Re: [ccp4bb] Symmetry Related molecules
On 08/05/2011 05:22 AM, Albert Guskov wrote: have a look at SuperSym plugin for pymol http://www.pymolwiki.org/index.php/SuperSym Or the Supercell script. It has less features than SuperSym but does not require cctbx module. http://pymolwiki.org/index.php/Supercell Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Symmetry related molecules
symmetry related molecules can be generated in pymol by : 1. opening the coordinates in pymol 2. Actions, generate, symmetry mates, radius
[ccp4bb] MR with ensemble containing multiple models
Dear all, I have several similar models which can be superimposed. (looks like NMR solved structure) Then I made those superimposed models to be a single ensemble in phaser. My question is: what would be the difference of running phaser with this kind of ensemble and with an ensemble which include only one model? As I have B factor information in PDB, the uncertainty in model has already been considered even if I just provide one model. Is that right? Would that really be more helpful to test an ensemble with multiple models superimposed? What would happen if those superimposed models are not quite similar, or they can not superimposed well( some distance between them can be observed)? Many thanks, G
Re: [ccp4bb] MR with ensemble containing multiple models
Hi G, Dear all, I have several similar models which can be superimposed. (looks like NMR solved structure) Then I made those superimposed models to be a single ensemble in phaser. My question is: what would be the difference of running phaser with this kind of ensemble and with an ensemble which include only one model? As I have B factor information in PDB, the uncertainty in model has already been considered even if I just provide one model. Is that right? Would that really be more helpful to test an ensemble with multiple models superimposed? Although I am not aware of any systematic study, there are indications that an ensemble can be a better model than a single model with B-factor weighting (check out the phaser MR tutorial with toxd). For one thing, an ensemble will weight up the structurally conserved parts of the model, while this is not guaranteed with B-factors (although both tends to weight up the core and weight down the surface). Also, B-factors are normally restricted to describe an isotropic uncertainty, but ensembles can describe complex motions of loops, etc. What would happen if those superimposed models are not quite similar, or they can not superimposed well( some distance between them can be observed)? It is possibly a good idea to do a weighted superposition, so that only the structurally similar parts are superposed (this is automatically done by the SSM algorithm). If there are still major deviations, you can consider trimming these residues away. This is something that can be done automatically with ensembler (currently in PHENIX, but eventually to be included in CCP4 as well). BW, Gabor Many thanks, G
Re: [ccp4bb] Mixed Iso/Aniso in refmac5
I think Garib has looked into this and introduced an option to specify residues range for iso/aniso B refinement in one of the latest refmac versions. He'll probably jump into the thread soon to clarify this option. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ethan Merritt [merr...@u.washington.edu] Sent: Thursday, August 04, 2011 6:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mixed Iso/Aniso in refmac5 On Thursday, 04 August 2011, Yuri Pompeu wrote: Hello everyone, How does refmac5 pick atoms for B-factor refinement, particularly with the mixed option enabled? In the MIX option, it simply keeps the atom treatment as it is given in the input file. Atoms with an ANISOU record are refined anisotropically, the remaining atoms are not. In the case of modeling anisotropy using TLS, the atom selection is done in a separate file *.tls or *.tlsin. Ethan I dont see a place for entering a manual selection, eg resname FMN... Thank you
Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Dear Catarina, When TLS is involved in refinement using a script, the keyword tlsout addu should be added to produce a coordinate file containing the full B factor. The latest REFMAC interface (in CCP4i) has a button Add TLS contribution to XYZOUT in the folder of TLS Parameters which will add this keyword. There are three ways to convert file so it contains full B factors: 1. You can convert your PDB file so it contains full B factors using the server at http://deposit.rcsb.org/adit/REFMAC.html 2. Convert locally using the script at http://deposit-beta.rcsb.org/tlsanl/tlsanl_script.csh Run tlsanl_script.csh pdbfile (note: CCP4 should be installed on your local machine prior to running the script) 3. Convert using CCP4i package * Find the file of TLS parameters TLSOUT that corresponds to the coordinate file, or if necessary extract the TLS parameters from the PDB file using the CCP4 program tlsextract * Use CCP4's tlsanl to put the full B factor in the PDB coordinate file, available in the GUI interface as the task Analyse TLS parameters. Be sure to set the keyword BRESID T in this interface. Please let us know if we can be of any further help. Sincerely, Rachel Green *** Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu __ PDB 40: Celebrate four decades of innovation in structural biology Oct 28-30, 2011 at Cold Spring Harbor Laboratory http://meetings.cshl.edu/meetings/pdb40.shtml ** On 8/3/2011 1:47 PM, Catarina Silva wrote: Dear all, I am trying to deposit a pdb containing TLS groups. PDB instructions states: As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records. I did run Refmac with TLS parameters and, as such, I would expect that all the values necessary to pdb deposition would be on the pdb coming out from refmac. However, when I deposit the pdb a 'serious error' comes up, not allowing me to deposit the coordinates: You will NOT be allowed to proceed for deposition unless these issues are corrected. *TLS and ANISOU/RESIDUAL B-FACTORS.* As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records.Your entry contains TLS records but no ANISOU records OR Residual B-factors. Please correct this and reupload your structure for validation I don't really understand why these supposed missing values are not already contained in the pdb file, and I can't figure out how to get them. Does anyone knows how to fix this situation? Thanks in advance! Catarina Silva
Re: [ccp4bb] Mixed Iso/Aniso in refmac5
Thank you for reminding me. There is a way to define residue ranges for mixed refinement. I think I did it by Boaz's request. Keyword should be something like (there are ways of selecting particular atoms of residues, but I am not sure I have tested that thoroughly): brefine mixed anisou residues from resnumber chain to resnumber chain atoms list of atoms Full description of the keywords for mixed refinement is in this document (anisotropic refinement section): http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html Thus option should be available from the latest ccp4 (but you need to use keyword, there is no buttons for this on the interface yet) Please let me know if it does not do what it is designed for. Regards Garib On 5 Aug 2011, at 11:51, Boaz Shaanan wrote: I think Garib has looked into this and introduced an option to specify residues range for iso/aniso B refinement in one of the latest refmac versions. He'll probably jump into the thread soon to clarify this option. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ethan Merritt [merr...@u.washington.edu] Sent: Thursday, August 04, 2011 6:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mixed Iso/Aniso in refmac5 On Thursday, 04 August 2011, Yuri Pompeu wrote: Hello everyone, How does refmac5 pick atoms for B-factor refinement, particularly with the mixed option enabled? In the MIX option, it simply keeps the atom treatment as it is given in the input file. Atoms with an ANISOU record are refined anisotropically, the remaining atoms are not. In the case of modeling anisotropy using TLS, the atom selection is done in a separate file *.tls or *.tlsin. Ethan I dont see a place for entering a manual selection, eg resname FMN... Thank you Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] Position available with Rigaku Europe - Sales Engineer, Life Sciences Division
Sales Engineer, Life Sciences - Rigaku Europe http://www.rigaku.com/jobs.html Role – Rigaku Europe based in Sevenoaks UK is looking for a motivated individual who can demonstrate their ability to work effectively both in a team and independently. Enthusiasm and strong organisational skills are highly advantageous in this role. The successful candidate will be responsible for sales of products related to X-ray diffraction of proteins, robotic equipment used for the crystallisation of proteins and biological X-ray scattering (BioSAXS) techniques. Education and Experience – Candidates will preferably have a proven sales record and ideally have experience of either X-ray diffraction equipment or be able to show experience and understanding of high-level technical sales processes. The role will focus on the candidates’ ability to effectively communicate the merits of Rigaku instruments to our existing and prospective customers. Excellent oral and written communication skills are essential and in particular fluent spoken-English is required, but this does not necessarily need to be the candidate’s first language. Additionally, the candidate will be expected to have a good level of computer literacy. Salary – Negotiable competitive basic plus commission Applications are invited from candidates based both within the UK and continental Europe. The candidate must be prepared, and be able to travel without restriction both within and outside Europe for a significant proportion of time. A full and clean driving license is required. Rigaku Europe is an equal opportunities employer. Closing Date: all applications should be received before 31st August 2011 Genuinely interested candidates should send their CV and a covering letter by post or e-mail to: Dr Mark Benson Unit B6, Chaucer Business Park Watery Lane, Kemsing Sevenoaks, Kent TN15 6QY, England Tel: +44 1732 763 367 Informal enquiries or CV’s can be sent to mark.ben...@rigaku.com
[ccp4bb] [CCP4] movie for side chain flip
Hi all, Sorry for a little bit out of topic question. Morph Serve is the only online server I know to make movie for protein motion. But what I want to do is to make a movie to show one single side chain flip. It seems Morph could not do this. Does anyone know a way to do that? Thank you. King regards, Wenhe
Re: [ccp4bb] [CCP4] movie for side chain flip
On Fri, 2011-08-05 at 15:48 +0100, WENHE ZHONG wrote: Hi all, Sorry for a little bit out of topic question. Morph Serve is the only online server I know to make movie for protein motion. But what I want to do is to make a movie to show one single side chain flip. It seems Morph could not do this. Does anyone know a way to do that? Thank you. King regards, Wenhe You can make morphs using Chimera http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera In this case, all you will need will be the two models with everything identical except the flipped side chain. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Hi, On Fri, Aug 5, 2011 at 5:27 AM, Rachel Kramer Green kra...@rcsb.rutgers.edu wrote: ** (...) There are three ways to convert file so it contains full B factors: (...) in fact, more: 4. The command phenix.tls model.pdb combine_tls=true will combine TLS from PDB file header with 'residual' B from ATOM records. phenix.tls model.pdb extract_tls=true will split the total B-factor in ATOM records into TLS component and 'residual' part. Pavel.
Re: [ccp4bb] Symmetry Related molecules
Thank you all, Best On Fri, 05 Aug 2011 09:19:55 +0200, Thomas Holder wrote: On 08/05/2011 05:22 AM, Albert Guskov wrote: have a look at SuperSym plugin for pymol http://www.pymolwiki.org/index.php/SuperSym Or the Supercell script. It has less features than SuperSym but does not require cctbx module. http://pymolwiki.org/index.php/Supercell Cheers, Thomas -- Yuri Pompeu
[ccp4bb] [CCP4]data processing I222 vs pointless I121
Hi All, Recently I did some soaking experiments for crystals. Most of them did not change their space group (I222). But one of them seems to be a little bit different (I222 --- I121). The following is the pointless data: (the data was processed by Mosflm under space group I222) Laue GroupLklhd NetZc Zc+ Zc-CCCC- Rmeas R- Delta ReindexOperator 1 I 1 2/m 1 ** 0.687 2.55 8.25 5.71 0.83 0.57 0.32 0.52 0.0 [-h,-k,l] 2 P -1 0.171 2.02 8.54 6.52 0.85 0.65 0.32 0.45 0.0 [-h,-k,1/2h+1/2k+1/2l] - 3I m m m 0.050 6.98 6.98 0.00 0.70 0.00 0.42 0.00 0.0 [h,k,l] 4 I 1 2/m 1 0.050 0.22 7.09 6.87 0.71 0.69 0.42 0.42 0.0 [k,-h,l] 5 I 1 2/m 1 0.043 0.06 7.05 6.99 0.70 0.70 0.42 0.42 0.0 [h,-l,k] Best Solution:space group I 1 2 1 Reindex operator: [-h,-k,l] Laue group probability: 0.687 Systematic absence probability: 1.000 Total probability: 0.687 Space group confidence: 0.595 Laue group confidence 0.595 Unit cell: 104.1 108.6 264.890 90 90 54.32 to 3.41 - Resolution range used for Laue group search 54.32 to 2.25 - Resolution range in file, used for systematic absence check Number of batches in file:400 The data do not appear to be twinned, from the L-test : WARNING: The chosen output crystal system is different from that used for integration of the input file(s). You should rerun the integration in the chosen crystal system because the cell constraints differ. The input crystal system is body-centred orthorhombic (Cell: 104.1 108.6 264.890 90 90) The crystal system chosen for output is body-centred monoclinic (Cell: 104.1 108.6 264.890 90 90) I couldn't see the difference between I222 and I121. May I ask do I need to go back to the Mosflm process step and choose other space group for the processing? Thank you. King regards, Wenhe
