Search results for "look through"

Re: [phenixbb] Error determining reference matches

by Pavel Afonine

Hi Dan, the only way we can help (= debug the problem, fix it or/and suggest a work-around) is if we can reproduce it here locally. To do this we need all inputs and commands necessary to reproduce the refinement run that crashed. Please send files to me (not to whole mailing list) and I will look myself or redirect to a respective developer. Thanks, Pavel On 8/30/13 4:32 PM, Dan McNamara wrote: > Hi all, > > I am encountering a strange crash when running phenix.refine through > the command line with reference model restraints turned on. The > references point to two different PDB files, one labeled as chain A > and one labeled as chain B. > > This error occurs whether I have my refinement model in P1 with 192 > chains or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH > (96). It appears to fail to align the reference models to the > sequences in the refinement model. This error does not occur with > other smaller target structures under 25 chains and reference models > used with the same installation of phenix. > > I am hoping for any advice on why this might be happening or how I > might get around it. > > ================== Extract refinement strategy and selections > ================= > > Refinement flags and selection counts: > individual_sites = True (401472 atoms) > torsion_angles = False (0 atoms) > rigid_body = True (401472 atoms in 192 groups) > individual_adp = False (iso = 0 aniso = 0) > group_adp = True (201984 atoms in 25824 groups) > tls = False (0 atoms in 0 groups) > occupancies = False (0 atoms) > group_anomalous = False > > n_use = 401472 > n_use_u_iso = 401472 > n_use_u_aniso = 0 > n_grad_site = 0 > n_grad_u_iso = 0 > n_grad_u_aniso = 0 > n_grad_occupancy = 0 > n_grad_fp = 0 > n_grad_fdp = 0 > total number of scatterers = 401472 > *** Adding Reference Model Restraints *** > determining reference matches automatically... > Traceback (most recent call last): > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py", > line 92, in run > master_params=customized_master_params) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py", > line 501, in __init__ > log=self.log) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 147, in __init__ > self.get_reference_dihedral_proxies() > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 460, in get_reference_dihedral_proxies > log=self.log) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 323, in process_reference_groups > moving_chain = mod_h) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py", > line 426, in _ssm_align > ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 215, in residue_groups > return cls( match = match, indexer = indexer ) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 176, in __init__ > self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) ) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 173, in get > assert identifier in indexer, "Id %s missing" % str( identifier ) > AssertionError: Id ('A', 1, ' ') missing > > Best, > Dan > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 5 months

Re: [phenixbb] measuring the angle between two DNA duplexes

by Pavel Afonine

Hi Tim, thanks for the reference! There is a number of instances where this approach is useful. In Phenix this is also used to determine density map peak sphericity (see cctbx/maptbx/sphericity.h) and to get initial values for refinement of anisotropic ADPs from map peaks. Sure I will play with this and visit as many corner cases as I could think of! All the best, Pavel On 1/21/14, 1:25 AM, Tim Gruene wrote: > Hi Pavel, > > that's the method described in > http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based > on the moments of inertia (a computer scientist might name it > differently). I am not sure, though, you would get the desired result > for short helices. E.g. a helix defined by three atoms the eigenvalue > would point roughly in the direction of the external phosphates, which > is far from parallel with the helix axis. > > Best, > Tim > > On 01/21/2014 04:20 AM, Pavel Afonine wrote: >> Hi Ed, >> >> interesting idea! Although I was thinking to have a tool that is a >> little more general and a little less context dependent. Say you have >> two clouds of points that are (thinking in terms of macromolecules) two >> alpha helices (for instance), and you want to know the angle between the >> axes of the two helices. How would I approach this?.. >> >> First, for each helix I would compute a symmetric 3x3 matrix like this: >> >> sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) >> sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) >> sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 >> >> where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over >> all atoms, and (xc,yc,zc) is the coordinate of the center of mass. >> >> Second, for each of the two matrices I would find its eigen-values and >> eigen-vectors, and select eigen-vectors corresponding to largest >> eigenvalues. >> >> Finally, the desired angle is the angle between the two eigen-vectors >> found above, which is computed trivially. >> I think this a little simpler than finding the best fit for a 3D line. >> >> What you think? >> >> Pavel >> >> >> On 1/20/14, 2:14 PM, Edward A. Berry wrote: >>> >>> Pavel Afonine wrote: >>> . . >>> >>>> The underlying procedure would do the following: >>>> - extract two sets of coordinates of atoms corresponding to two >>>> provided atom selections; >>>> - draw two optimal lines (LS fit) passing through the above sets >>>> of coordinates; >>>> - compute and report angle between those two lines? >>>> >>> This could be innacurate for very short helices (admittedly not the >>> case one usually would be looking for angles), or determining the axis >>> of a short portion of a curved helix. A more accurate way to >>> determine the axis- have a long canonical duplex constructed with its >>> axis along Z (0,0,1). Superimpose as many residues of that as required >>> on the duplex being tested, using only backbone atoms or even only >>> phosphates. Operate on (0,0,1) with the resulting operator (i.e. take >>> the third column of the rotation matrix) and use that as a vector >>> parallel to the axis of the duplex being tested. >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years

Re: [phenixbb] alternatives to RMSD

by Tim Gruene

Hi Pavel, if the B-value would correspond to a cloud of possible locations, one should be able to move an atom within the cloud without altering the R-value and other quality indicators and without a refinement program moving the atom back to where it came from. In my experience this is not the case, why I prefer the (original) scientific interpretation of the B-value as to model of harmonic motion rather than its statistical. That is also the reason why I am not a friend of exorbital B-values in PDB-files. I think they tend to fudge poor modelling. Cheers, Tim On 07/07/2014 10:02 PM, Pavel Afonine wrote: > Hi Tim, > > consider two atoms located at say 1A distance apart. In one case their > B-factors are 1A**2 and in the second case their B-factors are 100A**2. > In the first case these are two individual atoms and measuring distance > between them makes sense, while in the second case atoms virtually > coincide (within the cloud of their possible locations, given their > B-factor) and therefore measuring distance between them isn't very > meaningful. Using the map would differentiate these two scenarios, while > usual way of computing RMSD would not. I guess this is what I was trying > to say in my previous post. > > Whether the values of a metric of choice are intuitive or not is a > separate question. After all you can always calibrate your expectations > using examples with known answer. > > Pavel > > > On 7/7/14, 3:47 AM, Tim Gruene wrote: >> Hi Patrick, >> >> why don't you superimpose only the matching segments and report their >> RMSD? It is the common procedure for RMSD's from superpositions to >> report the aligned residues together with the RMSD. >> >> The advantage compared to a map CC is similar to that of R_sym over >> R_meas: readers have a better concept (from experience) of what the >> numbers mean. >> >> Best, >> Tim >> >> On 07/02/2014 05:15 PM, Patrick. C wrote: >>> Hi Phenix users, >>> >>> I am not a crystallographer but I though you guys might be a good >>> place to ask >>> this question. >>> >>> I have 2 super secondary structures, A and B and they consist of >>> Helix-turn-Strand >>> >>> Due to the turn the two structures have a poor RMSD because the two >>> flanking >>> fragments of Helix and Strand are far from each other but when I >>> superimpose the >>> two fragments individually(helixA with helix B and standA with >>> strandB in Pymol >>> they align very well). >>> >>> Now, is there a way to express this instead of using the RMSD? >>> When the two structures align well the RMSD is very good but a slight >>> movement >>> and the RMSD is awful. >>> But looking at the two structures I can see they follow the same path >>> through space. >>> >>> Thank you, >>> Patrick >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> 3D Earth Screensaver Preview <http://www.inbox.com/earth> >>> *Free 3D Earth Screensaver* >>> Watch the Earth right on your desktop! Check it out at >>> www.inbox.com/earth >>> <http://www.inbox.com/earth> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

11 years, 7 months

Re: [phenixbb] Coot mutation of Asp residue to isoAsp residue

by Xiao Lei

Hi Zhejie, For the 1AT6 structure, I downloaded its density in coot using "fetch density from EDS", but when I found the IAS at 101 position and try to do real space refine, it gives an error that "Refinement setup failure. Failed to find restraints for IAS." I do not know how to fix this but it seems to me it's caused by incomplete restraints dictionary or monomer library in ccp4? Thanks. Xiao On Tue, Aug 18, 2015 at 10:42 AM, Xiao Lei <xiaoleiusc(a)gmail.com> wrote: > Hi Zhijie, > > Thank you very much for the information. For step 1 you mentioned, I can > get monomer with L-Asp but it seems I can not drag it (or I do not know how > to do) and can not delete or modify it to become isoAsp. I will try play > around more though. > > Xiao > > On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li(a)utoronto.ca> wrote: > >> Hi Xiao, >> >> IsoAsp is essentially an L-Asp linked with next aa through its side chain >> (beta) carboxyl. So the mutation button won’t help you. You need to build >> in a new L-ASP, which is treated as a covalently linked ligand (HETATM >> records), instead of a standard residue (ATOM records) of the protein chain. >> >> A practical method might be: 1) delete the original Asp, 2) import a free >> L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the >> density, delete one oxygen atom on the beta-carboxyl and change the >> residue’s numbering and chain id to fit it into the sequence, 3) edit the >> PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside >> the chain). >> >> For step 3, you may need to rename the ASP to something else (IAS was >> used for isoASP in older pdb, so I would go with IAS ) so that coot won’t >> try to make a regular peptide bond using its main chain carboxyl during >> real space refinement. Of course you will need to make a cif file for the >> “new” compound too. I guess you can make a copy of ASP.cif from the monomer >> library and change everything in it to IAS. I think if you have placed the >> IAS to the right location and its ends are in bonding distance with the >> neighbouring aa residues you may not need to do anything for refmac. For >> phenix.refine you will need to add a bond description to the .edit file for >> each linkage the IAS makes to the neighboring aas. >> >> You may take a look at the structure 1AT6 and its PDB file. The residue >> IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the >> chain and there are two LINK records in the header to indicate its linkage >> to neighbouring aas (LINK records are normally not generated or needed >> during refinement using refmac or phenix.refine). >> >> >> Zhijie >> >> >> >> *From:* Xiao Lei <xiaoleiusc(a)gmail.com> >> *Sent:* Monday, August 17, 2015 6:50 PM >> *To:* PHENIX user mailing list <phenixbb(a)phenix-online.org> >> *Subject:* [phenixbb] Coot mutation of Asp residue to isoAsp residue >> >> Dear Phenixbb members, >> >> I suspect one Asp residue in my model may be an isoAsp (isomerization of >> Asp). I am asking if there is way to mutate Asp residue to >> isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in >> Mac OS X10.10.5)? >> >> I know there is a mutation button on coot, but the mutated aa lists are >> all natural amino acids. If I have to delete the Asp residue first and then >> build isoAsp into the density map, is there a way in coot to build an >> isoAsp residue in map? >> >> Thanks ahead. >> >> Xiao >> >> ------------------------------ >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> >

10 years, 5 months

[phenixbb] Re: phenixbb Digest, Vol 237, Issue 1 (out of office)

by Elisabeth Laurent

Thank you for your e-mail. I am out of office until September 15th, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 12.9.25 20:35 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. atom selection for elements anisotropic rest TLS (Georg Mlynek) 2. Re: atom selection for elements anisotropic rest TLS (John Bacik) 3. adding together (James Holton) 4. Re: adding together (Petrus Zwart) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Sep 2025 08:17:54 +0200 From: Georg Mlynek <georg.mlynek(a)univie.ac.at> Subject: [phenixbb] atom selection for elements anisotropic rest TLS To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <676e375c-3d60-438c-adc8-8f6942afb591(a)univie.ac.at> Content-Type: text/plain; charset=UTF-8; format=flowed Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. ------------------------------ Message: 2 Date: Wed, 10 Sep 2025 18:38:38 +0000 (UTC) From: John Bacik <mxjpb(a)yahoo.com> Subject: [phenixbb] Re: atom selection for elements anisotropic rest TLS To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org>, Georg Mlynek <georg.mlynek(a)univie.ac.at> Message-ID: <40790919.1197232.1757529518607(a)mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Hi Georg, if you are trying to refine anisotropic B-factors for a Mn or Mg element only I do not think you need TLS parameters for that. One way to refine specific elements would be in Refinement settings/Modify start model/B-factors/tick "Convert to anisotropic" and select for the Mn or Mg element. Any element that is formatted as anisotropic will remain so through subsequent rounds of refinement. All the best,John On Wednesday, September 10, 2025 at 01:18:06 AM CDT, Georg Mlynek <georg.mlynek(a)univie.ac.at> wrote: Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 3 Date: Fri, 12 Sep 2025 11:28:47 -0700 From: James Holton <jmholton(a)lbl.gov> Subject: [phenixbb] adding together To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <e2697b82-63b6-4b06-addb-f3c583d10851(a)lbl.gov> Content-Type: text/plain; charset=UTF-8; format=flowed Greetings Phenix developers! I have what I hope is a quick question. I'm trying to add a stack of phased structure factors together. Specifically from separate runs of phenix.fmodel. Normally, I'd use sftools for this, but the distributed version has a size limitation. According to Tom's phenix chatbot, I can use phenix.maps for adding two sets of structure factors togetheiotbx.reflection_file_editor, but it only works from the GUI (and I want to add 1000 mtz files together). phenix.xmanip looks promising too, but again, seems to want a pdb and an mtz. Is there a recommended way to do this? I've already asked this on CCP4BB, but I wanted to get the Phenix take on these kinds of manipulations. Thank you, -James Holton MAD Scientist ------------------------------ Message: 4 Date: Fri, 12 Sep 2025 11:34:35 -0700 From: Petrus Zwart <phzwart(a)lbl.gov> Subject: [phenixbb] Re: adding together To: James Holton <jmholton(a)lbl.gov> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <CA+_q3A1hONE54pVQJ70H10Y9fskYZL-haw_BrMuZq150a8cG=w(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" https://claude.ai/public/artifacts/f390c669-b8c7-4776-a4bc-1761b110bba0 On Fri, Sep 12, 2025 at 11:29 AM James Holton <jmholton(a)lbl.gov> wrote: > Greetings Phenix developers! > > I have what I hope is a quick question. I'm trying to add a stack of > phased structure factors together. Specifically from separate runs of > phenix.fmodel. Normally, I'd use sftools for this, but the distributed > version has a size limitation. According to Tom's phenix chatbot, I can > use phenix.maps for adding two sets of structure factors together, but > it seems to only want to combine an mtz with a pdb. There is > iotbx.reflection_file_editor, but it only works from the GUI (and I want > to add 1000 mtz files together). phenix.xmanip looks promising too, but > again, seems to want a pdb and an mtz. Is there a recommended way to do > this? > > I've already asked this on CCP4BB, but I wanted to get the Phenix take > on these kinds of manipulations. > > Thank you, > > -James Holton > MAD Scientist > > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s -- ------------------------------------------------------------------------------------------ Peter Zwart Staff Scientist, Molecular Biophysics and Integrated Bioimaging Berkeley Synchrotron Infrared Structural Biology Biosciences Lead, Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 ------------------------------------------------------------------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org ------------------------------ End of phenixbb Digest, Vol 237, Issue 1 ****************************************

4 months, 4 weeks

Re: [phenixbb] conversion from h3 to r3 with phenix apps

by Green, Todd

Thanks for taking the time to look at this Peter and Vaheh and other for that matter. I have processed multiple datasets in p1, p222, r3, and p23. I'll try to compile a something from the log files to submit for further questions that I have. I think it is possible that some of my datasets could be twinned, I'm certainly looking into it. xtriage doesn't seem to think so for the couple of datasets that i have run through it so far, although in some of the lower symmetry sg there are a few twin laws which indicate so, xtriage seems to attribute it to orientation of ncs. I'm also doing molecular replacement in each of the space groups. Also in some of the datasets, I have alternating lattice lines of heavy and light reflections. Thusly without carefully selecting spots and the light reflections will not be chosen and the wrong lattice will be assigned(ie. the lower density spots get skipped). It goes without saying that some of the datasets are not optimal but its what i have at the moment. One of the first red flags for me in regard to it not being cubic (at least one of the datasets), was that if i processed two seperate wedges of data from the same crystal not using the same indexing then tried to merge the datasets together the r-merge would be .4+. If i used xtriage to determine an appropriate reindexing operator then merged the data, the r-merge would be .08. I didn't think alternate indexing was possible for the cubic space group (other than for the assignment of +/- reflection). So even though in my case it is Se-met data, i didn't think that the difference of 30+ percent between alternative indexings could be possible. I thought this might be indicating that I didn't have a true p23 space group. Is my thinking correct here? Also in some of the datasets, I have alternating lattice lines of heavy and light reflections. Thusly without carefully selecting spots, the light reflections will not be chosen and the wrong lattice will be assigned. It goes without saying that some of the datasets are not optimal but its what i have at the moment. Are the rows of light reflections typically indicative of pseudo-symmetry? I believe that I will have 20 copies of a hetero-complex in the cubic setting and 120 in orthorhombic which should have i believe a packing similar to the cubic crystal. thanks in advance- Todd -----Original Message----- From: phenixbb-bounces(a)phenix-online.org on behalf of Peter Zwart Sent: Fri 8/10/2007 5:24 PM To: PHENIX user mailing list Subject: Re: [phenixbb] conversion from h3 to r3 with phenix apps Hi Todd, This table tells me that the data in P1 doesn't merge very well and that limits for what is reasonable are maybe set to tight for your case. Try using the keyword tanh_location=0.11 and see what happens. Just looking at the table though, there seem to be a number of options to be considered: P1: one unused symmetry operator present with R value equal 10%. Not a good sign, sg is too low P432: ONe operator has an R value of 47%. Not a good sign, sg is too high A couple of flavours of R3. | R 3 :h (x+z,y-z,-x+y+z) | 0.148 | 0.148 | 0.256 | 0.103 | | R 3 :h (-x+y+z,x+z,y-z) | 0.153 | 0.153 | 0.256 | 0.103 | | R 3 :h (y-z,-x+y+z,x+z) | 0.164 | 0.164 | 0.256 | 0.103 | | R 3 :R | 0.169 | 0.169 | 0.256 | 0.103 | From the last column it is clearly seen that an operator is present with a R-value equal to 10%, but is not used in the point group. The point group might be too low. The flavours of R32 don't work, as a operator is used that has a high R value: | R 3 2 :h (-x+y+z,x+z,y-z) | 0.484 | 0.489 | 0.109 | 0.103 | R 3 2 :h (y-z,-x+y+z,x+z) | 0.486 | 0.492 | 0.109 | 0.103 These options are nice(ish): | P 2 3 | 0.134 | 0.169 | 0.478 | 0.478 | | | P 2 2 2 | 0.109 | 0.110 | 0.481 | 0.478 | | | P 4 2 2 (b,c,a) | 0.181 | 0.486 | 0.480 | 0.478 | | Do you have any indication that your data is twinned? Peter Green, Todd wrote: > > I'm actually not sure that it's not orthorhombic. I know looking at > the cell lengths and angles makes it very inviting to the cubic cell > and i have been working with that as a possibility. i do have a real > good suspicion that I have a pseudo-cubic cell. I can do molecular > replacement in the cubic space group but am missing some density that > I think should be there. I wanted to do molecular replacement in the > rhombohedral setting and ultimately the lower symmetry space group too > and see if I pick that density up. This is why I wanted to know how to > convert the h3 to r3 setting. the h3 cell is a nightmare for my computer! > > as a side note not all of the crystals, process in the primitive > lattice, but all process as rhombohedral. That probably means that I > have a two different types of crystals more than anything else, etc > etc etc. cross-xtal averaging is another reason to i wanted to figure > out the setting difference. > > I have previously run one of my datasets processed in p1 thru Xtriage, > it said: > > Exploring higher metric symmetry > > The point group of data as dictated by the space group is P 1 > the point group in the niggli setting is P 1 > The point group of the lattice is P 4 3 2 > A summary of R values for various possible point groups follow. > > ------------------------------------------------------------------------------------------------ > | Point group | mean R_used | max R_used | mean R_unused > | min R_unused | choice | > ------------------------------------------------------------------------------------------------ > | P 1 | None | None | 0.362 > | 0.103 | <--- | > | P 2 3 | 0.134 | 0.169 | 0.478 > | 0.478 | | > | P 4 | 0.152 | 0.488 | 0.377 > | 0.164 | | > | C 1 2 1 (z,x+y,-x+y) | 0.489 | 0.489 | 0.337 > | 0.103 | | > | P 4 2 2 (c,a,b) | 0.266 | 0.481 | 0.481 > | 0.478 | | > | P 1 1 2 | 0.110 | 0.110 | 0.221 > | 0.103 | | > | P 2 1 1 | 0.107 | 0.107 | 0.290 > | 0.110 | | > | R 3 2 :R | 0.481 | 0.483 | 0.109 > | 0.103 | | > | C 1 2 1 (x+y,-x+y,z) | 0.492 | 0.492 | 0.269 > | 0.103 | | > | P 2 2 2 | 0.109 | 0.110 | 0.481 > | 0.478 | | > | C 2 2 2 (x-y,x+y,z) | 0.190 | 0.478 | 0.339 > | 0.103 | | > | P 4 (c,a,b) | 0.454 | 0.476 | 0.272 > | 0.110 | | > | C 1 2 1 (x+y,z,x-y) | 0.483 | 0.483 | 0.351 > | 0.103 | | > | C 1 2 1 (-x+y,z,x+y) | 0.486 | 0.486 | 0.351 > | 0.103 | | > | P 1 2 1 | 0.103 | 0.103 | 0.343 > | 0.110 | | > | R 3 2 :h (x+z,y-z,-x+y+z) | 0.488 | 0.492 | 0.109 > | 0.103 | | > | P 4 2 2 (b,c,a) | 0.181 | 0.486 | 0.480 > | 0.478 | | > | R 3 :h (x+z,y-z,-x+y+z) | 0.148 | 0.148 | 0.256 > | 0.103 | | > | C 2 2 2 (z,x-y,x+y) | 0.426 | 0.489 | 0.309 > | 0.110 | | > | R 3 2 :h (-x+y+z,x+z,y-z) | 0.484 | 0.489 | 0.109 > | 0.103 | | > | C 2 2 2 (-x+y,z,x+y) | 0.386 | 0.486 | 0.327 > | 0.110 | | > | P 4 2 2 | 0.243 | 0.492 | 0.386 > | 0.169 | | > | R 3 :h (-x+y+z,x+z,y-z) | 0.153 | 0.153 | 0.256 > | 0.103 | | > | R 3 :h (y-z,-x+y+z,x+z) | 0.164 | 0.164 | 0.256 > | 0.103 | | > | P 4 3 2 | 0.362 | 0.492 | None > | None | | > | C 1 2 1 (x-y,x+y,z) | 0.478 | 0.478 | 0.269 > | 0.103 | | > | R 3 2 :h (y-z,-x+y+z,x+z) | 0.486 | 0.492 | 0.109 > | 0.103 | | > | R 3 :R | 0.169 | 0.169 | 0.256 > | 0.103 | | > | P 4 (b,c,a) | 0.419 | 0.475 | 0.290 > | 0.110 | | > | C 1 2 1 (z,x-y,x+y) | 0.481 | 0.481 | 0.337 > | 0.103 | | > ------------------------------------------------------------------------------------------------ > > R_used: mean and maximum R value for symmetry operators *used* in this > point group > R_unused: mean and minimum R value for symmetry operators *not used* > in this point group > The likely point group of the data is: P 1 > > Possible space groups in this point groups are: > Unit cell: (375.144, 375.711, 377.723, 90.002, 90.034, 90.094) > Space group: P 1 (No. 1) > > what does this say to you? > > Thanks in advance- > Todd > > > > > -----Original Message----- > From: phenixbb-bounces(a)phenix-online.org on behalf of Peter Zwart > Sent: Fri 8/10/2007 4:35 PM > To: PHENIX user mailing list > Subject: Re: [phenixbb] conversion from h3 to r3 with phenix apps > > Hi Todd, > > Are you sure this is not cubic? You could run xtriage and find out > relatively easely. > > I suggest you give phenix.xmanip a try for reindexing or try to use the > following one-liner: > > iotbx.reflection_file_converter data.sca > --change-of-basis=to_niggli_cell --sca=niggli.sca > > Cheers > > Peter > > > > Green, Todd wrote: > > > > Hello all, > > > > I have what i believe to be a rhombohedral crystal that has an > > insanely large cell with the hexagonal setting: > > > > 533.026 533.026 652.887 90.000 90.000 120.000 > > > > and a modestly large cell comparatively with the rhombohedral setting: > > > > 377 377 377 90 90 90 > > > > I should be able to easily reindex to the smaller cell in scalepack > > but for some reason i'm not getting it to work correctly. Rather than > > struggle further on a friday afternoon, i figured that i'd give a > > phenix app a try. i assume xtriage can do this, can someone point me > > in the correct direction? > > > > thanks in advance- > > Todd > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > This email was scanned with Mcafee's Anti-Virus appliance, but this > is no guarantee that no virus exists. You are asked to make sure you > have virus protection and that it is up to date. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > This email was scanned with Mcafee's Anti-Virus appliance, but this is no guarantee that no virus exists. You are asked to make sure you have virus protection and that it is up to date.

18 years, 5 months

Re: [cctbxbb] bootstrap.py build on Ubuntu

by Billy Poon

Hi David, I don't have a fix yet, but here is a workaround. It seems like setup.py is looking for libz.so instead of libz.so.1, so you can fix the issue by making a symbolic link for libz.so in /usr/lib64. sudo ln -s /usr/lib64/libz.so.1 /usr/lib64/libz.so This requires root access, so that's why it's just a workaround. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Sat, Jun 11, 2016 at 5:05 PM, Billy Poon <bkpoon(a)lbl.gov> wrote: > Hi David, > > Sorry it look so long! Setting up all the virtual machines was a time sink > and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a little > tricky. > > It looks like Ubuntu 16.04 moved its libraries around. I used apt-get to > install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1 > file in /lib/x86_64-linux-gnu and in /usr/lib64. > > I have not gotten it to work yet, but I'm pretty sure this is the issue. > I'll have to double-check 12.04 and 14.04. > > As for Pillow, I did test it a few months ago, but I remember there being > API changes that will need to fixed. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman(a)gmail.com> > wrote: > >> Hi Billy, >> >> I'm replying on this old thread because I have finally got round to >> trying a bootstrap build for DIALS out again on Ubuntu, having waited for >> updates to the dependencies and updating the OS to 16.04. >> >> The good news is, the build ran through fine. This is the first time I've >> had a bootstrap build complete without error on Ubuntu, so thanks to you >> and the others who have worked on improving the build in the last few >> months! >> >> The bad news is I'm getting two failures in the DIALS tests: >> >> dials/test/command_line/tst_export_bitmaps.py >> dials_regression/test.py >> >> Both are from PIL >> >> File >> "/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py", >> line 401, in _getencoder >> raise IOError("encoder %s not available" % encoder_name) >> IOError: encoder zip not available >> >> Indeed, from base_tmp/imaging_install_log it looks like PIL is not >> configured properly >> >> -------------------------------------------------------------------- >> PIL 1.1.7 SETUP SUMMARY >> -------------------------------------------------------------------- >> version 1.1.7 >> platform linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32) >> [GCC 5.3.1 20160413] >> -------------------------------------------------------------------- >> *** TKINTER support not available >> *** JPEG support not available >> *** ZLIB (PNG/ZIP) support not available >> *** FREETYPE2 support not available >> *** LITTLECMS support not available >> -------------------------------------------------------------------- >> >> Any ideas? I have zlib headers but perhaps PIL can't find them. >> >> On a related note, the free version of PIL has not been updated for >> years. The replacement Pillow has started to diverge. I first noticed this >> when Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system >> python produced failures because it no longer supports certain deprecated >> methods from PIL. I worked around that in r24587, but these things are a >> losing battle. Is it time to switch cctbx over to Pillow instead of PIL? >> >> Cheers >> >> -- David >> >> On 7 January 2016 at 18:12, Billy Poon <bkpoon(a)lbl.gov> wrote: >> >>> Hi all, >>> >>> Since wxPython was updated to 3.0.2, I have been thinking about updating >>> the other GUI-related packages to more recent versions. I would probably >>> update to the latest, stable version that does not involve major changes to >>> the API so that backwards compatibility is preserved. Let me know if that >>> would be helpful and I can prioritize the migration and testing. >>> >>> -- >>> Billy K. Poon >>> Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> Lawrence Berkeley National Laboratory >>> 1 Cyclotron Road, M/S 33R0345 >>> Berkeley, CA 94720 >>> Tel: (510) 486-5709 >>> Fax: (510) 486-5909 >>> Web: https://phenix-online.org >>> >>> On Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter(a)lbl.gov> >>> wrote: >>> >>>> David, >>>> >>>> I notice that the Pango version, 1.16.1, was released in 2007, so >>>> perhaps it is no surprise that the latest Ubuntu does not support it. >>>> Maybe this calls for stepping forward the Pango version until you find one >>>> that works. I see that the latest stable release is 1.39. >>>> >>>> This would be valuable information for us..Billy Poon in the Phenix >>>> group is supporting the Phenix GUI, so it might be advisable for him to >>>> update the Pango version in the base installer. >>>> >>>> Nick >>>> >>>> Nicholas K. Sauter, Ph. D. >>>> Computer Staff Scientist, Molecular Biophysics and Integrated >>>> Bioimaging Division >>>> Lawrence Berkeley National Laboratory >>>> 1 Cyclotron Rd., Bldg. 33R0345 >>>> Berkeley, CA 94720 >>>> (510) 486-5713 >>>> >>>> On Thu, Jan 7, 2016 at 8:54 AM, David Waterman <dgwaterman(a)gmail.com> >>>> wrote: >>>> >>>>> Hi again >>>>> >>>>> Another data point: I just tried this on a different Ubuntu machine, >>>>> this time running 14.04. In this case pango installed just fine. In fact >>>>> all other packages installed too and the machine is now compiling cctbx. >>>>> >>>>> I might have enough for comparison between the potentially working >>>>> 14.04 and failed 15.04 builds to figure out what is wrong in the second >>>>> case. >>>>> >>>>> Cheers >>>>> >>>>> -- David >>>>> >>>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman(a)gmail.com> >>>>> wrote: >>>>> >>>>>> Hi folks >>>>>> >>>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following the >>>>>> instructions here: >>>>>> http://dials.github.io/documentation/installation_developer.html >>>>>> >>>>>> This failed during installation of pango-1.16.1. Looking >>>>>> at pango_install_log, I see the command that failed was as follows: >>>>>> >>>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../.. >>>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\" >>>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\" >>>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED >>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include >>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2 >>>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c -fPIC >>>>>> -DPIC -o .libs/fribidi.o >>>>>> In file included from fribidi.h:31:0, >>>>>> from fribidi.c:28: >>>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or directory >>>>>> >>>>>> The file glib.h appears to be in base/include/glib-2.0/, however this >>>>>> directory was not explicitly included in the command above, only its >>>>>> parent. This suggests a configuration failure in pango to me. Taking a look >>>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant >>>>>> lines: >>>>>> >>>>>> configure:22227: checking for GLIB >>>>>> configure:22235: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>>> configure:22238: $? = 0 >>>>>> configure:22253: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>>> configure:22256: $? = 0 >>>>>> configure:22304: result: yes >>>>>> >>>>>> but this doesn't tell me very much. Does anyone have any suggestions >>>>>> as to how I might proceed? >>>>>> >>>>>> Many thanks >>>>>> >>>>>> -- David >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> cctbxbb mailing list >>>>> cctbxbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> >>>> >>> >>> _______________________________________________ >>> cctbxbb mailing list >>> cctbxbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >>> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >

9 years, 7 months

[phenixbb] Re: Multiple Linux users access same project directory

by André Graça

Thank you, Guillaume, for the reply! I realized that I was very unspecific in my original email. My query is specific to access to the Phenix GUI by multiple users, not the Phenix command line programs nor the access to the files in the Phenix directory through terminal or file explorer. I wonder if there is a possibility, even just read-only would be good enough, for 2 or more users to see the same Phenix projects in the GUI. The use case is for those users that do not have command line experience but need to audit the projects from time to time. I don't see such a user digging into the submit and log files of a job. Another use case would be for the sys Admin to quickly have a comprehensive overview of the projects without having to parse the files. I am not very optimistic there is a solution for what I am looking for, but anyway if there is a place to learn otherwise, then this is the right forum. Happy weekend everyone! André ________________________________ From: Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> Sent: Friday, October 10, 2025 4:32:32 PM To: André Graça <andre.graca(a)umu.se>; phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: Re: Multiple Linux users access same project directory Hi André, There is nothing specific to Phenix in that, and it also depends what you mean by "access". If you want all accounts to have read and write permissions to a project directory: don't try that. It's a recipe for headaches at best, disasters at worst. It's really much better to require people to coordinate and communicate (which they would have to do anyway if working on the same project) than to give all permissions to everyone and hope everything will go smoothly. It won't. Files will get overwritten unexpectedly. It is generally a reasonable assumption on the part of each user that the files they create shouldn't be modified by other accounts, and giving them a system that doesn't offer this guarantee is only going to confuse everyone using it. If you want one account to own the project directory with all other accounts able to inspect the results (but not overwrite anything!): 1) Set up a directory where these projects will go. Give it a meaningful name: I like something simple like /data. You want this on a separate partition (ideally even on a separate physical disc), because if it is on the same partition as the OS and your users fill it up with their files (as they invariably do), your system will become unstable. 2) Give all accounts all permissions to this directory: chmod 777 /data 3) Voilà! Now all accounts can create files there. With the typical default umask (see https://en.wikipedia.org/wiki/Umask ), all accounts will have read permissions to all files, but only the account owning a given file will have write permissions to that file. If this is not the case on your system, you need to either change the umask for each account to define the default permissions of newly created files (the changes will apply only to files created after it, so you would need to update permissions of all files created before that change) or define groups and use the group-level permission to achieve the same effect. Now, I don't know how Phenix deals with a read-only project directory. You can for sure read all files with external programs. But maybe the Phenix GUI needs to write to some state files within the project even when not modifying the files being worked on; if this is the case, it will likely complain. It is easy to find out (simply try it), and harmless (since none of the project files can be overwritten if an account that didn't create them is accessing them with read-only permission). I hope this helps, Guillaume ________________________________ From: André Graça <andre.graca(a)umu.se> Sent: Friday, October 10, 2025 4:06:07 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Multiple Linux users access same project directory Hi everyone, Is there any possibility to set up Phenix so multiple Linux users of the same Linux machine can access the same project directory? Thank you, André _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

4 months

Re: [phenixbb] measuring the angle between two DNA duplexes

by Phil Evans

One way that I've used for alpha-helices is to start with an ideal model with it's axis along say z, then get the rotation required to fit the ideal helix to the model. This works even for short helices Phil On 21 Jan 2014, at 09:25, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de> wrote: > Hi Pavel, > > that's the method described in > http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based > on the moments of inertia (a computer scientist might name it > differently). I am not sure, though, you would get the desired result > for short helices. E.g. a helix defined by three atoms the eigenvalue > would point roughly in the direction of the external phosphates, which > is far from parallel with the helix axis. > > Best, > Tim > > On 01/21/2014 04:20 AM, Pavel Afonine wrote: >> Hi Ed, >> >> interesting idea! Although I was thinking to have a tool that is a >> little more general and a little less context dependent. Say you have >> two clouds of points that are (thinking in terms of macromolecules) two >> alpha helices (for instance), and you want to know the angle between the >> axes of the two helices. How would I approach this?.. >> >> First, for each helix I would compute a symmetric 3x3 matrix like this: >> >> sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) >> sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) >> sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 >> >> where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over >> all atoms, and (xc,yc,zc) is the coordinate of the center of mass. >> >> Second, for each of the two matrices I would find its eigen-values and >> eigen-vectors, and select eigen-vectors corresponding to largest >> eigenvalues. >> >> Finally, the desired angle is the angle between the two eigen-vectors >> found above, which is computed trivially. >> I think this a little simpler than finding the best fit for a 3D line. >> >> What you think? >> >> Pavel >> >> >> On 1/20/14, 2:14 PM, Edward A. Berry wrote: >>> >>> >>> Pavel Afonine wrote: >>> . . >>> >>>> The underlying procedure would do the following: >>>> - extract two sets of coordinates of atoms corresponding to two >>>> provided atom selections; >>>> - draw two optimal lines (LS fit) passing through the above sets >>>> of coordinates; >>>> - compute and report angle between those two lines? >>>> >>> >>> This could be innacurate for very short helices (admittedly not the >>> case one usually would be looking for angles), or determining the axis >>> of a short portion of a curved helix. A more accurate way to >>> determine the axis- have a long canonical duplex constructed with its >>> axis along Z (0,0,1). Superimpose as many residues of that as required >>> on the duplex being tested, using only backbone atoms or even only >>> phosphates. Operate on (0,0,1) with the resulting operator (i.e. take >>> the third column of the rotation matrix) and use that as a vector >>> parallel to the axis of the duplex being tested. >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years

Re: [cctbxbb] Module versioning (was Re: Debian Package)

by Picca Frédéric-Emmanuel

On Sat, 1 Sep 2012 11:35:04 +0200 Radostan Riedel <raybuntu(a)googlemail.com> wrote: Hello, I cam back from longer holidays that I expected :). It is always good ;) > > 1. Each and every cctbx developer becomes aware of so-versioning. Let's say a module is at 2.3.4, so we have > > env.SetVersionInfo(vers="2.3.4") > > and then a change is made to the C++ code. The developer responsible for that change should then figure out the new c.r.a and then add a comment > > env.SetVersionInfo(vers="2.3.4", #next release# vers="c.r.a") > > It would then be easy to automate an edit en-masse before release that would change that line and all its sisters to > > env.SetVersionInfo(vers="c.r.a") > > That's basically a formalised version of your proposition in your answer to Johan earlier. > > > > 2. Cctbx developers would not care about so-versioning and before a Debian release, the cctbx Debian maintainers would go through each call to SetVersionInfo to set the right c.r.a, based on a careful examination of the commits, complemented by asking questions to the core cctbx developers (or simply open questions on this forum). > I'd of course like the first extreme better. For starters it would be great if > everyone feels responsible for the "current" number. I'm not a c++ developer and > I don't know if thats easy? To my opinion the first solution whould be the best one also for other distribution. Indeed this is a "social" problem, developpers of the C++ librarty should learn about ABI/API compatibility like expected by most distributions when it comes to do some "long term" support into an integrated environment. The person who did the change is the only one which know the implication of the changes. Now during the build of a Debian package we have some tools that could detect API modifications and the build can fail if a library without a so number bump, remove a symbols. So it is a round trip collaboration, we can check if a so bump is requiere by a build of the futur next stable release, Identify the problem and explain to the person in charge of the C++ library how to modify the corresponding so number. After a few roundtrip (release) I think that peoples whould understand how to deal with thoses numbers. > > > There are relatively very few shlibs compared to Python modules. Keeping track of the version of all of the latter by hand would be an enormous amount of work. I don't think we can get it done cheaply with some automatic keyword expansion if we want proper major.minor.patch or worse something as involved as so-versioning. > Maybe it can be good to look on other projects how they are doing this. As a > python developer I'm always expecting different API's when it comes to new > upstream versions. I checked the policy for Debian and there seems to be nothing > special in versioning extensions and modules. Maybe Justin can tell us something > about Gentoo. I'd say we don't need to worry about it for now. Yes excepted if you distribut python extension used by other third party to build other extension. A good example is the python-numpy package. It was a nightmare for distribution before they introduce an API and ABI number. the public C API/ABI of this extension is now following a sort of so number and when someone build a package relying on this python-numpy extension the dh_numpy helper generate the right binay dependencies, based on the ABI number maintained by the numpy upstream. there is a dependency on python-numpy-abix. Exemple for the scipy package Package: python-scipy Version: 0.10.1+dfsg1-4 Installed-Size: 34405 Maintainer: Debian Python Modules Team <python-modules-team(a)lists.alioth.debian.org> Architecture: i386 Provides: python2.6-scipy, python2.7-scipy Depends: python-numpy (>= 1:1.6.1), python-numpy-abi9, python (>= 2.6.6-7~), python (<< 2.8), libamd2.2.0 (>= 1:3.4.0), libblas3 | libblas.so.3 | libatlas3-base, libc6 (>= 2.3.6-6~), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), liblapack3 | liblapack.so.3 | libatlas3-base, libquadmath0 (>= 4.6), libstdc++6 (>= 4.1.1), libumfpack5.4.0 (>= 1:3.4.0) Recommends: g++ | c++-compiler, python-dev, python-imaging So the same think should be proposed if third party package rely on C python extension of cctbx. But indeed it mean, you need to care about the versionning of your public C API/ABI. Cheers Frederic -- GPG public key 4096R/4696E015 2011-02-14 fingerprint = E92E 7E6E 9E9D A6B1 AA31 39DC 5632 906F 4696 E015 uid Picca Frédéric-Emmanuel <picca(a)synchrotron-soleil.fr> GPG public key 1024D/A59B1171 2009-08-11 fingerprint = 1688 A3D6 F0BD E4DF 2E6B 06AA B6A9 BA6A A59B 1171 uid Picca Frédéric-Emmanuel <picca(a)debian.org>

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