Re: [ccp4bb] Phaser and Molrep gave different solutions
Hi, It's not a bad idea to read the Phaser manual for molecular replacement; see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement Soon after the start, in a table on the right hand side, there is: TFZ score 5, have I solved it ? No. Hence with a TFZ score of 3.8 you do not have a solution using Phaser. Fred. Hubing Lou wrote: Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures
this is of course possible with PyMOL, try this: pdbid, chain = '1a00', 'A' cmd.fetch(pdbid, async=0) cmd.symexp('__neighbors', pdbid, pdbid + ' and chain ' + chain, 5.0) print 'Number:', len(cmd.get_object_list('(__neighbors*)')) cmd.delete('__neighbors*') cmd.delete(pdbid) Cheers, Thomas On 07/14/2011 01:48 PM, sukanta mondal wrote: I know, in PyMOL using 'symexp' possible to generate symmetry related molecules for a given crystal structure. But I'm looking for some program/software (for batch) by which I can find out the number of symmetry related molecules (distance cutoff= 5A) interacting with a given chain in a crystal structure. Thanking you, suku NIBIO, Osaka -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Phaser and Molrep gave different solutions
Have you tried using the DNA as your search model? - I have had success this way round - certainly more phasing power than your protein model, I guess. Also, refine with your DNA in place, and your phases/ map should improve - hopefully allowing you to place your protein molecules with ease. Tony. Sent from my iPhone On 21 Jul 2011, at 12:40, Hubing Lou louhub...@gmail.commailto:louhub...@gmail.com wrote: I was worried as well with the low TFZ score. Usually successful cases with score 8. I am still puzzled why Phaser and Molrep gave different solutions. Does this mean molecular replacement do not work out in this case so more crystals have to be prepared? A little more information might be helpful to dissolve the problem here. The model I used is a protein-DNA complex. The protein was Chainsaw editted but the DNA sequence was directly borrowed from the original model. Best, Hubing On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic mailto:frederic.velli...@ibs.frfrederic.velli...@ibs.frmailto:frederic.velli...@ibs.fr wrote: Hi, It's not a bad idea to read the Phaser manual for molecular replacement; see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement Soon after the start, in a table on the right hand side, there is: TFZ score 5, have I solved it ? No. Hence with a TFZ score of 3.8 you do not have a solution using Phaser. Fred. Hubing Lou wrote: Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
[ccp4bb] SLOW CCP4 Interface
Dear all, my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with Fedora core 15 2.6.38.8-35.fc15.x86_64 . Any ideas where to go from here? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Post-doc position available
A 2-year postdoctoral position is available in the laboratory of Dr. A. Dessen at the Institut de Biologie Structurale in Grenoble, France, to study structure and function of new bacterial virulence factors. The laboratory has state-of-the-art equipment for biochemistry and crystallography studies, and the postdoctoral fellowship will involve protein purification, crystallization, data collection at the synchrotron, and structure solution and refinement. The IBS is a member of the Partnership for Structural Biology and thus has preferential access to equipment and techniques available on the PSB site, which also includes the EMBL, the ILL, and the ESRF. Any inquiries should be sent to andrea.des...@ibs.fr.
Re: [ccp4bb] Phaser and Molrep gave different solutions
Dear Hubing, One maybe stupid question: Your are sure the space group is P21 and not P2 or even something else? Did you test other possible space groups? Choosing the wrong space group could exactly lead to the results you observe. Best, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hubing Lou Sent: Thursday, July 21, 2011 6:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phaser and Molrep gave different solutions Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
Re: [ccp4bb] Phaser and Molrep gave different solutions
I also processed with Imosflm and ran Pointless, it was P21. Also it was indicated by the Intensity systematic absences in HKL2000 scale.log file. Best, Hubing On Thu, Jul 21, 2011 at 8:44 PM, herman.schreu...@sanofi-aventis.comwrote: ** Dear Hubing, One maybe stupid question: Your are sure the space group is P21 and not P2 or even something else? Did you test other possible space groups? Choosing the wrong space group could exactly lead to the results you observe. Best, Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Hubing Lou *Sent:* Thursday, July 21, 2011 6:46 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Phaser and Molrep gave different solutions Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
Re: [ccp4bb] SLOW CCP4 Interface
Was a SELinux issue. Jan Dohnalek On Thu, Jul 21, 2011 at 1:44 PM, Jan Dohnalek dohnalek...@gmail.com wrote: Dear all, my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with Fedora core 15 2.6.38.8-35.fc15.x86_64 . Any ideas where to go from here? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410 -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector
We could use HKL2000 for Pilatus 6M detector a few months ago in our lab. We upgraded our HKL2000 to Version 0.98.701 and asked a new license file to include Pilatus 6M detector. Yu 2011/7/20 Petr Leiman petr.lei...@epfl.ch Dear all, What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M detector? Thank you, Petr -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] hello
Dear all, I have facing one problem during the refinement of my protein . Actually in my protein there are some modified amino acids are present like Cystein is modified into CME which i can get easily from monomer libraray in coot . but after refinement in Pdb text file indicated some gaps while in the structures there are no gap in between these amino acids so if any one suggest me what to do. I would appreciate your kind suggestions. LINKR GLU A 142 LEU A 144 gap LINKR SER A 328 GLY A 330 gap LINKR LEU A 138 GLU A 140 gap LINKR GLU A 126 ASP A 130 gap LINKR SER A 246 GLY A 248 gap Many thanks for your time Best regards Afshan
Re: [ccp4bb] hello
Hello Afshan, Maybe the programm that you use for refinement need specific entry with restraint for your modified amino acids. More precisely, i think about the *.cif file for exemple. HTH. Nicolas Le 21/07/11 17:13, Afshan Begum a écrit : Dear all, I have facing one problem during the refinement of my protein . Actually in my protein there are some modified amino acids are present like Cystein is modified into CME which i can get easily from monomer libraray in coot . but after refinement in Pdb text file indicated some gaps while in the structures there are no gap in between these amino acids so if any one suggest me what to do. I would appreciate your kind suggestions. LINKRGLU A 142 LEU A 144gap LINKRSER A 328 GLY A 330gap LINKRLEU A 138 GLU A 140gap LINKRGLU A 126 ASP A 130gap LINKRSER A 246 GLY A 248gap Many thanks for your time Best regards Afshan -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Concentrating a protein solution - subbu
Dear All: We have been trying to crystallize a protein which is large - 100 kDa. This is soluble but the best we can get is about 1 mg/mL. It did crystallize but did not diffract well. Efforts to increase the concentration has been unsuccessful. I am wondering whether there are methods that others use to increase the concentration other that using amicon columns. Any help will be appreciated. Thanks Subbu
Re: [ccp4bb] Concentrating a protein solution - subbu
You could try loading a small 1ml HiTrap (or similar) Q or S column with your protein - and knocking it off it in one go with high salt, alternatively micro-dialysis against a solution containing PEGs can also work well. Tony Sent from my iPhone On 21 Jul 2011, at 17:54, Narayanan Ramasubbu ramas...@umdnj.edu wrote: Dear All: We have been trying to crystallize a protein which is large - 100 kDa. This is soluble but the best we can get is about 1 mg/mL. It did crystallize but did not diffract well. Efforts to increase the concentration has been unsuccessful. I am wondering whether there are methods that others use to increase the concentration other that using amicon columns. Any help will be appreciated. Thanks Subbu
Re: [ccp4bb] Phaser and Molrep gave different solutions
Hi, Although it's pretty much true that if TFZ8, the solution is correct, there are hard cases where a correct solution has a significantly lower TFZ score. Also, we've been finding that TFZ scores are generally lower for monoclinic space groups like P21, at least in the search for the first molecule. (Among other things, the search for the first molecule in a polar space group only covers a plane, so there are fewer independent trials.) Rob Oeffner has been doing some detailed statistics, which we're analysing so that we can give better rules of thumb. However, a TFZ of 3.8 for the second molecule (where the search is 3-dimensional) is a bad sign. One of the earlier posts suggested looking just for the DNA, which sounds like a good idea. It's possible that the relative orientation of the protein and DNA is different enough that the complex model doesn't work, so it might well be worth trying the DNA and protein components separately. Good luck! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 21 Jul 2011, at 11:39, Hubing Lou wrote: I was worried as well with the low TFZ score. Usually successful cases with score 8. I am still puzzled why Phaser and Molrep gave different solutions. Does this mean molecular replacement do not work out in this case so more crystals have to be prepared? A little more information might be helpful to dissolve the problem here. The model I used is a protein-DNA complex. The protein was Chainsaw editted but the DNA sequence was directly borrowed from the original model. Best, Hubing On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi, It's not a bad idea to read the Phaser manual for molecular replacement; see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement Soon after the start, in a table on the right hand side, there is: TFZ score 5, have I solved it ? No. Hence with a TFZ score of 3.8 you do not have a solution using Phaser. Fred. Hubing Lou wrote: Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
[ccp4bb] Protein expression, purification and crystallization
Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena
Re: [ccp4bb] Concentrating a protein solution - subbu
Hi Subbu, You got crystals at 1mg/ml so you probably don't need to concentrate your protein any higher, especially since you suggest that concentrating beyond that is problematic. Instead, you may want to try to optimize the crystallization condition you have already identified. Some possible things to try: additive screen, include specific ligands, different temperature, different ratios of protein solution to crystallization solution, seeding, different crystallization methods (hanging vs. sitting drop, batch, diffusion,...), ... good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Thu, 21 Jul 2011, Narayanan Ramasubbu wrote: Dear All: We have been trying to crystallize a protein which is large - 100 kDa. This is soluble but the best we can get is about 1 mg/mL. It did crystallize but did not diffract well. Efforts to increase the concentration has been unsuccessful. I am wondering whether there are methods that others use to increase the concentration other that using amicon columns. Any help will be appreciated. Thanks Subbu
[ccp4bb] PDBe introduces UniPDB - a UniProt-PDB sequence-coverage widget
Hi all, As part of its recent summer update, the Protein Data Bank in Europe (PDBe; http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for graphical display of the coverage in the PDB of any UniProt entry (e.g., http://pdbe.org/unipdb?uniprot=P19909). The widget can be used on the PDBe website or included in your own web pages. For a quick overview of the functionality of the widget, see this illustration: http://www.ebi.ac.uk/pdbe-apps/widgets/html/unipdbsnap.png Note how the PDBlogos instantly reveal which are X-ray or NMR entries, which entries contain DNA or ligands, etc. Pressing the button Related PDB sequences (to the left in the top bar of the widget) will launch a FASTA search of the PDB using the UniProt sequence. The results will be presented (and can be analysed) in the PDBeXplore browser (http://pdbe.org/fasta). A simple way to make a link or bookmark to the UniPDB widget for your favourite protein is to use a URL in the following format: http://pdbe.org/unipdb?uniprot=P29373 (replacing P29373 by the UniProt code of your chosen protein, either its UniProt name, e.g. NGF_MOUSE, or its accession number, e.g. P01139). Incorporating the UniPDB widget in your own web pages is so easy even I can do it: http://xray.bmc.uu.se/gerard/unipdb_pdbportfolio.html - Why UniPDB? --- UniProt (http://www.uniprot.org/) is the primary resource for information about protein sequence and function and the PDB is the single global archive of 3D structures of biomacromolecules and their complexes. Many PDB entries contain proteins that are also archived in UniProt. As a biologist interested in a particular protein, you may want to find out which entries in the PDB (if any) contain structures for (parts of) your favourite protein, and how these structures map to the UniProt sequence. Structural biologists often work on partial sequences (e.g., stably folded domains) and sometimes have to modify the natural sequence to facilitate expression or crystallisation or to allow investigation of the effect of a mutation on the behaviour of the protein (such as catalytic activity or ligand-binding specificity). In addition, the same structure can be determined many times, e.g. in different laboratories, with different techniques, under different conditions, with different ligands, etc. For these reasons, it is not always easy to do sequence-based searches of the PDB and synthesise the results into an overview of what structural information is available for which parts of your favourite protein. This problem is addressed by the UniPDB widget. It uses the up-to-date mappings between UniProt sequences and PDB entries that are provided by the SIFTS resource (a collaboration between the UniProt and PDBe teams at the EBI; http://pdbe.org/sifts). SIFTS provides mappings from PDB entries to other bioinformatics resources as well, including Pfam (sequence-based protein domains), CATH and SCOP (both of these are structural fold classifications). For more information about UniPDB (including instructions on how to include it in your own web pages), see: http://pdbe.org/unipdb - We hope that you will find the UniPDB tool useful. As always, we welcome constructive criticism, comments, suggestions, bug reports, etc. through the feedback button at the top of any PDBe web page. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Protein expression, purification and crystallization
If you are eligible, I'd highly recommend the EMBO courses in Europe or the CSHL courses in the US on those subjects. Reading is a good start but will not be enough if you want to do real work.for strategy considerations, there is always Ch 3 and 4 in le livre. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hena Dutta Sent: Thursday, July 21, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein expression, purification and crystallization Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena
Re: [ccp4bb] Concentrating a protein solution - subbu
See below. I believe Ray intended this to be sent to the entire bb and especially to Subbu! And in reading Ray's message, I am reminded that I forgot to mention what he may be hinting at. You should also try to optimize by creating a fine grid screen around your identified condition varying in particular pH and precipitant concentration. best, Eric On Thu, 21 Jul 2011, ray-br...@att.net wrote: What is the pI? Perhaps the protein will be more soluble close to this pH? You could increase the salt and/or add some glycerol or a cofactor? Normally crystallization is most affected by the pH, 2 - 10% glycerol or temperature 4 - 25 degrees C. Cheers Ray Brown _ From: Eric Larson larso...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thu, July 21, 2011 1:40:51 PM Subject: Re: [ccp4bb] Concentrating a protein solution - subbu Hi Subbu, You got crystals at 1mg/ml so you probably don't need to concentrate your protein any higher, especially since you suggest that concentrating beyond that is problematic. Instead, you may want to try to optimize the crystallization condition you have already identified. Some possible things to try: additive screen, include specific ligands, different temperature, different ratios of protein solution to crystallization solution, seeding, different crystallization methods (hanging vs. sitting drop, batch, diffusion,...), ... good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Thu, 21 Jul 2011, Narayanan Ramasubbu wrote: Dear All: We have been trying to crystallize a protein which is large - 100 kDa. This is soluble but the best we can get is about 1 mg/mL. It did crystallize but did not diffract well. Efforts to increase the concentration has been unsuccessful. I am wondering whether there are methods that others use to increase the concentration other that using amicon columns. Any help will be appreciated. Thanks Subbu
[ccp4bb] JLigand: Handedness related issue
Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using JLigand. The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue? I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur
[ccp4bb] JLigand: Handedness related issue
Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using JLigand. The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue? I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur
[ccp4bb] A new historical structural achievement
Dear CCP4BB, Forgive me for soap boxing, but yesterday the first structure of a GPCR/Gprotein complex was released (PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=3SN6, article: http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature10361.html). Recently a student preparing for their dissertation asked this board for its opinion about the most significant recent structural accomplishment, and among many things the progress on GPCRs was mentioned (albeit as being cute, I think). Reading this work from Kobilka and Sunahara's two groups, I am floored by what it must have taken to achieve this - particularly if you know how hard and how long people have tried (both past and present) to get a GPCR/Gprotein complex structure. It is my opinion that this structure was something of a holy grail for the GPCR community. So, even if you don't usually follow the developments of membrane crystallography, I wanted to invite your attention to this historical achievement in the GPCR field; and I hope you will join me in congratulating the scientist involved in this work. Cheers~ ~Justin
Re: [ccp4bb] JLigand: Handedness related issue
Hi Vineet, I did not used JLIGAND so far, so I cannot explain what happend, but maybe the quickest solution would be a manual intervention in the cif-files. Type at at the chirality remark positiv or negativ or whatever nomenclature is used and save it again. I do it sometimes for my ligands when I genereated the wrong stereoisomer or the description for the racemate. Good Luck Christian Am Donnerstag 21 Juli 2011 23:10:01 schrieb Vineet Gaur: Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using JLigand. The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue? I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur
[ccp4bb] Intensity-Weighted Reciprocal Lattice
Hello ccp4 phenix BB members, I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections. Any tips or recommendations would be appreciated. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu