Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Vellieux Frederic
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

Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

2011-07-21 Thread Thomas Holder
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

Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Hubing Lou
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

Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Antony Oliver
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.

[ccp4bb] SLOW CCP4 Interface

2011-07-21 Thread Jan Dohnalek
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

[ccp4bb] Post-doc position available

2011-07-21 Thread Karen Fulan Discola
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

Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Herman . Schreuder
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

Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Hubing Lou
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

Re: [ccp4bb] SLOW CCP4 Interface

2011-07-21 Thread Jan Dohnalek
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

Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector

2011-07-21 Thread zhang yu
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

[ccp4bb] hello

2011-07-21 Thread Afshan Begum
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

Re: [ccp4bb] hello

2011-07-21 Thread Nicolas Foos
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

[ccp4bb] Concentrating a protein solution - subbu

2011-07-21 Thread Narayanan Ramasubbu
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

Re: [ccp4bb] Concentrating a protein solution - subbu

2011-07-21 Thread Antony Oliver
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

Re: [ccp4bb] Phaser and Molrep gave different solutions

2011-07-21 Thread Randy Read
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

[ccp4bb] Protein expression, purification and crystallization

2011-07-21 Thread Hena Dutta
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

2011-07-21 Thread Eric Larson
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

[ccp4bb] PDBe introduces UniPDB - a UniProt-PDB sequence-coverage widget

2011-07-21 Thread Gerard DVD Kleywegt
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

Re: [ccp4bb] Protein expression, purification and crystallization

2011-07-21 Thread Bernhard Rupp (Hofkristallrat a.D.)
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

Re: [ccp4bb] Concentrating a protein solution - subbu

2011-07-21 Thread Eric Larson
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

[ccp4bb] JLigand: Handedness related issue

2011-07-21 Thread 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

[ccp4bb] JLigand: Handedness related issue

2011-07-21 Thread 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

[ccp4bb] A new historical structural achievement

2011-07-21 Thread Justin Hall
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

Re: [ccp4bb] JLigand: Handedness related issue

2011-07-21 Thread Christian Roth
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

[ccp4bb] Intensity-Weighted Reciprocal Lattice

2011-07-21 Thread Michael Thompson
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