Re: [ccp4bb] Possible sulphate
Rex Palmer wrote: What seems to be a possible sulphate has been identified in our electron density. What steps could/should be taken to confirm or consolidate this assignment that would satisfy referees? Rex Palmer Birkbeck College If you place a sulphate and it refines in a sensible way - temperature factors for the group more or less agreeing that is good. Is there a decent set of H bonds? Was there sulphate available in the medium? is there a anom peak marking the S position - but you need good data to hope to find this - you can verify quality by checking all other S in the crystal Eleanor
Re: [ccp4bb] Phasing statistics
You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179
Re: [ccp4bb] Follow up to TLS, NCS and refinement
A thought - are these molecules related by a non-crystallographic translation involving 0.5 along any axes. In such a case it is easy to get the space group wrong, and assign a 1 axis when it is really only a pseudo 21. if that happends your refinement will stick.. I think that at that resolution you should keep on NCS restraints till the model is complete, but maybe relax them once it is all built. it is always tricky though to decide on the best protocl.. Eleanor Daniel Bonsor wrote: Hello again! Following my previous question, there was something wrong with the staring model for molecular replacement. Now that is sorted, I have 8 complexes in the ASU. After a few rounds of refinement with NCS and isotropic Bfactors, both the Rfactor and Rfree get stuck at 30% and 36%, respectively. I have only just noticed that I am trying to model ~43000 atoms with ~95000 unique reflections (98% complete, at 2.58 Angstrom resolution). Is this the reason why the R factors are stuck and I should start the refinement again from scratch using overall Bfactors with NCS and switch to TLS once my Rfactor is less than 30% and possibly reduce the number of reflections used for Rfree (currently using the standard CCP4 5%) Any input would be greatly appreciated! Dan
Re: [ccp4bb] applying B_factor and scale correction to an MTZ
I thought truncate applied the scale but not the B value. you can use CAD to apply a scale - see the documentattion.. And yo can rerun truncate to check that you now have a fle with B =0, nd scale = 1.. but why do you want to do that? All refinement will rescale your output Fs to the model more reliably than a Wilson plot. Eleanor Francois Berenger wrote: Hello, Is there a tool to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file? After applying these corrections, is there another way than redoing wilson to check that the output MTZ is on absolute scale? Thanks a lot, Francois.
Re: [ccp4bb] Phasing statistics
Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] Phasing statistics
I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. On 12/04/2010 12:10, Anastassis Perrakis wrote: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] Phasing statistics
Hi Tassos, my personal opinion is, that I would like to see the usual phasing statistics. At least to me, they provide hints how well the structure was determined, analogous to the R-factor/Free-R-factor providing hints how well the structure was refined. It would be good if SHELXE would print out those statistics before any density modification. Best regards, Dirk. Am 12.04.10 13:10, schrieb Anastassis Perrakis: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Phasing statistics
Hiya Frank Well my take on it would be that they did a certain experiment - which includes phasing datasets - and we have an expectation to see all the steps reported. Good structures are not the 'be all' and 'end all'. Reporting data is not merely to convince readers that this is not a 'made up' structure. It is like in mathematics when you don't just report the correct answer but your 'show your workings' as my old maths teacher used to say. So maybe phasing statistics are pretty important in that respect. And it would be good to have datasets with experimental phases deposited. I should've done this with my 1e3h years ago as the experimental phases (which, as I recall, you were a friendly advisor on ;) were included in the refinement target (CNS mlhl). SeMet phases are usually good - but ones from other heavy atoms it might be nice to see too. There used to be a heavy atom database for such like things - not sure of the current status of that. see you all the best Martyn Martyn Symmons Cambridge From: Frank von Delft frank.vonde...@sgc.ox.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 12 April, 2010 12:24:50 Subject: Re: [ccp4bb] Phasing statistics I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. On 12/04/2010 12:10, Anastassis Perrakis wrote: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] OCA Search System is Alive and Searching
With OCA your program/script can, for example, - GET PDB ON-HOLD structures related to tuberculosis http://oca.weizmann.ac.il/oca-bin/ocaids?hl=TUBERCULOSIS - GET structures that contain ligand BTN and that belong to Author Freitag http://oca.weizmann.ac.il/oca-bin/ocaids?m=du;ht=BTN;au=Freitag OCA is a powerful, fast returning, scriptable Search Engine and Database that allows programmatic access to structure/function data integrated from several databases (PDB, OPM, SGKB, OMIM, etc), updated weekly. The complete list of data sources is available at http://oca.weizmann.ac.il/oca-docs/sources.html For the programmatic user, the complete list of current parameters to select data and formats, including simple examples, is available at http://oca.weizmann.ac.il/oca-docs/faq.html . If your application requires other modes, data or features, please write to o...@weizmann.ac.il For the human user, OCA's web interface provides intuitive access to data from an interface viewable with Any Browser. Please report problems or send special requests to o...@weizmann.ac.il As of today, OCA is being mirrored on 29 sites worldwide. If you want to become an OCA mirror or simply to run your own local copy, learn how to at http://oca.weizmann.ac.il/oca-docs/download.html -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D)
Re: [ccp4bb] Phasing statistics
As Tassos correctly says, the 'usual phasing statistics' are utterly irrelevant to phasing a structure with SHELXE. SHELXC/D/E adopt a minimalist approach, and input and calculate only what is needed to get a map that is good enough to interpret. For example, in order to calculate RCullis one would need to know the exact composition of the crystal and the f values of all the elements present, information that may well not yet be known correctly. Rather than printing a value that should probably be changed later and is not used in the phase determination, I prefer not to calculate it at all. By chance a paper Experimental phasing with SHELXC/D/E: combining chain tracing with density modification has just appeared as Open Access: Acta Cryst. D66 (2010) 479-485. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 12 Apr 2010, Dirk Kostrewa wrote: Hi Tassos, my personal opinion is, that I would like to see the usual phasing statistics. At least to me, they provide hints how well the structure was determined, analogous to the R-factor/Free-R-factor providing hints how well the structure was refined. It would be good if SHELXE would print out those statistics before any density modification. Best regards, Dirk. Am 12.04.10 13:10, schrieb Anastassis Perrakis: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone:+49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de ***
[ccp4bb] chi1 definition in proteins
Dear ccp4 users, I have found contadictory classifications in side-chain dihedral chi1, namely for gauche(+) and gauche(-), and I would like to know the actual convention. It seems that in general for polymers G- (gauche(-) ?) and G+ (gauche(+) ?) correspond to dihedral angles -60 and +60 degrees, according to http://goldbook.iupac.org/C01088.html, but I also find exanples where chi1 is defined by dihedral N-CA-CB-CG with gauche(-) and gauche(+) corresponding to dihedral angles +60 and -60 degrees (reversing the IUPAC naming above). Does anyone knows what is the accepted convention ? A reference? Thanks. Carlos -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt www.itqb.unl.pt
[ccp4bb] Postdoctoral position at the Scripps Research Institute
Please bring this position to the attention of anyone in your lab who might be interested. Thanks, Kendall The Scripps Research Institute Palm Beach Co, Florida Post-doctoral Position: Nuclear Receptor Signaling and Structure-Based Drug Design The Scripps Research Institute has established a major science center in Palm Beach County, Florida, focusing on biomedical research, technology development and drug design. A post-doctoral fellowship position is available to study nuclear receptor signaling and structure based drug design in the laboratory of Associate Professor Kendall Nettles. Candidates should have a PhD degree and experience in protein crystallography and/or a good background in molecular biology and protein biochemistry. The laboratory is equipped with robots for high throughput cloning, protein purification, solution mixing and crystallization, and automated crystal visualization. The institute has a home source, and dedicated time at SSRL and APS. We use a variety of structural and molecular approaches to understand the connections between small molecule ligand, receptor structure and function, and endocrine physiology. Ongoing projects include investigation of the structural basis for tissue and pathway specific signaling through the estrogen and glucocorticoid receptors, signal transduction across the RXR heterodimer interface, and structure-based drug design. The fellow will interact closely with the Drug Discovery, Advanced Technology, and Genomics groups at Scripps Florida to take advantage of other automated technologies, including robots for small molecule screening and transfection. Please send curriculum vitae, a brief statement describing research experience and scientific interests and the names of at least two references to: Kendall W. Nettles, PhD Associate Professor, Department of Cancer Biology The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 Email: knett...@scripps.edu
Re: [ccp4bb] Phasing statistics
Hi Dirk - I am afraid I still don't agree and will try to defend my thesis a bit further. First, as eorge explained why in SHELXE these things are meaningless anyway, so the answer to that referee is simple: SHELXE that was used for calculating phase probabilities; that precludes reporting of conventional phasing statistics as explained by the software authors (cite paper) (no need to look at my course notes any more now that the paper is out, thanks George!) I also just had a look in my PhaserEP log file. I could not find PP and Rcullis. So what? I did nto even miss them in the first place. Should I get worried I did not solve the structure? Should any of you get worried about it? Its 2.2 A data, all of it got autobuilt, Rfree is 21%, 98% molprobity percentile. On top, although FOM is supposed to be an estimate of the cosine of the phase error ... some programs estimate it well, and others less well. There is some interesting literature, that even the programs that I thought are doing it really well, were not doing it that well in SAD cases (even if I find this 'semantics' in some extent). As for Frank's argument, I fully agree low resolution cases are a different ball game (talking about ball games, I usually agree with Frank, he is much bigger than me, and its healthier to agree with him, since I play football with him one every two years at the Gordon). A 4 A case, or anything below 3.0-3.2 A, warrants very careful documentation of how maps were calculated, since its the quality of the experimental maps rather than quality of the refinement that will likely dominate model quality. For higher resolution were nearly complete models are autobuilt from the modified maps, i find the reporting of anything more than the FOM (to satisfy my curiosity) a bit of a nuisance. Best - tassos On Apr 12, 2010, at 13:58, Dirk Kostrewa wrote: Hi Tassos, my personal opinion is, that I would like to see the usual phasing statistics. At least to me, they provide hints how well the structure was determined, analogous to the R-factor/Free-R-factor providing hints how well the structure was refined. It would be good if SHELXE would print out those statistics before any density modification. Best regards, Dirk. Am 12.04.10 13:10, schrieb Anastassis Perrakis: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- *** Dirk Kostrewa Gene Center,
Re: [ccp4bb] Phasing statistics
Frank- Are you referring to our colleagues personal qualities, or the projects on which they work? :) From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Frank von Delft (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Phasing statistics
Hi Tassos, On Mon, Apr 12, 2010 at 04:10:57PM +0200, Anastassis Perrakis wrote: As for Frank's argument, I fully agree low resolution cases are a different ball game (talking about ball games, I usually agree with Frank, he is much bigger than me, and its healthier to agree with him, since I play football with him one every two years at the Gordon). I agree too ... especially since big Frank is sitting 2 metres away from me right now ;-) A 4 A case, or anything below 3.0-3.2 A, warrants very careful documentation of how maps were calculated, since its the quality of the experimental maps rather than quality of the refinement that will likely dominate model quality. In those cases I find an overall value always less meaningful than a more detailed break-down versus resolution (similar to SHELXC output - which would be my preferential stat to be reported for SHELXC/D/E solved structures). Often, a 3A dataset might only have meaningful heavy atom phases to 4-5A - and then the whole procedure for calculating maps, density modification, NCS averaging, automatic building etc becomes quite impoprtant. After all, a missing domain in those cases might just be due to very poor initial heavy atom phases that were misleading density modification procedures into flattening it away. So a good description of the procedure is even better (even if it is only in supplementary material) than just a number in some table 1. I like the phasing power statistics as three numbers: - what is the value in the lowest resolution range It often shows issues with overloads, poor beamstops etc - which can be a big problem later on. - at what resolution does it drop below 1.0 This gives me an idea what the initial, purely heavy-atom phased map will look like (and how one can improve the phases to the full resolution of the data). - overall value Not very useful, I find. For higher resolution were nearly complete models are autobuilt from the modified maps, i find the reporting of anything more than the FOM (to satisfy my curiosity) a bit of a nuisance. Yes (although I still like the phasing power better - but this looks quite different for different phasing programs I guess). As long as it isn't the FOM after density modification which can be highly overestimated. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Phasing statistics now and once
Well, Frank, your membranous by their science (not very frequently) colleagues will say - first of all look on the properly calculated electron density maps first of all - good map will be manifested by continuity, shape, accordance to the secondary structure elements etc. For us/them (membranous colleagues) evolution of many one-number qualifiers such as PP and FOM (very important), Rcullis (less important) during phasing progress was/is absolutely necessary parameters to observe to guide phase development . Values of the standard deviations of differences between heavy atom and protein phases are important to judge the validity of the phases, they should be ideally 51.96 and 90 (in degrees) for non-centric and centric reflections respectively (Maybe Eleanor will remind us a source of these numbers). They correlate with linear and exponential parts of the scale factors. These values are calculated and printed by MLPHARE, which recently is forgotten, ignored and even despised by many newcomers. BTW MLPHARE was one of the first phasing program that properly calculated FOM (usually low) and not overestimated , ready to please crystallographer (usually high) FOM, accompanying non-interpratable electron density map. Many excellent phasing parameters are also supplied by SHARP, a vintage brand tool for the manual development of phases in extremely difficult cases. Rumors also claim the superiority of phasing and reported phasing statistics in HKL3000. To conclude: For automatique protein structure solutions cases - who cares about one number qualifiers? Good auto-tracing algorithms will never trace wrong structure. It you get your structure from ARP/wARP it is most probably correct. However, for cases that usually go to the most prestigious journals (reciprocality of resolution - impact factor can be observed frequently), the demand for several well defined parameters that will properly describe overall quality of phasing should be revived to bring back from dusty pages of complementary materials concise, but full description back into the main pages. And if there is no place for that according to the publishers policies, publish in journals such as Acta Crystallographica, that provide such place. When authors claim experimental structure solution - ALL experimental data used for phasing, such as heavy atom derivative data sets with anomalous signal in them, complete MAD and SAD data, heavy atom coordinates etc. that will give ability TO RE-SOLVE the structure MUST BE deposited in PDB or elsewhere. Who knows, maybe by availability of the data, decorations even higher than publication in prestigious journals will be shaken and snapped off from the gleaming uniforms of the royal hussars, or even will not be given in the first place, to clean the protein crystallography from the reappearing stench of forgery, intentional or not - alike. 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: ++972 547 459 608 On Apr 12, 2010, at 14:24 , Frank von Delft wrote: I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. On 12/04/2010 12:10, Anastassis Perrakis wrote: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the
Re: [ccp4bb] Phasing statistics now and once
I like the ideal of calling SHARP 'vintage'. ;-) Indeed, it gets better by the time, but at the same time i like having a sip or two all the time, and not wait for it to really mature! Maybe Gerard can hint if major releases of SHARP are always coinciding with good years in the valley of Bordeaux. On the other hand, I must say that in my view 'resolving' the structures in the PDB would have little to benefit from knowing the experimental phases. Having the 'native' data available is the major need there and we have achieved 99% last year. What I would love to be able to deposit is images - if nothing else I would know were to look for them ten years down the row ... A. On Apr 12, 2010, at 17:04, Felix Frolow wrote: any excellent phasing parameters are also supplied by SHARP, a vintage brand tool for the manual development of phases P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] Zalman and coot: flipping polarisation?
Dear all, we recently purchased a couple of Zalman monitors. While on machines with an NVIDIA Quadro FX580 (Debian Stable), installation was simply plug-and-play, one machine with a NVIDIA Quadro FX1700 (Debian Testing) the sense of rotation by dragging the mouse is inverted: while moving the mouse down, the front face of molecular and map seem to move up. The effect is inverted and corrected by flipping the glasses, i.e. by using the left-eye glass on the right eye and vice versa. The effect is also corrected by dragging the window to its maximum size instead of using the maximising button. And according to the user it is even structure-dependent, i.e., with some PDB-/ MTZ-files it works correctly, with others it works invertedly. Some wikis on the web describe the solution by moving the window by a pixel. Is there by now a way to automatically invert the polarisation state so that one can use the maximised window? Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] job opportunity: protein expression scientist, Glasgow UK
Please direct applications to the email address below. Thanks, Andrew Protein Expression Scientist Starting Salary: £22,100 to £37,100 depending on experience The Beatson Institute Drug Discovery Programme will become established as an Industry Standard Unit, exploiting world class research within the Beatson Institute, the Cancer Research UK network and beyond to discover novel anticancer therapies. Fragment screening by NMR and SPR, structure-based design and high throughput assay will be critical to success. We are seeking an experienced protein expression scientist to design and execute protein expression and purification strategies to enable in vitro screening, structural biology, NMR and biophysical methods. Duties and Responsibilities: *Vector design and cloning in E.coli and baculovirus expression systems, coordination of external gene synthesis requests. *Expression and purification in milligram quantities of protein for crystallisation, NMR, biophysical methods and in vitro assays *Efficient maintenance of SOPs and lab book records Qualifications and Experience/Skills *BSc/MSc in a biological science with a minimum of 3 years hands-on experience of cloning, expression and purification or a relevant PhD with a minimum of 2 years experience as described. *Familiarity with requirements of SPR, NMR (including expression of labelled proteins) and protein crystallisation would be an advantage as would crystallisation experience. *Good communication and teamworking skills *Ability to coordinate multiple projects in parallel Applications with CV and names of three referees should be sent to Drug Discovery Programme, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD or by email to beat...@beatson.gla.ac.uk Closing date for applications is 30 April 2010.
[ccp4bb] How to show ligand in the protein pdb as sticks..??
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[ccp4bb] How to show the ligand in my protein as sticks....???
Dear all i'm trying to show ligand which is in the pdb of my protein as sticks, but it is showing the folowing message in the pymol Tcl/Tk GUI. You clicked /1204//X/TL1`0/C10 Selector: selection sele defined with 45 atoms. but it not responding to that command. can any one help..?? thank you. Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
Hussain, You can do a couple things. (1) At the PyMOL command line type: as sticks, organic (2) Create an organic selection using the mouse via the object menu, A Generate Selection Organic. PyMOL makes a new selection for you (if there is at least one organic small molecule). Then, from the new selection select S As Sticks. By the way, A Generate Selection means select A for your protein of choice, then from that menu select Generate then Selection, ... and so on. Hope this helps, -- Jason On Mon, Apr 12, 2010 at 2:15 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear all i'm trying to show ligand which is in the pdb of my protein as sticks, but it is showing the folowing message in the pymol Tcl/Tk GUI. You clicked /1204//X/TL1`0/C10 Selector: selection sele defined with 45 atoms. but it not responding to that command. can any one help..?? thank you. Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
--- On Mon, 12/4/10, Jason Vertrees jason.vertr...@schrodinger.com wrote: From: Jason Vertrees jason.vertr...@schrodinger.com Subject: Re: [ccp4bb] How to show the ligand in my protein as sticks??? To: Hussain Bhukyagps hsn...@yahoo.com Cc: CCP4BB@jiscmail.ac.uk Date: Monday, 12 April, 2010, 6:33 PM Hussain, You can do a couple things. (1) At the PyMOL command line type: as sticks, organic (2) Create an organic selection using the mouse via the object menu, A Generate Selection Organic. PyMOL makes a new selection for you (if there is at least one organic small molecule). Then, from the new selection select S As Sticks. By the way, A Generate Selection means select A for your protein of choice, then from that menu select Generate then Selection, ... and so on. Hope this helps, -- Jason On Mon, Apr 12, 2010 at 2:15 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear all i'm trying to show ligand which is in the pdb of my protein as sticks, but it is showing the folowing message in the pymol Tcl/Tk GUI. You clicked /1204//X/TL1`0/C10 Selector: selection sele defined with 45 atoms. but it not responding to that command. can any one help..?? thank you. Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 Dear Jason Vertrees, my ligand is a metal complex. I followed the way you suggested me, but still i'm not able solve it. by the way i generated new selection but it is not working for lines and sticks. it is working with spheres and dots and also nb_spheres etc.. thank you Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
Dear Jason Vertrees, My ligand is a metal complex. i followed the way u suggested to me, but still i'm not able to solve it. it is working for spheres, dots, nb_spheres etc.. But not sticks and lines. By the way i'm able to generate thank U... Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
Hussain, Spheres, dots, non-bonded spheres are for atoms. Sticks and lines show bonds. This indicates that your metal isn't bound to anything. If you like, feel free to send me the file or a snippet of it and I'll take a look. PyMOL does have some weirdness when it comes to figuring out proper bonding, especially in things like heme groups: you might have to do some bond-editing yourself. Good luck, -- Jason On Mon, Apr 12, 2010 at 3:14 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear Jason Vertrees, My ligand is a metal complex. i followed the way u suggested to me, but still i'm not able to solve it. it is working for spheres, dots, nb_spheres etc.. But not sticks and lines. By the way i'm able to generate thank U... Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
[ccp4bb] Need isolated crystals
Dear all, I am getting protein crystals in clusters. How can I achieve isolated crystals. Thanks Amit Sharma
Re: [ccp4bb] Need isolated crystals
One way to separate crystal cluster is to poke them with a tiny probe, e.g. Hampton Research HR-217. Then scoop up a single crystal or large fragment for screening/data collection. Cheers. On 4/12/2010 3:31 PM, Amit Sharma wrote: Dear all, I am getting protein crystals in clusters. How can I achieve isolated crystals. Thanks Amit Sharma -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Need isolated crystals
Have you tried anything, yet? The list of answers can be quite long. A couple of keywords: - micro-seeding - macro-seeding - cross-seeding - additive screens - extend to purification protocol - change temperature, pH, etc. - have you search around the current conditions ... if you describe a little what you have done so far we can also get an idea of your status of experience and adapt the answers accordingly. Kind regards, Tim On Tue, Apr 13, 2010 at 01:01:29AM +0530, Amit Sharma wrote: Dear all, I am getting protein crystals in clusters. How can I achieve isolated crystals. Thanks Amit Sharma -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
