[ccp4bb] Phasing@Home event

[Claudia Millán Nebot]

Dear CCP4bb community,

We are glad to announce the first Phasing@Home event, an online meeting
devoted to presenting XDS, ARCIMBOLDO, Phaser and SHELX software and their
use in challenging phasing cases.



Confirmed speakers and members of the teams:

Institut de Biologia Molecular de Barcelona (IBMB-CSIC): Isabel Usón,
Claudia Millán, Ana Medina, Iracema Caballero, Elisabet Jimenez, Albert
Castellví, Giovanna Petrillo, Josep Triviño

Cambridge Institute for Medical Research (CIMR): Randy Read, Airlie McCoy,
Rob Oeffner, Kaushik Hatti, Massimo Sammito, Tristan Croll

University of Konstanz: Kay Diederichs

University of Goettingen: George Sheldrick

Instituto de Biociencias, Universidade Estadual Paulista (UNESP): Rafael
Borges


The full schedule can be found under:
http://chango.ibmb.csic.es/phasingathome

The meeting will hosted via Zoom and is free of charge but you will need to
pre-register here:
https://www.eventbrite.co.uk/e/phasinghome-tickets-107673520398



The event will be held online on the 13th and 14th of July. Talks will be
short and focused on covering the advanced usage of the software, so
participants are expected to be familiar with the basics already or to
browse some basic material provided by us in advance. Interaction among
speakers and participants will be through a Discord (https://discord.com/)
server.


Please note that this event is limited to 25 external participants and
provided they meet the requirements of presenting some challenging dataset,
the acceptance upon registration will be on a first-come, first-served
basis.


With best wishes,



Claudia Millán and Massimo Sammito



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Re: [ccp4bb] MR for coiled coil structure

[Claudia Millán Nebot]

Dear Mark and Shengyang,

indeed, as Mark pointed out, we have a special mode in ARCIMBOLDO_LITE
devised to tackle coiled-coil structures. Trough the ccp4i interface this
will be available as an option you can tick when running an ARCIMBOLDO_LITE
job. A tutorial is available on our website (
http://chango.ibmb.csic.es/tutorial_coiled) and you can also contact us
directly if you have any questions regarding its use.

As for Mark's comment on beta structures, they are always more challenging
for a number of reasons, but we have been successful in solving some of
them using our libraries of general folds in ARCIMBOLDO_BORGES. There is
also an example on our website (http://chango.ibmb.csic.es/tutorial) but if
you have any particular question regarding parameterization or you need to
generate a library of a fold that it is still not available trough CCP4 you
can contact us and well be happy to help.

Best wishes,

Claudia




Claudia Millán (cmn...@ibmb.csic.es)

Crystallographic Methods Group

http://chango.ibmb.csic.es

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

LinkedIn: es.linkedin.com/in/claudiamillan/


ResearchGate:
https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf

Twitter: https://twitter.com/cheshireminima




El mié., 10 jul. 2019 a las 10:01, Mark J van Raaij ()
escribió:

> This sounds like a case for the Arcimboldo program developed by the Uson
> group (http://chango.ibmb.csic.es/), of which three versions are in CCP4
> (Borges, Lite and Shredder).
> This will use short secondary structure elements in a mixed MR/ab initio
> approach.
> We almost never get it to work with our well-diffracting beta-structured
> proteins :-(, but for alpha-helical proteins it apparently has a really
> good success rate.
>
> a recent paper on use of Arcimboldo for coiled coils is here:
> https://journals.iucr.org/d/issues/2018/03/00/cb5097/
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
>
>
> On 10 Jul 2019, at 10:00, Shengyang Jin  wrote:
>
> Dear all,
>
> We recently acquired a data set (2.0 A, P222) for a coiled coil protein
> (according to Itasser, QUARK, Robetta, and Phaser).
> Matthews coefficient indicates 1 copy of protein per ASU. Sequence of the
> protein is quite novel with no apparent homolog in PDB.
> We tried to to MR with various models (ab initio or homology based) but
> with little success.
>
> We then tried to use AMPLE, but in ccp4 it always returned this error:
> __main__.py: error: unrecognized arguments: -use_arpwarp True
> (if we untick arpwarp and choose buccaneer instead, it returns -use_arpwarp
> False)
>
> Could anyone help?
>
> Thank you very much.
>
>
> Shengyang Jin
> Nanyang Technological University
> Singapore
>
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[ccp4bb] ECM31 Software Fayre

[Claudia Millán Nebot]

Dear colleagues,

The ECM31 in Oviedo in approaching, and as in previous editions, there will
be a crystallographic software fayre (https://ecm31.
ecanews.org/en/software-fayre.php). The fayre will be held all 4 days of
the ECM31 during the lunch breaks, from 12:30 to 13:45h. At this event, the
developers of academic and/or open-source software will present their
latest developments and demonstrate the use of their software. All
registered participants of the Congress can attend to these sessions (no
separate registration necessary). In order to participate as a speaker,
check the available 25 min slots at http://www.cryst.chem.uu.
nl/lutz/software_fayre.html

With best regards,

Claudia Millán and Martín Lutz



Claudia Millán (cmn...@ibmb.csic.es)

Crystallographic Methods Group

http://chango.ibmb.csic.es

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

LinkedIn: es.linkedin.com/in/claudiamillan/


ResearchGate:
https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf

Twitter: https://twitter.com/cheshireminima



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Re: [ccp4bb] query about ab initio phasing about Arcimboldo_Lite

[Claudia Millán Nebot]

Dear Madhurina,

we answered this question offline, but as it may be of more general
interest I wanted to comment on the problem, which was happening with an
old ccp4 release. Arcimboldo was in the menu of the Windows interface while
there is no Windows version for any of the arcimboldo programs. It is good
to update as it eliminates known problems like this and anyway programs are
getting better all the time.
In any case, a log file and .html output will be produced straightaway,
reporting on the outcome of checks for compatibility of the version with
phaser and shelxe as well as the soundness of the input. The .html file
will be updated as the job proceeds if the program is running. Time will
depend on the hardware and parameterization but the case described should
take less than two hours.

Best wishes,

Claudia Millán



Claudia Millán (cmn...@ibmb.csic.es)

Crystallographic Methods Group

http://chango.ibmb.csic.es

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

LinkedIn: es.linkedin.com/in/claudiamillan/


ResearchGate:
https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf

Twiiter: https://twitter.com/cheshireminima



2018-02-18 13:41 GMT+01:00 Madhurima Roy :

> Dear all,
>
> I am trying to solve a crystal structure of a small protein of molecular
> weight 7 kDa. Since the molecular replacement failed I am trying to run ab
> initio phasing method Arcimboldo_lite under CCP4 suite. I have 2.4 angstrom
> dataset whose scaled mtz file has been given as input for Arcimboldo_lite.
>
> It has been two days the program still running. Can anyone tell me how
> much time does the program needs to give the result?
>
> What will be the output of the program ?
>
>
> Madhurima
>

Re: [ccp4bb] Arcimboldo, ShelxE, Windows

[Claudia Millán Nebot]

Dear Daniel,

All three Arcimboldo programs run only on Linux or Mac machines, so it is
not a problem with shelxe. We should change the appearance on the windows
interface and give a more sensible error message. Thanks for pointing it
out.

Best,

Claudia

El 8 jul. 2017 23:40, "Bonsor, Daniel"  escribió:

Dear All,


Does Arcimboldo actually run on WIndows as I can see it is installed and so
is ShelxE, but I have a warning in the GUI saying "ShelxE is not found and
option to run on 'this machine' is disabled. Is this a bug, do I need alter
something so get it to recognize ShelxE or it does not run because I am
using WIndows and I should get a Mac or Linux.


Thanks for any input or solving this problem.


(This problem is seen in arcimboldo_lite, arcimboldo_borges and arcimboldo
_shredder).


Dan


Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201

Re: [ccp4bb] MR solution for a helical protein

[Claudia Millán Nebot]

Dear Madhu,

At the resolution that you mention, which is at the edge of the resolution
limit for ARCIMBOLDO_LITE, and considering that you have already some
information about the possible fold, I would suggest you to use our tool
ARCIMBOLDO_SHREDDER, as it will derive fragments starting from your distant
homolog template, and refine them against the experimental data, increasing
the possibilities of convergence of your MR trial.

The current version of CCP4i1 has already an interface to
ARCIMBOLDO_SHREDDER, which will be updated again in the next days, and you
can use the spherical mode for your case.

Best wishes,

Claudia Millán

2017-01-02 14:34 GMT+01:00 Madhu Sudhan :

> Dear all,
>
>
>
> We are trying to solve a protein structure of 37KDa using molecular
> replacement method. Protein secondary structure indicates that it has
> 4-Heat repeat (α-helical hair pin) i.e. 16 α-helices. It has about 40%
> sequence identity  with templates in PDB, using which we tried MR, but we
> are unable to find a solution using MOLREP, PHASER, BALBES, MRBUMP, MORDA
> etc.
>
> This protein has two iron molecules also and data were collected at home
> source using Cu Ka radiation with 1.5418 A wavelength at 2.5 A resolution.
> Its highest homology PDB template is also having 16 α-helices with
> horseshoe shaped structure.
>
>
>
> We are also trying to use Arcimboldo tool (in the CCP4 7.0)  to find the
> structure solution, but it is taking a long time on our computers (8-core).
>
> So I will be grateful if anyone can provide us suggestions
>
> 1. Any program which can provide us good working model having only α-helical
> content.
>
> 2. In case we know our model, how can we optimize Arcimboldo tool with our
> helical model (we can generate from homologous PDB)
>
>
>
> Thanking you in advance,
>
>
> Madhusudhan
>

Re: [ccp4bb] Help with MR result

[Claudia Millán Nebot]

Hi Liuqing,

As Eleanor suggested, if your structure is expected to contain alpha
helices, you might
want to give ARCIMBOLDO_LITE a try, as your resolution is still within the
scope of the method.
In case you have any suspicion of the fold that might be and it contains
beta sheets,
you can try ARCIMBOLDO_BORGES with our precomputed libraries.

Good luck,

Claudia

2016-10-26 15:53 GMT+02:00 SUBSCRIBE CCP4BB Liuqing Chen <519198...@163.com>
:

> Hello!
> I have a crystal diffracted to 2Å, and have no homology structure.  As, i
> can't repeat the crystallization, so i try using Balbe and MorDa program,
> the MorDa give a partial model with Q socre 0.46,  Rwork/Rfree 0.50/0.51.
> it's hard to rebuilt using coot, and when i use Buccaner  or Arp/warp， it's
> built model worse.
> I don't know what to do?
> can anyone give me some suggestions?
> Thanks
> Liuqing Chen
>
>

Re: [ccp4bb] Phaser going into infinite loop in Ample

[Claudia Millán Nebot]

Dear Dale,

as George points out, you may be interested in trying ARCIMBOLDO, as it has
been successfully applied to coiled coil proteins recently, as in the case
of
Franke et al (2014)  Open Biology, 4. p. 130172 or  Sammito et al (2013)
Nature Methods 10: 1099-1101 . Different models can be searched for,
starting from single helices with or without sidechains, going to
precomputed libraries of helices in parallel or antiparallel configurations.

If you need help or support to use it, please feel free to ask any question.
Best wishes,

Claudia



Claudia Millán

2015-04-22 6:56 GMT+02:00 Dale Tronrud de...@daletronrud.com:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1


We are having a problem with AMPLE and hope someone can help.

The protein is about 70 amino acids long and we suspect it forms a
 coiled-coil.  Our previous attempts at molecular replacement have
 failed so we hoped that AMPLE, with its ability to generate a variety
 of potential models, would do the trick.

Our problem is that all of our CPU cores are consumed by Phaser
 jobs that are not making progress.  With this protein Phaser decides
 that it will look for 11 copies in the asymmetric unit.  For a few of
 the possible ensembles it fails to find even one copy and gives up.
 That's fine with us.  For other ensembles it finds a handful of
 possible first positions, goes on to look for a second and fails, then
 goes back to try to place a second copy again.  We presume that the
 intent is to lower the acceptance criteria in the second pass, but in
 actuality Phaser simply repeats the same search that failed before and
 fails again.  The leads to an infinite loop.

Once all the cores are occupied in this futile endeavor AMPLE makes
 no further progress.

How can we get Phaser to either try harder to place a molecule or
 to give up?

We are using CCP4 6.5.008 and the copy of Phaser that came with it.
  We used CCP4i to create a script which we modified slightly and ran
 using the at command.  The command is:

 /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
 - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
 - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
 /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
 /usr/local/rosetta-3.5 -frags_3mers
 /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
 /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
 - -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
 True -shelx_cycles 15 -use_arpwarp False

 Any help is appreciated,
 Dale Tronrud
 Sarah Clark
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Re: [ccp4bb] molecular replacement with poor model

[Claudia Millán Nebot]

Dear Ursula,

If you have a resolution around 2.0 A you can try some of the following:

- Expand the partial solution with shelxe autotracing feature.

- Do a search with ARCIMBOLDO_LITE using the partial solution. You can fin
the program at http://chango.ibmb.csic.es/arcimboldo_lite. Then, instead of
searching for ideal alpha helices, you can input your solution and search
for 2 copies.

Hope it helps. Best,

Claudia



Claudia Millán (cmn...@ibmb.csic.es)

Crystallographic Methods Group

http://chango.ibmb.csic.es

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

LinkedIn: es.linkedin.com/in/claudiamillan/
http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/

ResearchGate:
https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf



2014-12-12 22:38 GMT+01:00 Ursula Schulze-Gahmen uschulze-gah...@lbl.gov:

 I am trying molecular replacement with a very poor model. The model
 consists mainly of 1 long helix and two slightly bent antiparallel helices.
 After dividing it into 2 fragments, I was able to find a solution for one
 of the fragments ( at least I think so after looking at maps, packing,
 refinement etc). But even if I place the first solution as fixed ensemble
 in phaser, I cannot find a solution for the second fragment ( 18% sequence
 identity). From the structure of the model and the packing it seems clear
 where the fragment should go roughly.

 Are there any other programs other than phaser that might be able to solve
 this problem? I tried already epmr and mr_rosetta without success.
 I also tried to just superimpose the complete model onto the partial
 solution. This results in quite nice packing, but doesn't refine. Is there
 a rigid program refinement program with very large convergence?

 Ursula

 --
 Ursula Schulze-Gahmen, Ph.D.
 Project Scientist
 UC Berkeley, QB3
 360 Stanley Hall #3220
 Berkeley, CA 94720-3220
 (510) 643 9491

[ccp4bb] Tool for calculating RMSD

[Claudia Millán Nebot]

Hello everyone :)

I would like to know if it exist some tool that allows to calculate RMSD
between 2 pdbs that are identic, but just displaced in space. It should not
make a superposition, beause if this is the case it will just say that RMSD
is 0 .
I know is not such a difficult problem in terms of scripting, but i was
wondering if there are tools already.

Claudia Millán (cmn...@ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain