[ccp4bb] CCP4 7.1 released

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, CBuc

Re: [ccp4bb] Fwd: Refmac error

ect 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: >

Re: [ccp4bb] Trying to "digest" PISA results

720 is not an impressive size for a stable interface, but it may do depending on molecule size and exact chemistry of the interface (h-bonds, salt bridges, disulphides, charges etc etc). Everything is subject to chemical environment and concentration, as usual. For these entries, PISA gives diss

Re: [ccp4bb] Biological assembly

Dear Kavya, If I understand your question correctly, it is about the choice of asymmetric unit for your deposition. In case of dimeric asymmetric unit (ASU), there are, indeed, a few valid possibilities and you arrive to just one of them in the course of structure solution. What you decide to d

Re: [ccp4bb] Biological assembly

Dear Bostjan, >> In case when ASU has the same multiplicity (number of chains) as the >> probable biological assembly, the latter is an ASU as well. In such a >> case, the PDB suggests to choose ASU in the form of that assembly, purely >> for simplicity. It seems to me that this is not an unreason

Re: [ccp4bb] Hydrophobic interactions

google on "pisa pdbe" -- Eugene From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Luthra,Amit [alut...@uchc.edu] Sent: Wednesday, December 14, 2011 8:34 PM To: ccp4bb Subject: [ccp4bb] Hydrophobic interactions Hi Everyone I have to calculate hydroph

Re: [ccp4bb] Opinion on automation

This is actually very true, I simply want to support/enforce Liz's statement by adding that ccp4i indeed provides for both ends: from elementary scripts, useful for experts, to a rather large-scale automated processing where low-level details are not on the front page, which is more useful for a

Re: [ccp4bb] van der Waals distances

plus exchange interaction :) On 21 Mar 2012, at 13:42, David Mueller wrote: > Aren't all forces between atoms and molecules electrostatic in origin? > > > Cheers > > > > On 3/21/12 8:27 AM, "Ed Pozharski" wrote: > >> On Wed, 2012-03-21 at 10:16 +0100, Rubén Sánchez Eugenia wrote: >>> In Ph

[ccp4bb] Collaborations Workshop (CW11) on 3-4 March 2011

Posted on behalf of Simon Hettrick, The Software Sustainability Institute: If you want to use software to advance your research, the Collaborations Workshop (CW11) on 3-4 March 2011 is the perfect opportunity to meet the researchers, software developers, funders and other software experts that

Re: [ccp4bb] CCP4 for iphones

Is there a real need? Eugene On 25 Feb 2011, at 19:54, Jacob Keller wrote: > Hello All, > > is there a ccp4 app for iphones yet? Has any structure been solved on > an iphone? I know BR uses an iphone to drive his robots, but what > about structures? > > (A question for Friday afternoon...) >

Re: [ccp4bb] Ubuntu 10.10 64-bit and COOT

coot has to be installed separately, it is not included in ccp4 6.1.13. It is best to get coot binaries from Paul Emsley directly, just google on "coot emsley" and look for download pages, then choose ubuntu tarball. Best, Eugene. On 7 Mar 2011, at 18:27, Pranjal Mahanta wrote: > Hi, > I just

[ccp4bb] Scientific programmer positions at CCP4

looking for computation/IT/PX-related job and may be interested in joining us. Many thanks and best of luck to all prospective candidates, Eugene. __ Eugene Krissinel, PhD Group Leader for CCP4 Research Complex at Harwell Rutherford Appleton Laboratory Harwell

Re: [ccp4bb] PISA server

I did not see anything terribly wrong with PISA after I suggested PDBe to turn off PISA's job logging. Because of the latency of distributed file system, the log was jammed from time to time, which resulted in 10-minute delay with getting to the service (PISA is configured to try log for 10 minu

[ccp4bb] Scientific programmer positions at CCP4

. Best regards, Eugene. __ Eugene Krissinel, PhD Group Leader for CCP4 Research Complex at Harwell Rutherford Appleton Laboratory Harwell Science & Inoovation Campus Didcot, Oxfordshire OX11 0FA United Kingdom Phone: +44 (1235) 56 7725 Email: eugene.kr

Re: [ccp4bb] Fwd: superpose atom selection

Only bear in mind that superpose relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs. Eugene. On 14 Apr 2011, at 15:45, goslar wrote: > (Should have) found it! > http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection > Did not fully RTM.

Re: [ccp4bb] Histogram/Plot of Buried Surface Areas

Dear Jacob, I do not have exactly what you are asking about but some clues. I am not fond of using buried surface area as an indicator of anything in particular and always use energy estimates, however unreliable they may be. In J.Comp.Chem. 31(1),133-143, I put a probability plot for PISA to g

Re: [ccp4bb] generate large symmetry model

PDBCur (CCP4) should be able to generate the unit cell at once, which then should be translated to 3x3x3 "cube". All may be done within a single run of PDBCur, a simple keyword input is required. Same job is doable with PDBSet. Eugene On 30 Jun 2011, at 15:36, Petr Leiman wrote: > Apologies fo

Re: [ccp4bb] PISA question

Dear Tongqing No there is no such option in CCP4's PISA, but I put this on the list for further developments. Regrettably PDBe changed the interface after I moved out and I cannot help you with that. However, you may ask them to put that option back. Sorry, Eugene. On 23 Aug 2011, at 17:16,

Re: [ccp4bb] solvent excluded area and binding affinity

PISA can give you such estimate, you may try standalone pisa in CCP4 or on-line (google on "EBI PISA") Eugene On Thu, Apr 1, 2010 at 8:36 AM, Mike England wrote: > Hi All, > > I would greatly appreciate your comments on following: > > I would like to know the quantitative relation between "Solv

Re: [ccp4bb] noncovalent interactions

Depending on what exactly you are looking for, you may try PDBeMotif: http://www.ebi.ac.uk/pdbe-site/pdbemotif/ PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Eugene On Wed, May 12, 2010 at 6:02 PM, gauri misra wrote: > Hi, > Which  free online servers are best for calculation of non

Re: [ccp4bb] Structure Based Sequence Alignment

I believe SSM does just that: http://www.ebi.ac.uk/msd-srv/ssm/ Eugene On Tue, May 25, 2010 at 7:39 PM, Muhammed bashir Khan wrote: > Dear All; > > Can some body tell me a website for structure based sequence alignment, > which can also pin point the similar and identical residues in different

Re: [ccp4bb] BSA

PISA's interface area is 1/2 of sum BSAs for the interfacing structures. If you go to interface details, you also get total area of structures and their individual BSAs. The latter I should think would be an overinterpretation if used. Eugene. On Wed, May 26, 2010 at 1:45 PM, Sollepura Yogesha

Re: [ccp4bb] which software can calculate binding energy

In addition to what was rightly said, the problem is actually on both, theoretical and experimental, ends. What is taken as "experimental value" is not very well defined, and figures may vary quite significantly, simply because enthalpy change depends on the precise chemical environment your protei

[ccp4bb] Biotherapeutics Postdoc opportunity available (Pfizer)

On behalf of Dr. Sandeep Kumar (Pfizer): Pfizer Inc: Working together for a healthier world Founded in 1849, Pfizer is the world's premier biopharmaceutical company taking new approaches to better health. We discover, develop, manufacture and deliver quality, safe and effective prescription medici

Re: [ccp4bb] quaternary structure comparison

Dear Eike, depending on what your structure is - you can try interface search in PISA (google on "ebi pisa"). Select the most "representative" interface in your complex (the one that makes the non-standard arrangement) and see whether there are similar interfaces in the PDB. It shouldn't be a too

Re: [ccp4bb] Rosettadock/Robetta server Interface analysis

2. If there is another method of predicting binding affinities in silico you may want to have a look at PISA (google on "EBI PISA") Eugene

Re: [ccp4bb] Active site similarity search

PDBeSite was designed for this, see http://www.ebi.ac.uk/pdbe-site/PDBeSite/ Eugene On Fri, 10 Jul 2009, Raja Dey wrote: Hi, Sorry for asking a non-ccp4 question. Is there any way to mine the PDB to accumulate the structures which have similar binding site(ligand binding pocket) with t

Re: [ccp4bb] Active site similarity search

yes, you can upload a custom file there. Eugene. On Fri, 10 Jul 2009, Raja Dey wrote: Thanks to Eugene. I got an idea how to search PDB against a query structure locally. Raja From: Eugene Krissinel To: Raja Dey Cc: CCP4BB@jiscmail.ac.uk Sent: Friday

Re: [ccp4bb] Van der Waals contacts

I may have missed the original question, but the significance of VdW interactions in general should hugely depend on the context. Let's say, I would expect VdW in protein interfaces to have little effect, because it gets compensated, on average, by VdW with water molecules in dissociated state. Th

Re: [ccp4bb] LINKR in refmac

Ian, Perhaps someone from one of the PDB deposition sites could comment and verify my reading of this? let me take the liberty. Your reading of PDB documentation is absolutely correct. PDB format has got 3 types of links: SSBOND, LINK and CISPEP. And indeed, residue numbers have no significanc

Re: [ccp4bb] LINKR in refmac

Hi Ian, I may be wrong here, in which case Jawahar will correct me. I understand that to mean that it's the *order* of residues that must be identical, not the residues themselves, i.e. it's valid for residues to be omitted from the co-ordinate section (but not of course from the SEQRES section

Re: [ccp4bb] LINKR in refmac

If I were to deal with your example, I would look into distance profile between residues in coordinate section, which then gives answer to your question. OK that's interesting, I hadn't realised that the interatomic distances played an active role in determining connectivity: I had assumed the w

Re: [ccp4bb] Protein Protein interactions

Mariah, you may want to try PISA at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Eugene On Mon, 17 Aug 2009, protein.chemist protein.chemist wrote: Hello All, Can anyone tell me what are the programs used to find out the different interactions in a protein. I am talking about both int

Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface

Hello, PISA gives you quite a lot of information on hydrophobic interactions, down to atomic level (subject to interpretation). In the list of interfaces, PISA gives just the sum hydrophobic effect for each interface. If you click on interface number, it will take you to further details for the i

Re: [ccp4bb] Contact Surface Area

PISA reports ASA/BSA on residue level as well. Internally, it keeps information on atomic level (including ASA/BSA "per atom"), but the atom-level output was never done. The reason is, I could never imagine that such level of description has any good meaning. "Surface area" is an abstraction for _m

Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment

On Sun, Oct 18, 2009 at 10:00 AM, Shaun Lott wrote: > In my experience, DALI can be better than SSM at detecting distant > structural similarities. this is interesting. Do you take into account that, in difference of DALI, SSM has a control on the remoteness of structural hits that it delivers?

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

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

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: Volu

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

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 > Cc: > Subject: Re: [ccp4bb] CCP4 pac

[ccp4bb] 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 mailto:eugene.krissi...@stfc.ac.uk>> Date: 12 July 2013 12:47:26 GMT+01:00 To: mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [

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

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

Re: [ccp4bb] mmCIF as working format?

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 w

Re: [ccp4bb] mmCIF as working format?

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

Re: [ccp4bb] mmCIF as working format?

ISCMAIL.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 w

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

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 an

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

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

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

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

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

t; 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. > &

Re: [ccp4bb] CCP4 Setup manager

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 runni

[ccp4bb] CCP4 Release 6.4.0 out

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.php The release is avail

Re: [ccp4bb] CCP4 Release 6.4.0 out

o-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 > wrote: > >> Dear CCP4 Users, >> >> >> The CCP4 Core Group is very pleased t

Re: [ccp4bb] CCP4 Release 6.4.0 out

v University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il<mailto: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 mailto:eugene.krissi...@stfc.ac.uk>> wrote: Dear CCP4 Use

[ccp4bb] CCP4 Release 6.4.0 follow-up

ny problems with CCP4 software that they have encountered. Sincerely yours, Eugene Krissinel -- Scanned by iCritical.

Re: [ccp4bb] Conflicting Qt on OS X 10.6

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

Re: [ccp4bb] Comparison of Water Positions across PDBs

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

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

nnouncement or until new updates are reported available by your ccp4i. Many thanks, Eugene Krissinel Begin forwarded message: From: Andrey Lebedev mailto:andrey.lebe...@stfc.ac.uk>> Date: 6 November 2013 12:52:31 GMT To: mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Joint CC

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

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 Co

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

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, discont

Re: [ccp4bb] Coot error

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 a

Re: [ccp4bb] PyMol and Schrodinger

> 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 a

Re: [ccp4bb] PyMol and Schrodinger

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 se

Re: [ccp4bb] Superpose

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 s

Re: [ccp4bb] Superpose

)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 : > >> I would say the guess is a wrong one. SS superposition is used only as a >

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

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 s

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

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

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

nt of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il<mailto:mbfro...@post.tau.ac.il> Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 3, 2014, at 14:47 , Eugen

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

ww.cnb.csic.es/~mjvanraaij > > > > > > On 3 Jun 2014, at 13:47, Eugene Krissinel 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 >> o

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

n tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel 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 > origina

Re: [ccp4bb] CCP4-6.4.0 Update 018

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 t

[ccp4bb] Scientific programmer position at CCP4 Core Group

/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

[ccp4bb] Scientific Programmer Position at CCP4 Core Group

- 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

[ccp4bb] CCP4 Workshop at ECM-32

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

[ccp4bb] CCP4 Computational Scientist

, 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

[ccp4bb] PISA server @ CCP4

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. -- Scanned by iCritical.

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

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

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

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 fou

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

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

Re: [ccp4bb] superpose bug?

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 m

Re: [ccp4bb] superpose bug?

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, ra

Re: [ccp4bb] asymmetric homotrimer in the asu

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). Per

[ccp4bb] CCP4 Release 6.5

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] CCP4 Release 6.5

e; 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 a

Re: [ccp4bb] RMSD of dimers

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

[ccp4bb] CCP4 6.5 Windows-32

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.

[ccp4bb] CCP4 Scientific Programmer Position at CCP4 Core

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

[ccp4bb] CCP4 Scientific Programmer Position at CCP4 Core Group

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

[ccp4bb] CCP4 6.3.0 release

Dear All, We're very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.3.0 (Settle) 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, and delivers a

Re: [ccp4bb] Structure alignment

Dear Theresa, You could use Gesamt from CCP4 6.3.0, which will align a given range of residues in one protein onto a range of residues from another protein. Just run $CCP4/bin/gesamt for usage instructions and selection syntax, or use Structure Superposition from CCP4i. Best, Eugene On 23 J

Re: [ccp4bb] Angle between monomer of a dimer

I believe $CCP4/bin/superpose does the same Eugene On 24 Aug 2012, at 11:44, Paul Emsley wrote: > On 23/08/12 20:08, Nikolina Sekulic wrote: >> Dear Appu, >> >> I had similar issue once. You can use Coot to overlay two structures and get >> the rotation matrix >> >> a1 a2 a3 >> b1 b2 b3 >>

[ccp4bb] CCP4 Update

ight 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. -- Scanned by iCritical.

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

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 -- Scanned by iCritical.

[ccp4bb] CCP4 Updates

lease 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, Eugene Krissinel. -- Scanned by iCritical.

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

an 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 -

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

bourne), 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 -- Scanned by iCritical.

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

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 CCP

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

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 s

Re: [ccp4bb] residues forming the surface of a cavity

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 -- Scanned by iCr

Re: [ccp4bb] CCP4 update 6.3.0 006

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 ou

Re: [ccp4bb] CCP4superpose_only superpose interesting residues

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 Subj

Re: [ccp4bb] fragment searching

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 u

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