

Please note that October 1st, Monday, is the application deadline for the joint 
EMBL-CCP4 training course European School for Macromolecular Crystallography 
(ESMAX). Please take this last opportunity and make your application 
electronically using the link:

http://www.embl-hamburg.de/training/events/2012/ESMAX-12/index.html

The Course will take place at the EMBL Hamburg Outstation, the DESY synchrotron 
site, during the period:

Monday November 19th to Monday November 26th, 2012.

The ESMAX-2012 school will build upon the traditions of the forefront of 
training in structural biology – the M2M workshops and the CCP4 crystallography 
schools and will include a range of activities addressing essential steps in 
determining biomolecular structures. In particular, the courses will have 
practicals on the use of synchrotron radiation and beamline equipment, sample 
handling and carrying out an experiment, followed by an intense course on data 
processing, structure solution, model building and validation using top-ranked 
software packages.

The number of places is restricted to 20.

Speakers and tutors include G. Bourenkov (Hamburg), C. Carolan (Hamburg), M. 
Cianci (Hamburg), Z. Dauter (Argonne), K. Diederichs (Konstanz), W. Kabsch 
(Heidelberg), J. Kallio (Hamburg), R. Keegan (Harwell), E. Krissinel (Harwell), 
V. Lamzin (Hamburg), A. Lebedev (Harwell), B. Lohkamp (Stockholm), W. Minor 
(Charlottesville), G. Murshudov (Cambridge), S. Panjikar (Melbourne), N. Pannu 
(Leiden), H. Powell (Cambridge), T. Schneider (Hamburg), T. Schwede (Basel), T. 
Wiegels (Hamburg).

The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan, Eugene 
Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider


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[ccp4bb] Joint EMBL-CCP4 training course in macromolecular crystallography

[eugene . krissinel]

Dear All,

This is a reminder that the application deadline for the joint EMBL-CCP4 
training course European School for Macromolecular Crystallography (ESMAX) is 
now just a week ahead (October 1st).

The Course will take place at the EMBL Hamburg Outstation, the DESY synchrotron 
site during the period:

Monday November 19th to Monday November 26th, 2012. 

The ESMAX-2012 school will build upon the traditions of the forefront of 
training in structural biology – the M2M workshops and the CCP4 crystallography 
schools and will include a range of activities addressing essential steps in 
determining biomolecular structures. In particular, the courses will have 
practicals on the use of synchrotron radiation and beamline equipment, sample 
handling and carrying out an experiment, followed by an intense course on data 
processing, structure solution, model building and validation using top-ranked 
software packages.

Speakers and tutors include G. Bourenkov (Hamburg), C. Carolan (Hamburg), M. 
Cianci (Hamburg), Z. Dauter (Argonne), K. Diederichs (Konstanz), W. Kabsch 
(Heidelberg), J. Kallio (Hamburg), R. Keegan (Harwell), E. Krissinel (Harwell), 
V. Lamzin (Hamburg), A. Lebedev (Harwell), B. Lohkamp (Stockholm), W. Minor 
(Charlottesville), G. Murshudov (Cambridge), S. Panjikar (Melbourne), N. Pannu 
(Leiden), H. Powell (Cambridge), T. Schneider (Hamburg), T. Schwede (Basel), T. 
Wiegels (Hamburg).

The number of places is restricted to 20. Applications can be made 
electronically via the link 

http://www.embl-hamburg.de/training/events/2012/ESMAX-12/index.html

The deadline for applications is October 1st, 2012.

The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan, Eugene 
Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider



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[ccp4bb] CCP4 Update

[eugene . krissinel]

Dear CCP4 Users,

Following the release of ccp4 6.3.0, CCP4 core team sets up an update mechanism 
for moderate modifications of Suite's components between the releases. It is 
expected that updates will be essential for CCP4 maintenance and will make 
patch releases less frequent or even redundant, while delivering bug fixes and 
new features much more efficiently than before. Please take a moment to install 
CCP4 update functionality as described below.

While update mechanism will be integrated in all future CCP4 releases, it needs 
to be installed manually in CCP4 6.3.0. When installed, the updater checks for 
new updates automatically, and issues a message when new updates are available. 
After that, updates can be installed in a few mouse clicks. If, for some 
reason, you find a particular update undesirable, it can be removed with 
auto-reverting your CCP4 setup to the pre-update state. Note that the update 
mechanism cannot be used with CCP4 versions lower than 6.3.0, therefore, please 
upgrade to the latest CCP4 release if you have not done it so far. For upgrade, 
proceed to CCP4 download pages at http://www.ccp4.ac.uk/download/ .

Detail update installation instructions are given in

http://www.ccp4.ac.uk/download/update_manual.html

The document may seem to be lengthy, however, installation should not take more 
than a few minutes:

1) download update client (archived) using an appropriate link in the above 
manual
2) unpack the archive into the top of CCP4 directory ( C:/CCP4/6.3/ in Windows, 
ccp4-6.3.0/ in Linux/Mac OSX)
3) run the update client (update.exe/update/Update.app) _from CCP4 directory_ 
by double-clicking on it in your file browser
4) install 1st update
5) (re-)start ccp4i, and see new Manage Updates button in the bottom-right 
corner of ccp4i window.

If this does not work for you for any reason, please (re-)read update manual 
for details. If that does not help as well, please write to us.

Thank you for using CCP4,

Eugene Krissinel.



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