Re: [ccp4bb] mtz/cif file for depostion
Dear all, thanks to all who answered. Gemmi and uniqueify did not help, "Export MTZ" from the toolbar did. "Merge experimental data objects to MTZ" from "Export and Deposition" did not help me. I think, it's not the programs, though. The problem now seems to me the missing Fs. "Export MTZ" seems to convert to Fs without asking. Trying to upload Iplus and Iminus only for validation (or deposition) did not work. I thought it would be better (closer to the experimental data) to use I instead of F, and therefor intentionally tried to deposit Is only. Is it really obligatory to deposit F? Wouldn't it be better to deposit I instead of F? Greetings Gottfried Am Freitag, den 09-02-2024 um 23:39 schrieb Jon Cooper: >From your refmac refinement job in i2, this should give you the combined mtz? test.jpg Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent with Proton Mail [1] secure email. On Friday, 9 February 2024 at 17:54, Palm, Gottfried wrote: Dear all, I have problems preparing my experimental data (XRD) for deposition. I have two mtz files, which work well for refmac5, with an FREER column in one file and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged them into one mtz file with cad (in ccp4i). The validation server doesn't take two separate mtz files, but complains about missing data in the merged file. I guess because FREER ended up in "Columns common to all datasets" and the other columns in "Dataset #1: 356211/DEFAULT/NATIVE". Can I somehow move the FREER column to Dataset #1? With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in ccp4i2, the problem is the same. I also tried converting to cif many ways, but failed. I have used OneDep at EBI. Best Regards Gottfried - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 Links: -- [1] https://proton.me/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] mtz/cif file for depostion
Dear all, I have problems preparing my experimental data (XRD) for deposition. I have two mtz files, which work well for refmac5, with an FREER column in one file and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged them into one mtz file with cad (in ccp4i). The validation server doesn't take two separate mtz files, but complains about missing data in the merged file. I guess because FREER ended up in "Columns common to all datasets" and the other columns in "Dataset #1: 356211/DEFAULT/NATIVE". Can I somehow move the FREER column to Dataset #1? With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in ccp4i2, the problem is the same. I also tried converting to cif many ways, but failed. I have used OneDep at EBI. Best Regards Gottfried To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Handling of alternate main chain conformations in refmac
Dear all, specifically refmac developers, I have an unexpected observation, when refining alternate main chain conformations for residues 22 and following in refmac. Residue 21 has one conformation, residues 22-25 have two conformations. There are four chains. I have coordinates with PRO 21, A PRO 22 and B PRO 22, A PRO 23 and B PRO 23, ... In chain A and B A PRO 22 is connected to A PRO 23 and B PRO 22 is connected to B PRO 23. Refmac handles this correctly in chain A ATOM 134 N PRO A 21 55.911 -46.023 11.391 1.00 71.64 N ATOM 135 CA PRO A 21 54.636 -45.699 10.771 1.00 69.48 C ATOM 136 C PRO A 21 53.652 -45.003 11.712 1.00 75.85 C ATOM 137 O PRO A 21 53.737 -45.128 12.943 1.00 71.90 O ATOM 138 CB PRO A 21 54.132 -47.050 10.291 1.00 73.57 C ATOM 139 CG PRO A 21 54.732 -48.029 11.268 1.00 78.87 C ATOM 140 CD PRO A 21 56.095 -47.462 11.621 1.00 80.25 C ATOM 148 N APRO A 22 52.618 -44.384 11.088 0.40 83.27 N ATOM 149 N BPRO A 22 52.759 -44.118 11.211 0.60 75.47 N ATOM 150 CA APRO A 22 51.512 -43.751 11.796 0.40 84.16 C ATOM 151 CA BPRO A 22 51.849 -43.395 12.104 0.60 72.98 C ATOM 152 C APRO A 22 50.228 -44.579 11.869 0.40 87.98 C ATOM 153 C BPRO A 22 50.964 -44.325 12.947 0.60 75.21 C ATOM 154 O APRO A 22 49.906 -45.361 10.962 0.40 78.72 O ATOM 155 O BPRO A 22 50.724 -45.466 12.556 0.60 75.40 O ATOM 156 CB APRO A 22 51.372 -42.540 10.866 0.40 81.67 C ATOM 157 CB BPRO A 22 51.028 -42.492 11.157 0.60 70.57 C ATOM 158 CG APRO A 22 51.449 -43.146 9.482 0.40 81.76 C ATOM 159 CG BPRO A 22 51.348 -42.942 9.743 0.60 70.36 C ATOM 160 CD APRO A 22 52.449 -44.275 9.624 0.40 80.93 C ATOM 161 CD BPRO A 22 52.605 -43.766 9.788 0.60 71.03 C ATOM 176 N APRO A 23 49.460 -44.406 12.970 0.40 93.31 N ATOM 177 N BPRO A 23 50.456 -43.886 14.129 0.60 74.50 N ATOM 178 CA APRO A 23 48.118 -44.976 13.080 0.40 94.09 C ATOM 179 CA BPRO A 23 49.554 -44.724 14.943 0.60 74.34 C ATOM 180 C APRO A 23 47.344 -44.828 11.770 0.40 86.61 C ATOM 181 C BPRO A 23 48.202 -45.107 14.318 0.60 79.21 C ATOM 182 O APRO A 23 46.587 -43.879 11.580 0.40 78.80 O ATOM 183 O BPRO A 23 47.978 -44.905 13.125 0.60 87.29 O ATOM 184 CB APRO A 23 47.502 -44.164 14.238 0.40 99.79 C ATOM 185 CB BPRO A 23 49.389 -43.885 16.249 0.60 66.55 C ATOM 186 CG APRO A 23 48.683 -43.763 15.109 0.40 99.18 C ATOM 187 CG BPRO A 23 49.687 -42.465 15.832 0.60 65.08 C ATOM 188 CD APRO A 23 49.861 -43.632 14.158 0.40 98.24 C ATOM 189 CD BPRO A 23 50.763 -42.584 14.757 0.60 62.91 C in chain B, though, ATOM 10241 N PRO B 21 29.572 -19.212 60.309 1.00 70.15 N ATOM 10242 CA PRO B 21 28.640 -18.729 59.295 1.00 76.47 C ATOM 10243 C PRO B 21 28.922 -19.180 57.863 1.00 79.17 C ATOM 10244 O PRO B 21 30.034 -19.590 57.528 1.00 73.13 O ATOM 10245 CB PRO B 21 28.749 -17.216 59.453 1.00 79.61 C ATOM 10246 CG PRO B 21 30.155 -16.998 59.938 1.00 80.13 C ATOM 10247 CD PRO B 21 30.483 -18.180 60.824 1.00 74.66 C ATOM 10255 N APRO B 22 27.930 -18.968 56.964 0.40 81.02 N ATOM 10256 N BPRO B 22 27.885 -19.324 57.007 0.60 86.55 N ATOM 10257 CA APRO B 22 28.181 -18.795 55.531 0.40 79.63 C ATOM 10258 CA BPRO B 22 28.083 -19.897 55.672 0.60 85.45 C ATOM 10259 C APRO B 22 28.404 -17.322 55.153 0.40 74.57 C ATOM 10260 C BPRO B 22 28.612 -18.882 54.668 0.60 82.28 C ATOM 10261 O APRO B 22 27.496 -16.474 55.330 0.40 65.21 O ATOM 10262 O BPRO B 22 29.491 -18.064 55.017 0.60 75.63 O ATOM 10263 CB APRO B 22 26.878 -19.368 54.958 0.40 78.44 C ATOM 10264 CB BPRO B 22 26.664 -20.355 55.335 0.60 88.40 C ATOM 10265 CG APRO B 22 25.820 -18.874 55.924 0.40 77.98 C ATOM 10266 CG BPRO B 22 25.785 -19.289 55.969 0.60 84.77 C ATOM 10267 CD APRO B 22 26.494 -18.892 57.288 0.40 78.10 C ATOM 10268 CD BPRO B 22
[ccp4bb] solvent mask for partial ligands, addendum
Dear all, I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a main chain N, one of the ring nitrogens to a glutamate side chain. At occupancy 1.0 I get B-factors twice as high as the protein and negative difference density. Thus, I set the occupancy to 0.5 and get the whole EPE covered in positive difference density at 3 sig, peaking at 6 sig. This positive density is much larger than without EPE. On first glance, this looked contradictory to me: more positive density after putting more atoms there. I can only guess that the solvent at the place of the EPE is set to 0 (instead of 0.5), so I get positive density because of only 0.5 occupied EPE. Can I refine with half a ligand and half solvent? Greetings Gottfried I should add that I am refining with refmac version 5.8.0419. parameters: SCALE TYPE SIMPLE SOLVENT YES Sorry for the confusion because of hijacking another thread of the bulletin board. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] solvent mask for partial ligands
Dear all, I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a main chain N, one of the ring nitrogens to a glutamate side chain. At occupancy 1.0 I get B-factors twice as high as the protein and negative difference density. Thus, I set the occupancy to 0.5 and get the whole EPE covered in positive difference density at 3 sig, peaking at 6 sig. This positive density is much larger than without EPE. On first glance, this looked contradictory to me: more positive density after putting more atoms there. I can only guess that the solvent at the place of the EPE is set to 0 (instead of 0.5), so I get positive density because of only 0.5 occupied EPE. Can I refine with half a ligand and half solvent? Greetings Gottfried On Tuesday, 12-12-2023 at 09:50 Krieger, James M wrote: There is also discussion about this for chaperonins such as CCT and GroEL. It may be that beryllium fluoride works better. Best wishes James > On 12 Dec 2023, at 05:30, Matthew BOWLER wrote: > > Dear Jinyu, > we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where we confirmed it by both crystallography and 19F NMR > > In fact ALF3 does not exist as a trigonal bipyramid - all cases where this geometry is observed are likely MgF3 that does adopt this geometry and will replace the aluminium at pH values above 8 as Al will precipitate as AlOH. > > We only saw the water replacing the F when a catalytic residue charge was removed and proposed the hypothesis that phos transfer enzymes need to balance the charge in the active site exactly therefore selecting the neutral AlF3 over negative AlF4- that both exist in solution. > > Best wishes, Matt > >> On 2023-12-12 03:40, Friday wrote: >> Dear CCP4 community, >> I recently tried to use AlF3 to mimic the transition of an enzyme. In >> all the publications I can find, when mimicking the 3rd phosphate of >> the transition state, the AlF3 forms a trigonal bipyramid >> coordination, and the G(A)DP oxygen to the AL is about equal distance >> to that from the AL to the catalytic water oxygen (2.2A). >> However, I got a completely different geometry of ALF3, I think I have >> the ALF3OH bound and it's a tetrahedron geometry instead of trigonal >> pyramidal. The G(A)DP oxygen to the AL is about 3.1A and the AL to >> the catalytic water oxygen is about 1.8A. >> I am pretty sure it is not the ALF4 but the ALF3OH since the AL-OH >> distance is longer than the Al-F distance (1.8A verse 1.6A) and I have >> a very high resolution structure. >> Can anyone explain this to me, have you ever encountered this before? >> Your answer is much appreciated! >> Jinyu >> - >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- > Matthew Bowler > Project Leader MASSIF1@ESRF > European Molecular Biology Laboratory > 71 avenue des Martyrs > CS 90181 F-38042 Grenoble > France > === > Tel: +33 (0) 4.76.20.76.37 > Fax: +33 (0) 4.76.20.71.99 > > http://www.embl.fr/ > http://www.esrf.eu/MASSIF1 > https://twitter.com/id30_massif1 > https://www.embl.org/people/person/mbowler/ > === > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] effect of torsion angle definition in cif file
Dear all, I have a problem in fine tuning the cif file for my new ligand. I try to force a specific torsion angle, but coot doesn't "obey". The ligand has more than 50 atoms , so I tried with simple ethane diol, EDO. I copied the EDO.cif from the library and changed the C1-C2 torsion angle definition to EDO sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 1 After loading EDO in coot via "import cif dictionary" with "generate a molecule", regularize zone should now push the dihedral to 180°, because the periodicity was changed to 1. Instead, it refines to 58.86°. After manually setting it to 110° by "edit chi angles" it still refines to 58°. After setting it to 130° it refines to 179°. It thus behaves like periodicity 3, not periodicity 1. The modified cif file was correctly read, in "edit chi angles" it clearly states sp3_sp3_4 C1 C2 ref 180.00 per: 1. What am I missing? Greetings Gottfried To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] anomalous data usage
Dear all, I have a few questions handling (non) anomalous data: By default aimless seems to produce Iplus and Iminus columns. Can I force it to (also) create an Imean column? What does refmac do, when it gets Iplus and Iminus (and their sigmas) as input. Does it take only one of them or does it calculate and use Imean? Greetings Gottfried To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Full professorship in biochemistry, Greifswald, Germany
Dear all, the University of Greifswald is currently seeking to appoint a full professor (m/f) of biochemistry (Biochemie III). You can find the official advertisement at University-Homepage: https://www.uni-greifswald.de/universitaet/information/stellenausschreibungen/professuren/stellenausschreibung/n/w2-professur-fuer-biochemie-iii/ Euraxess: https://euraxess.ec.europa.eu/jobs/779824 To repeat some points, the topics protein biochemistry and modern biochemical-analytical methods are explicitely mentioned. Greifswald university has a research focus on proteomics and protein technologies open for extension and collaborations. A group using protein crystallography does exist in the institute (Prof. Lammers), so a pure focus on protein crystallography will have a hard time to convince the committee, but related fields are welcome. Using the new in house X-ray generator and crystallization facilities will be possible, though. Neighbouring groups also have equipment and expertise in various bioanalytical methods as ITC, SPR, fluorimetry, DLS. A 600 MHz NMR also exists in the institute which is currently run by the Biochemie III group. As written in the advertisement, applications of female scientists are particularly welcome. The deadline for the application is June 24, 2022. Best regards, Gottfried Dr. Gottfried Palm Synthetische und Strukturelle Biochemie Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4, D-17489 Greifswald Tel.: 03834 420 4393 -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Cysteine-S-Iodine interaction
Check the electron density (O, Cl, I ?) and the anomalous signal on your "iodine". Cysteine has an interesting chemistry and one is oxidation to the sulfenic acid, CSO, already mentioned. Probably, it is more common than we tend to expect and may be overlooked, because we don't look for it and because it is further oxidized to the sulfonic acid during purification. Even more unexpected is the sulfenylchloride, R-S-Cl. A redox sensor we worked on has a reactive cysteine which is oxidized (eventually to a disulfide) by hydrogenperoxide, most likely the mechanism goes via H2O2 + Cl- --> HOCl, RSH + HOCl --> RSCl, RSCl + RSH --> RSSR. Thus, sulfenylchloride has a physiological role, why not sulfenyliodide. I am not sure, if it is long lived enough to be ever crystallized, though. Greetings Gottfried Am Freitag, den 18-03-2022 um 09:04 schrieb Paul Emsley: On 17/03/2022 17:37, Mohd Syed Ahangar wrote: > > > I have been doing some protein crystal soaking with some covalently > binding fragments and in one structure I have got an extra density on > Cysteine but that density doesn't match with the expected fragment. > The fragment was in the form of iodide salt. when I fit the Iodine in > the density, it fitted fairly well than any other possible chemical > entity. From the density map it looks like something is covalently > bound to Cysteine. > Now my question is, can a sulphur atom of Cysteine have such an > interaction with Iodine. No, they are both electronegative, C-S-I is not a thing. > The distance between S and Iodine is 2.76A in this case as shown in > the attached figure. > I would be grateful if someone can shed some light on this. > Your map (this figure) is a textbook example of a covalently linked atom incorrectly refined with a non-bonded contact. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ligand binds to one molecule
Dear all, I don't think, there is much to add to the statement of Bernhard or James that different protomers in the asymmetric unit (must) have some difference in there contacts and therefore often in their conformation. What it doesn't answer is a chicken or the egg question: do the different environments in the crystal allow or force different conformations (e.g. open or closed loops) and/or different (active) site occupancies or do different states in an oligomer allow or force crystallization only in a packing and space group with multiple states? Latter could be due to an anti-cooperative binding to a dimer. We have seen this in the dimeric Tet repressor: wt binds the ligand (a tetracycline) in each monomer of the dimer with one chain in the asymmetric unit, but some of the mutants bind only one ligand per dimer (confirmed by ITC, Biochimica et Biophysica Acta, 2020). Despite the same packing, this forces reduction of space group symmetry from I422 to P422 (omitting screws). >From the crystal structures alone, I think, one cannot prove what comes first. From my gut feeling, in most cases multiple states in solution force multiple states in the crystal - in other words - I tend to say, multiple states in the crystal are "real" in the sense they also occur in solution. Does somebody want to comment on this? Greetings Gottfried Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp: As you stated, you have multiple protomers in the asymmetric unit, where they are free from crystallographic symmetry constraints. Generally that means different local environment for each protomer. Inspecting the sites in the different protomers (frequently related by various non-crystallographic symmetry operations) often can reveal plausible reasons for different occupancies. One hydrogen bond more or less for example can mean a difference of 4 orders of magnitude in Kd. Best, BR -Original Message- From: CCP4 bulletin board On Behalf Of Sent: Saturday, March 5, 2022 12:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ligand binds to one molecule Hello all, In homo-dimeric or homo-oligomeric protein crystal structures, what would be the reason for having a ligand (chemical compound or fragment) binds to one molecule and not all molecules in the asymmetric unit? I have soaked a fragment that has an affinity of 200 uM to a viral protein but I can only see it binds to one molecule (we have eight molecules in the AU). This is was also notable as well in some published PDB (dimeric protein). Any suggestions? Best wishes, Shymaa To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] the complex structure of protein and DNA
Dear Yang Meiting, I have not solved protein - DNA complexes, but I have seen many protein densities with more or less ligand bound. When the ligand has a carboxylate group but doesn't bind tight enough, often an acetate or sulfate groups binds instead. Depending on how clear you see the phosphates and how sure you can be that there is not only solvent but some kind of covalently linked atoms between them, you should consider the disappointing case of e mere chain of sulfates or phosphates (depends on your crystallization conditions). If you can wash some crystals and detect DNA in them, that would be a good reasurance. Best regards, Gottfried Am Freitag, den 17-12-2021 um 08:01 schrieb Petr Kolenko: Dear Yang Meiting, There are few things to know better about your structures first: 1) What is the resolution of the complex structure? 2) In what stage of structure refinement you are? Rwork/free would help. 3) Have you tried some automatic DNA building tools? I am not surprised that you can see only a fraction of DNA. I guess, solvent flattening may also decrease the visibility of this region. The only thing I would suggest now, do not expect to see the whole DNA immediately. Just start with the step-wise building if possible. The rest may appear in the later stage of model building. Best regards, Petr From: CCP4 bulletin board on behalf of Meiting Yang Sent: Friday, December 17, 2021 7:29:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] the complex structure of protein and DNA Dear all， We have determined two Crystal structures, with one is apo structure and the other is a complex of the same protein with double-stranded DNA. In the complex, the protein structure is clearly viible, but the DNA only can be seen several phosphate groups. We want to know how do we get the complete DNA structure. The space group of the apo structure is P222, one asymmetric unit including two protein molecules. The space group of the complex structure is P2, one unit containing two protein molecules, 5 phosphate groups just situated near one protein molecules. The binding ability of the DNA and the protein is about 1 μM. The DNA we used for crystallization is 18 bp double-stranded DNA, but now only 5 phosphate groups can be observed. The crystal we have identified is a complex rather than a monomer, the cell parameters of complexes and monomers are different. Here, we want to get some suggestions, to get the complexe that contain the entire DNA structure. Best regards. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Rigaku X-ray diffractometer open for bidding
Dear all, our previous Rigaku X-ray diffractometer is being offered by the VEBEG (auctions of used stuff from federal institutions in Germany) for the highest bid. It is only in German, but open to all bidders. https://www.vebeg.de/de/verkauf/suchen.htm?DO_SUCHE=1_MATGRUPPE=1170_AUS=2142260_LOS=2 The machine as a whole is not functioning. It doesn't power up and we don't know, which part(s) are responsible. We expect problems in (one of) the generator boards. Several parts should work, though: anode: one in the machine, which worked until the end of operation; a second one, which can be refurbished osmic mirror goniometer AFC12 detector: Saturn 92 CCD camera Cryotiger (cooling the CCD camera to -30°C) control unit for the CCD camera and goniometer, supplies the data to the frame grabber via glas fiber cable TMP, Part No 906116, Rebuilt, TMP, Varian, V81 TMP adapter, Part No 902123, Adapter, TMP-TV81 TRAFO for the high voltage generator Possibly defunct parts: TMP driver, Part No 1014563, Driver, TMP, PCB, Agilent, V81 (this board could be one of the parts which lead to failure of the system) 2 computers (frame grabber and data collection control) (as a set they don't boot properly anymore) Not part of the offer: Cryosystem Crystal camera Oil pump Chiller for anode Feel free to get in contact with us, jens.hop...@uni-greifswald.de, michael.lamm...@uni-greifswald.de, p...@uni-greifswald.de, we will be back in office on Oct 11th and might not answer the emails before. Greetings Gottfried Gottfried Palm Synthetic and Structural Biochemistry Institute for Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17489 Greifswald Germany To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] version for old AMD processors
Thanks Tim and Oleg for suggestions. The legacy version works and should be sufficient for my purpose. Maybe there could be a link or hint in the chapter "Old AMD processors" to avoid unnecessary questions. Greetings Gottfried On Thursday, 10-12-2020 at 12:46 Kovalevskiy, Oleg (STFC,RAL,SC) wrote: Dear Gottfried, If this is 64-bit AMD, there is legacy build of CCP4 for Linux available for download at the bottom of this page (under ‘Legacy systems’): http://www.ccp4.ac.uk/download/#os=linux Hope this helps. All the best, Oleg -- Dr Oleg Kovalevskiy CCP4 Core team UKRI Science and Technology Facilities Council Rutherford Appleton Laboratory Harwell Campus Didcot, Oxfordshire OX11 0QX UK From: CCP4 bulletin board Date: Thursday, 10 December 2020 at 15:08 To: ccp4bb Subject: [ccp4bb] version for old AMD processors Dear all, I am running into a "known issue" upon installing ccp4-7.1 on a pre2010 AMD machine. The download page says CCP4 7.1: Known issues ... Old AMD processors ... We are in the process of preparing an alternative release package for those processors. Is there a solution in the meanwhile? Greetings Gottfried To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] version for old AMD processors
Dear all, I am running into a "known issue" upon installing ccp4-7.1 on a pre2010 AMD machine. The download page says CCP4 7.1: Known issues ... Old AMD processors ... We are in the process of preparing an alternative release package for those processors. Is there a solution in the meanwhile? Greetings Gottfried To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] how to swap chain IDs
Hi Christian, couldn't you simply change the position in a text editor after changing chain IDs in coot? Atom IDs should renumber after reading and writing in coot, but conversion to cif will probably ignore the atom IDs anyway. Greetings Gottfried On Monday, 07-12-2020 at 19:19 Pavel Afonine wrote: Hi Christian, you can do it in Phenix PDBTools: GUI->Model Tools-> load files then Options->Other modifications look for Rename chain ID. Pavel On Mon, Dec 7, 2020 at 9:49 AM Christian GALICIA wrote: Hello, I'm trying to swap the chain IDs of a structure. I tried changing the IDs in coot and with PDBset, both change labels of the chains but not the atom positions nor numbering.Also, after the pdb file is converted to cif for deposition it displays in pymol in the original position making chain A not to be at the beginning of the sequence. I would appreciate if you would suggest a good way to achieve this. The structure is otherwise finished and will no go any other rounds of refinement. Thanks Christian -- Christian Galicia E-mail: cgali...@vub.be - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ligand bound to only one chain in the crystal
Dear all, the tenor seems to be, if you see the ligand in any of the monomers, that's the mode the ligand binds. We have seen other cases, though, too. Usually the protein I am thinking of (TetR(D)) crystallizes with one molecules /a.u. In solution it is an obligate dimer. The dimer is formed by a crystallographic axis. Each chain binds one ligand and for wt the binding constant is sub uM without noticable cooperativity. For some mutants we saw breakdown of this crystallographic axis (symmetry dereases from I4(1)22 to P4(3)2(1)2), though, and now one of the chains harbored a ligand, the other did not. It took some very careful measurements to check that these mutants bind the ligand anticooperatively, i.e. the first chain binds a ligand, the second of the monomer so much weaker that we couldn't measure it. So, in case of oligomers, keep cooperativity in mind. Greetings Gottfried On Tuesday, 27-10-2020 at 12:57 Ian Tickle wrote: Hi Christian I wouldn't worry: if the density is clear that nails it. You didn't say whether this is a soak or co-crystallization. I assume the former since you mention solvent channels. In my experience this is much more likely in the case of soaks, which can often (though not always) be rationalised by the kinetic effect (different rates of exchange of bound and free ligand due to different accessibilities), so the time to attain equilibrium can be much longer than your soaking time, whereas in the case of co-crystallizations it's obviously pre-equilibrated and determined purely by the binding affinity. Even if there are no obvious solvent channels leading from the bulk solvent to the binding sites, a soaked ligand can still get in (particularly if high-affinity which prevents it leaving again), because the protein can "breathe" opening up short-lived channels which close behind the ligand. Cheers -- Ian On Tue, 27 Oct 2020 at 10:29, Christian GALICIA wrote: Hello, In our structure only one chain in a crystallographic trimer (non-biological) shows a ligand bound to it (with clear density). There doesn't seem to be any channels (or lack of them) favoring that specific site. Can the community give your opinion on whether this can make the presence of the ligand or its biological role questionable, and give any examples of similar cases you might be aware of. Thank you. -- Christian Galicia Post Doctoral Scientist E-mail: cgali...@vub.be - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Accessing full list of programs in CCP4I2
distang to do a quick check on crystal contacts.. nd there must be more.. Eleanor On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried wrote: For occasions like Laus, it would be useful to further on have access to the CCP4 v7.0 Program Documentation, even if the programs are not updated as Christian explained. I was for instance looking for translating coordinates as in pdbset, but couldn't find a replacement in the ccp4i2 gui. Greetings Gottfried On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote: Ah I see! Great I can run it that way And yes, Eleanor, after I realized that list was gone, I was panicking that there are some random things I used to do with those programs would no longer be possible. Good to know that the command line versions are still there in the 7.1 distro. Best, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" wrote: yes Eleanor is right. command line still works.:-) fft is also in 7.1 distribution. On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson wrote: Oh Lau - how I miss that list! But if you just run fft online it is still distributed..wombat:Downloads eleanor$ fft hklin mapout LABIN FP= and so on.. On Tue, 7 Jul 2020 at 14:22, Christian Roth wrote: Hi Kelvin, well fft as single program is kind of not longer supported as is not ccp4i. In i2 internally, as well in communication with mg or coot, everything is done using map coefficients. Their are two options: First via i2: Use the unusual map coefficients Task and choose not to compare maps, but to generate the map coefficients plus a map (button is in Advanced tab) the standard grid parameters can be changed, but are actually optimized already. Second just save the map out of Coot (Export map) To avoid redundancy, the old fft task was discontinued. i2 works with coefficients, which generates smaller files and Coot provides all the functions to generate the map and is its own gui. Hope that explains a bit why things are how they are now. Cheers Christian On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin wrote: Hi Christian, I was in particular looking for the fft program (I couldn't find that using the method you described) just to convert an mtz into a .map. Before in version 7.0 I could just browse all programs, now it seems like I cannot do that (other than using the filter, and some seem to be missing) At the end I just used mtz2map in phenix. -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] On 06.07.20, 13:34, "Christian Roth" wrote: Hi Kelvin, not quite sure if I understand you correctly, but if you press the Task Manager button you get on the right sight a list of topics (import data, Molecular Replacemnt etc.) each point can be open up like a file tree to see all programs or pipelines available. You can search with the search field (Filter) on top for specific program names. Does that help? Cheers Christian On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin wrote: Hello, I am looking for a way to find the list of programs accessible using the new 7.1 CCP4I2 interface? Is this still possible or do I have to revert back to version 7.0? Best regards, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe fro
Re: [ccp4bb] Accessing full list of programs in CCP4I2
For occasions like Laus, it would be useful to further on have access to the CCP4 v7.0 Program Documentation, even if the programs are not updated as Christian explained. I was for instance looking for translating coordinates as in pdbset, but couldn't find a replacement in the ccp4i2 gui. Greetings Gottfried On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote: Ah I see! Great I can run it that way And yes, Eleanor, after I realized that list was gone, I was panicking that there are some random things I used to do with those programs would no longer be possible. Good to know that the command line versions are still there in the 7.1 distro. Best, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" wrote: yes Eleanor is right. command line still works.:-) fft is also in 7.1 distribution. On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson wrote: Oh Lau - how I miss that list! But if you just run fft online it is still distributed..wombat:Downloads eleanor$ fft hklin mapout LABIN FP= and so on.. On Tue, 7 Jul 2020 at 14:22, Christian Roth wrote: Hi Kelvin, well fft as single program is kind of not longer supported as is not ccp4i. In i2 internally, as well in communication with mg or coot, everything is done using map coefficients. Their are two options: First via i2: Use the unusual map coefficients Task and choose not to compare maps, but to generate the map coefficients plus a map (button is in Advanced tab) the standard grid parameters can be changed, but are actually optimized already. Second just save the map out of Coot (Export map) To avoid redundancy, the old fft task was discontinued. i2 works with coefficients, which generates smaller files and Coot provides all the functions to generate the map and is its own gui. Hope that explains a bit why things are how they are now. Cheers Christian On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin wrote: Hi Christian, I was in particular looking for the fft program (I couldn’t find that using the method you described) just to convert an mtz into a .map. Before in version 7.0 I could just browse all programs, now it seems like I cannot do that (other than using the filter, and some seem to be missing) At the end I just used mtz2map in phenix. -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] On 06.07.20, 13:34, "Christian Roth" wrote: Hi Kelvin, not quite sure if I understand you correctly, but if you press the Task Manager button you get on the right sight a list of topics (import data, Molecular Replacemnt etc.) each point can be open up like a file tree to see all programs or pipelines available. You can search with the search field (Filter) on top for specific program names. Does that help? Cheers Christian On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin wrote: Hello, I am looking for a way to find the list of programs accessible using the new 7.1 CCP4I2 interface? Is this still possible or do I have to revert back to version 7.0? Best regards, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin@epfl.ch [1] Phone: +41 21 69 30267 [2] If unreachable: +41 21 69 34494 [2] - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 Links: -- [1] mailto:kelvin@epfl.ch [2] tel:+41%2021%2069%C2%A030267
Re: [ccp4bb] text color in coot buttons
Paul's answer helped despite of my sparse infos, thanks. I am using open SuSE, either openSUSE Leap 42.3 or 15.1 I am using ccp4-7.0 and coot 0.8.9.2 downloaded from the CCP4 Download pages In the Application menu I could change Settings - Configure Desktop - Appearance - Workspace Theme - Look And Feel from default "openSUSE" to "Breeze Dark". This results in white text on gray background. Thanks again Gottfried On Thursday, 26-03-2020 at 17:53 Paul Emsley wrote: On 26/03/2020 16:46, Palm, Gottfried wrote: I have problems reading some of the text in coot. Example situation: I open the Ramachandran Dynarama. The I hover with the mouse over one of the dots for a residue. A small box appears, but the text is white on very light grey background. Most of the time impossible to read. I believe it is not a problem from coot, rather from some other setting somewhere, but I don't know where. Can I get a hint, what to change /set? When reporting issues with Coot it's often a good idea to tell us which version you are using, from where downloaded it and on which operating system and desktop you are trying to use it. For the record, I don't support ccp4 builds of Coot, but sometimes I help out. My guess is that this is some sort of Fedora system - try changing your desktop theme. Paul. - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] text color in coot buttons
Dear all, I have problems reading some of the text in coot. Example situation: I open the Ramachandran Dynarama. The I hover with the mouse over one of the dots for a residue. A small box appears, but the text is white on very light grey background. Most of the time impossible to read. I believe it is not a problem from coot, rather from some other setting somewhere, but I don't know where. Can I get a hint, what to change /set? Thanks Gottfried Gottfried Palm Universität Greifswald,Institut für Biochemie Felix-Hausdorff-Straße 4 D-17489 Greifswald To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names
The situation might not be so rare, if you consider 50% Lys and 50% Acetyl-Lys or other post-translational modifications. Gottfried On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote: If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the alternative residue is a Phe, then it would be ALEU and BPHE, both residues would have the same residue number, and reset the occupancies to fractions that sum to 1.0. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 6, 2019, at 1:36 AM, herman.schreu...@sanofi.com wrote: Dear Edwin, I do not know whether your question has been answered already, but the answer is simple: you have to define alternative conformations. Easiest is to generate them in coot with the “add alternate conformation” option in the right panel. You may have to delete the original unlabeled alternative conformation first though. Alternatively, if you want to keep the original coordinates, or if the alternative residue is different: say a Leu versus a Phe you can open the pdb file with an editor and generate the alternative conformation yourself: One of the residues gets an “A” in front of the residue name, e.g. ALEU, and the alternative residue a “B”, say BLEU. You also have to reset the occupancies to 0.5 for both conformations (or different fractions which add up to one). Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin Pozharski Gesendet: Montag, 4. Februar 2019 22:35 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names Belated happy 2019, everyone. For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same residue ID. Presented with a pdb file that has such feature, Refmac fails saying this ERROR: in chain A residue: 443 different residues have the same number There is an error in the input coordinate file At least one the chains has 2 residues with the same number Check above to see error ===> Error: Problem with coordinate file There are several ways of getting around this I can think of. Perhaps duplicate chain with strict NCS for all but the residue in question could work. Perhaps adding this residue as two separate chains and then adding enough LINK records to keep things in place could. Either solution here is inelegant and requires reformating pdb file back to sanity prior to deposition. Is there some way to allow different geometries for alternate conformers that is native to Refmac? Cheers, Ed. PS. I know that phenix.refine takes the mixed name pdb file straight up. I still want to be able to refine such structure with refmac (and buster, actually, but that's a question I already asked in the appropriate forum. Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse / - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 [1] - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 - UT Southwestern Medical Center The future of medicine, today. - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 Links: -- [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=533Wexf2P2dxZ7xNYAOkGTAhejw65fhzx7fdVjiaqR0=3CLcdo1WJ40rHm6l4rs8gd7nqHBgf_cZbvJjRgUfgHg= To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
