Re: [ccp4bb] DNA interaction 2D plot software
Hi, NUCPLOT is good. You could also try: http://utdallas.edu/~hnam/software.php#NuProPlot Sid Dr K S Sidhu Department of Biochemistry 1/61 Henry Wellcome Building Lancaster Road Leicester LE1 9HN Tel: 0116 229 7237 On 16 Oct 2013, at 20:35, Nicolas Foos nicolas.f...@afmb.univ-mrs.fr wrote: Hello, you can try Nucplot. http://www.ebi.ac.uk/thornton-srv/software/NUCPLOT/ Very usefull and tunnable to find and show dsDNA/protein complex. Hope to help. Nicolas Le 16/10/13 21:23, Eike Schulz a écrit : Hello everyone, I would like to display the interactions of a protein dsDNA complex in a simplified 2D plot, similar to what LIGPLOT does for protein ligand interactions. In many articles you find interactions displayed in such a way but as far as I know those are hand-made. In my experience LIGPLOT itself is suboptimal if there are too many interactions to display … Thanks a lot in advance for your suggestions. Eike
[ccp4bb] Vacant position in structural biology at the Department of Drug Design and Pharmacology, University of Copenhagen
Please see announcement below that can also be seen at http://www.ku.dk/english/available_positions/vip/ as Post doctoral position/assistant professor with application deadline November 1. If you wish to apply, you will need to use the link above to the electronic application system. All the best wishes Michael Gajhede Post doctural position/assistant professor Identification of compounds that are potential drugs targeting the putative breast cancer oncogene KDM5B The Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences at the University of Copenhagen is offering a two-year post doctoral position/assistant professor withinIdentification of compounds that are potential drugs targeting the putative breast cancer oncogene KDM5Bcommencing January 1 2014 or soon thereafter. The project is a collaboration between Assoc. Prof. Henrik Franzyk from the Natural Product Research group and the Chromatin Modifications group from Biostructural Research, both units located at the Department of Drug Design and Pharmacology. Brief project description The project aims at the identification of new peptide- and oligonucleotide-based scaffolds for potential drugs targeting the histone demethylase and putative oncogene KDM5B. The position will be anchored at the Biostructural Research section, Department of Drug Design and Pharmacology, University of Copenhagen. The Biostructural Research section provides the basis for structural and functional studies of a wide range of different proteins involved in health and disease. Further information For further information, please contact Professor Michael gajhede...@sund.ku.dkmailto:m...@sund.ku.dk, tel. +45 3533 6407. Qualifications required The preferred applicant will be an experimentally oriented scientist who preferably has experience with structural biology and enzymatic assays. The applicant should also have an interest in peptide chemistry. Terms of employment The terms of employment and payment are according to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. As an equal opportunities employer, the University of Copenhagen encourages all qualified applicants to apply, regardless of gender, age, religion and ethnic origin. Application Applications should include the following parts: 1) Application cover letter indicating motivation 2) Curriculum vitae 3) Copies of relevant diplomas 4) A complete list of publications indicating articles relevant to the position, including copies of these articles (max. 5) 5) Recommendation letters if relevant The parts must be clearly labeled with the above-mentioned numbers. Applications will not be taken into consideration, if the requirements listed above are not met. The application will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities. The University of Copenhagen encourages all interested in this position to apply. Please submit the application with the required attachments by clicking on apply online below. Only online applications will be accepted. The closing date for applications is 23:59, November 1 2013. Applications received after the deadline will not be considered. The Faculty of Health Sciences comprises app. 7500 students, app. 1500 PhD students and app. 3200 employees. The Faculty creates new knowledge and recognition through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions for the benefit of patients and the community. Apply onlinehttps://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/ApplicationForm.cfm?PortalID=3789VacatureID=611138 The University of Copenhagen actively influences current and future generations through excellent research, education and co-operation. UCPH is one of the highest ranked universities in Europe and is Denmark´s oldest university, founded in 1479. Today, the University has 37,000 students and 9,000 employees affiliated across six faculties: humanities, law, natural sciences, social sciences, health sciences and theology. www.ku.dk/english/. Frist: 01-11-2013 Arbejdsgiver: Det Sundhedsvidenskabelige Fakultet Michael Gajhede Professor Faculty of Health and Medical Sciences Biostructural Research University of Copenhagen Jagtvej 162 2100 Copnhagen Ø Denmark TEL +45 35336000 DIR +45 35336407 m...@sund.ku.dkmailto:m...@sund.ku.dk www.ku.dkhttp://www.ku.dk/ [Description: Description: Description: Description: Description: Description: SUND_bomaerke_UK] inline: image001.gif
[ccp4bb] Problematic PDBs
Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
[ccp4bb] AW: [ccp4bb] Problematic PDBs
Dear Lucas, I recently came accross a scientific comment on the 1.9 Å PDB structure 4i8e, where apparently a HEPES molecule had been misinterpreted as a disaccharide. See Ives Muller, acta cryst F96, 2013:1071-1076. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Lucas Gesendet: Donnerstag, 17. Oktober 2013 15:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Problematic PDBs Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
[ccp4bb] AW: [ccp4bb] Problematic PDBs
Sorry, it is acta cryst F69, not 96! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Schreuder, Herman RD/DE Gesendet: Donnerstag, 17. Oktober 2013 16:11 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] AW: [ccp4bb] Problematic PDBs Dear Lucas, I recently came accross a scientific comment on the 1.9 Å PDB structure 4i8e, where apparently a HEPES molecule had been misinterpreted as a disaccharide. See Ives Muller, acta cryst F96, 2013:1071-1076. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Lucas Gesendet: Donnerstag, 17. Oktober 2013 15:51 An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Problematic PDBs Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
Re: [ccp4bb] Problematic PDBs
On Thu, Oct 17, 2013 at 6:51 AM, Lucas lucasbleic...@gmail.com wrote: I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. This would be a good place to start: http://www.ncbi.nlm.nih.gov/pubmed/23385452 The retracted ABC transporter structures are also good, although less obvious to the untrained eye. I forget what the PDB IDs are but I'll see if I can dig them up. -Nat
Re: [ccp4bb] Problematic PDBs
From the original ABC transporter retraction: http://www.sciencemag.org/content/314/5807/1875.2.full The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for MsbA and 1S7B and 2F2M for EmrE have been moved to the archive of obsolete PDB entries You can get your hands on them via URLs like: ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/XML/js/1jsq.xml.gz Phil Jeffrey Princeton On 10/17/13 10:26 AM, Nat Echols wrote: On Thu, Oct 17, 2013 at 6:51 AM, Lucas lucasbleic...@gmail.com mailto:lucasbleic...@gmail.com wrote: I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. This would be a good place to start: http://www.ncbi.nlm.nih.gov/pubmed/23385452 The retracted ABC transporter structures are also good, although less obvious to the untrained eye. I forget what the PDB IDs are but I'll see if I can dig them up. -Nat
[ccp4bb] R-factor for radiation damage (R_d)
Dear all, I am using xds (with graphical interface xdsgui) to process several diffraction data of a membrane protein that I have crystallized. At the end, I run XDSSTAT in order to check the statistic parameters of the process and my attention is captured by the R_d plot: R_d drops during the firsts 10-15 frames and then reaches a maximum (20-30 frames). Then, its value remains quite stable (I suppose due to the radiation damage correction performed by xds). The trend seems the same that is shown in ActaCryst. (2006). D62, 96–101 where Some aspects of quantitative analysis and correction of radiation damage Fig.1(a)(b) where R_d (decay R-factor) was introduced. The question is: By considering that radiation damage increases during the data collection due to the progressive dose of radiation to which the crystal is subjected, why does the R_d drop during the first period of data collection? Thank you in advance for your answers. Danilo
Re: [ccp4bb] Problematic PDBs
On Thursday, 17 October, 2013 10:51:08 Lucas wrote: Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? 4KAP is a nice cautionary example of failing to properly refine a ligand after placement. - Open coot, download 4KAP + map from EDS. - Navigate to ligand and view difference density map. - Oops. - Now open up residue information for the ligand. Notice anything odd? For bonus points, look up the known ligation chemistry of this site. Notice that the binding pose of the 4KAP ligand does not match it. Ethan Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
Re: [ccp4bb] Problematic PDBs
I would start with 1E4M (residue 361 of chain M) and 1QW9 (170 of chain B). First show the model and then reveal the electron density. This promotes a healthy skepticism of PDB models and enforces the importance of always looking at a model in the context of the map. For model building I would recommend 2PWJ and 3SQK. In 3SQK the linker to the His tag in chain B was built using the wrong sequence. It is fairly easy to build a sequence into the density and then recognize what the linker actually is. In 2PWJ the wrong sequence was used up to residue 31. I've never been able to figure out how this error came to be. Some horrible, horrible mistake was made when sequencing the gene and the person who built the model believed the sequence more than the density. The model building required to correct 2PWJ is more challenging since a number of short cuts were made cutting out loops. If I recall, my model has about 10 more amino acids than the PDB model. In all of these cases the majority of the resides in each model are fine. 3SQK has been replaced with a corrected model (4F4J). Dale Tronrud On 10/17/2013 06:51 AM, Lucas wrote: Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
Re: [ccp4bb] Problematic PDBs
I use 2QNS for teaching. It is an egregious case of modeling ligand into noise. Also, the structure has many close contacts (e.g. HOH A351), poor stereochemistry (e.g. A58-A61), and incorrectly built water. Turn on symmetry to see the steric clash of the peptide ligand with itself. You can get the coordinates and maps from EDS. http://www.ncbi.nlm.nih.gov/pubmed/18611381 http://www.ncbi.nlm.nih.gov/pubmed/21827955 http://retractionwatch.wordpress.com/2011/08/16/ties-that-dont-bind-group-retracts-parathyroid-hormone-crystallography-paper/ http://retractionwatch.wordpress.com/2012/01/26/pnas-retraction-marks-second-for-crystallography-group/ John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edumailto:tanne...@missouri.edu http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html On Oct 17, 2013, at 8:51 AM, Lucas lucasbleic...@gmail.commailto:lucasbleic...@gmail.com wrote: Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
Re: [ccp4bb] Problematic PDBs
Yikes! This cuts close to my area. We occasionally have undergrads solve and refine carbonic anhydrase-sulfonamide structures as a part of a 4-hour biochemistry teaching lab. (We have a whole shelf-full of sulfonamides that make excellent teaching projects.) ___ Roger S. Rowlett Gordon Dorothy Kline 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 On 10/17/2013 12:55 PM, Ethan A Merritt wrote: On Thursday, 17 October, 2013 10:51:08 Lucas wrote: Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? 4KAP is a nice cautionary example of failing to properly refine a ligand after placement. - Open coot, download 4KAP + map from EDS. - Navigate to ligand and view difference density map. - Oops. - Now open up residue information for the ligand. Notice anything odd? For bonus points, look up the known ligation chemistry of this site. Notice that the binding pose of the 4KAP ligand does not match it. Ethan Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
Re: [ccp4bb] Problematic PDBs
Hi Lucas, this book ( http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysis/dp/0471201995/ref=sr_1_2?s=booksie=UTF8qid=1382044405sr=1-2keywords=structural+bioinformatics) brings nice examples of protein structures with unusual features in the structure validation chapter . I used it on my protein modelingcourse and it is definitely worth buying. I small list taken from the book (unless I am very much mistaken) includes these structures: 1. 2ABX 2. 1GMA 3. 1CYC 4. 3PGM 5. 1CTX 6. 2GN5 7. 2ATC 8. 1PYP 9. 4RCR 10. 1TRC HTH, --asn [ ]s --alessandro 2013/10/17 Lucas lucasbleic...@gmail.com Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
[ccp4bb] Postdoctoral Position
Postdoctoral position, Columbia University Medical Center, NYC Postdoctoral position is available in the lab of Alexander Sobolevsky at Columbia University, Department of Biochemistry and Molecular Biophysics ( http://www.cumc.columbia.edu/dept/gsas/biochem/faculty/ALEXANDERSOBOLEVSKY.htm ). The research in the lab is focused on structure and function of ion channels using different biophysical and biochemical techniques including X-ray crystallography, molecular biology and electrophysiology. Highly motivated and creative applicants interested in structure and function of ion channels are encouraged to apply. Applicants must have a PhD or equivalent academic degree within a relevant field and excellent organization and communication skills. Strong biophysical background, prior experience with structure/function of ion channels or/and knowledge of membrane protein expression, purification and crystallization techniques is advantageous, as is a strong publication record. Please send a letter stating your scientific interests, CV and contact information for 2-3 references to Alexander Sobolevsky at sobolevskyc...@gmail.com or as4...@columbia.edu as4...@columbia.edu
Re: [ccp4bb] questions
Thanks to all of those that sent in their comments. For those that have an interest in the consensus (after ~24 hours): For question one about the PDB deposition code- out of 10: 3 said in footnote, 2 said they had either seen or had put the deposition code in the materials and methods, and a majority indicated that it shouldn't matter, but from a pragmatic standpoint the editor is always right or house rules. There is no indication in the notes to authors for this journal, which would have been the obvious way to find out where this information should go. It was also pointed out that the IUCr journals helpfully put this on the front page, so again it shouldn't matter where it is in the text. For question two on the 'rotamer-quality score' from MolProbity- 6 guessed that what was meant was the number associated with poor rotamers (i.e. in this case 12) and possibly the percentage (2.3%), but no one was actually sure that this was the case. So although I guessed incorrectly, at least it was a bit of a sanity check for me, as I hate to miss the obvious. I also got some helpful hints as to how to improve this number. I'll go with the consensus and see whether I get another berating or relief at getting it correct. Thanks again to everyone for their comments. Cheers, tom From: Peat, Tom (CMSE, Parkville) Sent: Thursday, 17 October 2013 1:59 PM To: 'ccp4bb@jiscmail.ac.uk' Subject: questions Dear CCP4 community, I would like to tap into the collective wisdom of you folks on two questions, both of which have put me into the bad graces of a particular editor. The first question seems trivial, but I will ask it anyway- where would you put the PDB deposition code in a manuscript? I may be old fashioned, but I have put it in the footnotes just prior to the references (which also ends up being the acknowledgments section in some journals), into Table 1 or in some more chemistry oriented journals in the footnotes on the first page (often near the author information). I've been told that it obviously goes into the Materials and Methods section (where I cannot ever remember seeing it, but my memory seems to be fading with old age). I find this a little strange as I consider the final model to be a result and not a material used to produce data nor a method. But maybe people are now putting their results into the methods section. So opinions on this question are welcome. The second question is hopefully straight-forward. I was also asked to put a number in Table 1 which I am happy to do, but I don't understand how to get this number. I was asked to put the 'rotamer-quality score' from MolProbity into the table. I don't run MolProbity often, but the output I got from the server doesn't have a 'rotamer-quality score' that I can find (see attachment). Is there some option that I am missing that gives this elusive factor? I also took a look at the Chen et al paper (Acta Cryst D, 2010) on MolProbity and it mentions a rotamer-quality score for specific residues but doesn't refer to an overall score (which is what I am assuming is needed for a table). I already have the well known Ramachandran percentages (favourable, allowed /poor and outliers) in the table, so the editor clearly wants something different. When I took a guess by putting in the 'MolProbity score' I was basically called an idiot that can't follow directions. Help on this front would be appreciated as although I have been called worse things, it would be nice to eventually get what is being referred to. Thanks, tom Tom Peat CSIRO, Melbourne, Australia
