Re: [ccp4bb] Possibility of Quasi-crystal formation of heterodimeric protein complex

Dear Debiasish, it looks like you got spherulites. You might try to optimize the conditions or use these spherulites for microseeding. It worked for me once. Good luck! Mirella Sent from my iPhone On 24 Mar 2017, at 08:29, Camillo Rosano

[ccp4bb] Correct reading of HDF5 (meta)data

Dear All, There has been much discussion of XDS efficiently reading HDF5 data - this is of course highly desirable though not sufficient for the correct processing of the data. One thing which I think could very much help the community would be to have data published from beamlines where

Re: [ccp4bb] Possibility of Quasi-crystal formation of heterodimeric protein complex

Dear Debiasish, more than "quasicrystals" (crystal in which molecules adopt an ordered but aperiodic structure), to me the one in your photo looks like spherulites. You shouldn't be far for finding the right crystallization conditions: maybe change the pH of your precipitant

[ccp4bb] Cryo-EM positions at EMBL

Dear all, We invite applications for postdoc and support scientist positions in the Sachse laboratory at EMBL: Postdoctoral Fellow – Structural membrane biology cryo-EM http://s.embl.org/HD01058 Research Technician – Support scientist structural biology

[ccp4bb] PhD position at IGBMC, Strasbourg, France

Dear all, just a reminder that the deadline for applications is in one week. Best regards, Helgo On 23 January 2017 at 15:36, Helgo Schmidt < 0eb5ac628ee4-dmarc-requ...@jiscmail.ac.uk> wrote: Dear all, I’m looking for an enthusiastic and highly motivated PhD student to join my

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

Alex It seems that nobody has answered your question. I'm not sure what you can do in CCP4, but if I understand your question correctly, you can perform a comprehensive validation in Phenix complete with Ramachandran plot including clickable points relating to your residues which allow you to see

Re: [ccp4bb] Coot and pymol 3D on Mac Pro with NVIDIA Quadro FX4500

Dear ccp4 members, I am looking for a recommendation from users who still have older generations of a Mac Pro with the NVIDIA Quadro FX 4500 stereo card. My question is which generation of the Mac Pro... http://www.ebay.com/sch/Apple-Mac-Pro/111418/bn_649847/i.html .. is still compatible with

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

Thanks Pavel, is there a command that can tell secondary structure assignment based on Rama plot of each residue beside phi and psi? for example : A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix On Fri, Mar 24, 2017 at

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

May be not exactly what you want, but should be close: phenix.secondary_structure_restraints 1yjp.pdb then here you have options - for output format: format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage - for search (annotation method): search_method = *ksdssp mmtbx_dssp

[ccp4bb] coot fragment translation for nucleic acids

Although I have used Coot a lot for modeling protein structures, I have little experience using it for nucleic acids. I am trying to translate fragments of nucleic acid using the rotate/translate zone option in Coot. But I am unable to select a zone; instead the whole chain is selected when I am

[ccp4bb] Antibody modelling software

Hi all, can anyone recommend some user friendly software for modelling antibodies. Commercial or academic is fine. Thanks in advance for the help. Hugh

Re: [ccp4bb] Antibody modelling software

My Oxford colleague Charlotte Deane develops SAbPred: http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/WelcomeSAbPred.php Sent from tiny silly touch screen From: Hugh Morgan

Re: [ccp4bb] CCP4BB Digest - 23 Mar 2017 to 24 Mar 2017 (#2017-83)

Dear Alex, try MAIN "http://www-bmb.ijs.si/; it has a two way interface to Ramachandran plot, you can either display “HIS_RAMA” of individual clicked residues in displayed 3D model and also the other way around, you can click on residues in Ramachandran plot and center on the residue in 3D

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

On 03/23/2017 11:39 PM, Alex Lee wrote: Dear All, Is there a tool or software which can give Ramachandran information of individual residues in a plot? I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in Coot, not individual one. I also use

Re: [ccp4bb] Antibody modelling software

Try also the LYRA server http://www.cbs.dtu.dk/services/LYRA/ In my experience, most programs do an excellent job with the canonical CDR loops, but care must be taken when looking at the CDR3s. Hope this helps, Massimo Sent from my iPhone On 24 Mar 2017, at 20:18, Hugh Morgan

Re: [ccp4bb] coot fragment translation for nucleic acids

Dear Schulze-Gahmen, Which version of coot did you use? For me, Coot 0.8.4 works well in windows 8.1 system. It does not have a question in optimizing nucleic acids. best, Zhonghao chenzhonghao...@163.com From: Ursula Schulze-Gahmen Date: 2017-03-25 04:35 To: CCP4BB Subject: [ccp4bb]

[ccp4bb] Call reminder: XChem fragment screening at Diamond (and iNEXT)

Dear Protein Crystallographers This is a second reminder for proposals for performing crystal-based fragment screening at Diamond's XChem facility at beamline I04-1, for the next allocation period (Oct 2017 to April 2018). *The deadline for proposals is NEXT SATURDAY: 1st APRIL 5PM.*