Search results for "look through"

Re: [phenixbb] phenix.automr high zscore but too many clashes

by Andreas Förster

Hey Zach, remove the loops from your search model and rerun the MR. Alternatively, increase the maximum number of clashes allowed until you get a solution written out. See where your solutions clash. Again, if it's in a loop region, cut the loop and rerun. Your z-scores look great. (Notice that you have zed-scores when you run phaser through ccp4i and zee-scores when you run phaser through phenix.) Andreas zach powers wrote: > Hi, > > > I have a problem and i wonder if someone has had a similar experience. I > have been using phenix.automr program to find an MR solution for a > protein. When I ask Phaser to use copies=2 I find a number of solutions > with poor z-scores (3-4). When I ask it to use copies=3, I get great > Z-scores (see below) but no solution due to the high number of clashes > (>100!). > > As an x-ray newbie I am a bit perplexed of what to make of this: the > solution is not good because there is not enough space in the unit cell > to comfortably accommodate all three molecules yet the Z-score indicates > the structure is good. > > My structure does have several loops and these may be contributing to > the clashing residues. As a newbie I have a newbie question - what does > this mean (great z-score but no solutions)? Is this non-solution a > possible solution if I play with it, or is the packing simply too tight > and the Z-scores are not valid? > > In the meantime I am chopping my protein into sub-domains as recommended > in the Phaser documentation, but if anyone has seen something like this > before, any suggestions are welcome. > > thanks > zach charlop-powers > > > > > Packing Table: Space Group P 3 > ------------------------------ > Solutions accepted if number of clashes = 135 (lowest number of > clashes in list) > provided this number of clashes <= 10 (maximum number of allowed clashes) > # #Clashes # Accepted Annotation > 1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=10.4 > 2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=10.2 > 3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.8 > 4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.7 > 5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=10.5 > 6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.2 > 7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.1 > 8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=10.2 > 9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=9.1 > 10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.9 > 11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.8 > 12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.6 > 13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.6 > 14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.5 > 15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.3 > 18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=9.2 > 19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=9.1 > 20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.0 > 21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=8.0 > 22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 > TFZ=8.9 > 23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 > TFZ=7.8 > > 0 accepted of 23 solutions > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

16 years, 9 months

Re: [cctbxbb] Niggli-reduced cell C++ implementation

by Ralf Grosse-Kunstleve

Hi Martin, Let me know if you need svn write access to check in your changes. All I need is your sourceforge user id. Ralf On Fri, Mar 23, 2012 at 3:35 AM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: > Dear David and Rolf, > > thank you for your encouragement. > > David: I'm more than happy to port your implementation to cctbx if you're > happy with this. Of course I don't want to step on your toes so if you'd > rather do it yourself (or not at all) that's cool. > > There may be some licensing issues to sort out as it looks like cctbx has > a custom (non viral) license but the BSD license is likely compatible. > > On first impression I think a new class would be the way to go but I'd > have to look at the two algorithms in greater detail to be sure. > > All the best, > -Martin > > > On 22 March 2012 22:00, Ralf Grosse-Kunstleve <rwgrosse-kunstleve(a)lbl.gov>wrote: > >> Hi Martin, >> You're very welcome to add a C++ version of the Krivy-Gruber algorithm to >> cctbx if that's what you had in mind. >> I'm not sure what's better, generalizing the fast-minimum-reduction code, >> or just having an independent implementation. >> Ralf >> >> On Thu, Mar 22, 2012 at 2:24 PM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: >> >>> Dear Cctbx community, >>> >>> Firstly I'd like to say thank you to Rolf, Nicholas and Paul for their >>> expertly thought through implementation of the reduced cell algorithm. >>> I've found it to be extremely useful for my work. >>> >>> My code is all in C++ and I'd like to be able to use the Krivy-Gruber >>> algorithm. My understanding is that only the reduced (Buerger) unit cell >>> algorithm is implemented in C++ [1] which guarantees shortest lengths but >>> not unique angles. From my understanding the Krivy-Gruber would also >>> guarantee me uniqueness of unit cell angles, however this is only >>> implemented in Python [2]. Sorry to be so verbose, I just wanted to check >>> that I was on the right page. >>> >>> Would it be possible for me to implement the Krivy-Gruber in C++ by >>> adding in the epsilon_relative to the parameter and following the procedure >>> found in the python version? >>> >>> Many thanks, >>> -Martin >>> >>> [1] >>> http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1fas… >>> [2] >>> http://cctbx.sourceforge.net/current/python/cctbx.uctbx.krivy_gruber_1976.h… >>> >>> >>> >>> -- >>> Martin Uhrin Tel: +44 >>> 207 679 3466 >>> Department of Physics & Astronomy Fax:+44 207 679 0595 >>> University College London >>> martin.uhrin.10(a)ucl.ac.uk >>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Martin Uhrin Tel: +44 > 207 679 3466 > Department of Physics & Astronomy Fax:+44 207 679 0595 > University College London > martin.uhrin.10(a)ucl.ac.uk > Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

13 years, 10 months

Re: [phenixbb] temp files

by Tom Terwilliger

Hi James, Not the code (I hope), just any scripts that use these methods. Like this: mkdir /var/tmp/autosol phenix.autosol p9.sca 2 se temp_dir=/var/tmp/autosol Now the temp files go in /var/tmp/autosol and the output files go in AutoSol_run_xxx/ as usual All the best, Tom All the best, Tom T On Sat, Apr 24, 2021 at 11:59 AM James Holton <jmholton(a)lbl.gov> wrote: > Thank you Tom! > > Ok. So, in order to change the default I need to go through the code > looking for "temp_dir" and change things? > > > On 4/24/2021 10:16 AM, Tom Terwilliger wrote: > > Hi James, > > There is no overall Phenix temp directory specification, but most of the > temp_dir usage is from autosol/autobuild/ligandfit/map_to_model. Each of > these has the keyword "temp_dir=xxxx" which you should be > able to set to any directory you want (and local is better as you note). > Most programs using a temp_dir also have a keyword clean_up=True as well. > > All the best, > Tom T > > On Sat, Apr 24, 2021 at 10:51 AM James Holton <jmholton(a)lbl.gov> wrote: > >> Thank you Li-Wei >> >> Definitely not placing blame on one program. Phenix.autobuild is another >> big temp file producer. So is XDS. Clearly this ligand run was a case >> of a misconfigured, runaway task that never finished. However, the files >> lingered on disk, eating up inodes for 3 years! >> >> The reason I'm asking is I think there are significant performance >> increases to be gained by using fast, local storage for scratch files. >> This is not just in speed but storage and overall system/cluster >> performance. Very few things are more expensive than an NFS write! >> >> Does anyone know how to change the default temp file location across >> phenix ? Is this a cctbx thing? >> >> Thanks >> >> -James >> >> >> On 4/23/2021 9:38 PM, Li-Wei Hung wrote: >> > Hi James, >> > >> > I'll leave the global Phenix temp aspect to Billy. >> > For ligand identification specifically, the working directory is where >> > all the files are located. The program will purge most of the >> > intermediate files upon completion. If the user interrupted the runs >> > or if the program crashed at certain spots, the purge mechanism might >> > not kick in. Even so, it'd take many runs to accumulate 20e6 (2e7?) >> > files. In any case, you've got a point and I'll look into salvaging >> > intermediate files of ligand identification as soon as they are not >> > needed in the process. >> > >> > Thanks, >> > >> > Li-Wei >> > >> > On 4/23/2021 7:03 PM, James Holton wrote: >> >> Hello all, >> >> >> >> Is there a way to configure phenix at install time (or perhaps >> >> post-install) to put temporary files under /tmp ? I just had to >> >> delete 20e6 temp files over NFS from a single user's phenix ligand >> >> identification run. The delete took almost a month. >> >> >> >> Apologies if I am neglecting to look somewhere obvious in the >> >> documentation, >> >> >> >> Happy Weekend! >> >> >> >> -James Holton >> >> MAD Scientist >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > -- > Thomas C Terwilliger > Laboratory Fellow, Los Alamos National Laboratory > Senior Scientist, New Mexico Consortium > 100 Entrada Dr, Los Alamos, NM 87544 > Email: tterwilliger(a)newmexicoconsortium.org > Tel: 505-431-0010 > > > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

4 years, 9 months

Re: [phenixbb] Phaser SAD question

by Kitty Pattridge

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

16 years, 1 month

Re: [phenixbb] Phaser SAD question

by Kitty Pattridge

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

16 years, 1 month

Re: [cctbxbb] some thoughts on cctbx and pip

by Derek Mendez

I think its worth getting a cctbx-light pip build.. I think modules like cctbx miller, sgtbx are extremely useful. Also simtbx.nanoBragg. -Derek On Sun, Aug 18, 2019 at 10:48 PM Graeme.Winter(a)Diamond.ac.uk < Graeme.Winter(a)diamond.ac.uk> wrote: > Hi Aaron > > Re: talk about if interest > > I think it would be very useful to have a roadmap of where this is going, > the intentions and how we expect it to play with other cctbx-dependent > projects - have I missed this? Having it somewhere e.g. on the wiki would > be a big help > > Thanks Graeme > > On 17 Aug 2019, at 00:36, Aaron Brewster <asbrewster(a)lbl.gov<mailto: > asbrewster(a)lbl.gov>> wrote: > > Hi Luc, thanks. I did recall someone working on this a while back. > > For conda, there are a couple more things to finish and then we hope to > have cctbx available through conda. > > 1) There is work being done in a branch to make cctbx use boost in > standard locations (e.g. the system boost, or a conda boost). That will > allow us to use install boost by conda and not build it ourselves. ( > https://github.com/cctbx/cctbx_project/tree/conda_boost). Also, newer > versions of boost are being tested (up through 1.70). (This will also > enable python 3.7 support.) > 2) We need to work on getting a make install step in place so that we can > build the conda package and upload it. > 3) We want to split the dependencies up by builder (cctbx, cctbx-lite, > dials, phenix, etc.) into meta packages and their associated manifests. I > can talk more about this if there is interest. > > Thanks, > -Aaron > > > > On Fri, Aug 16, 2019 at 1:48 PM Luc Bourhis <luc_j_bourhis(a)mac.com<mailto: > luc_j_bourhis(a)mac.com>> wrote: > Hi, > > I did look into that many years ago, and even toyed with building a pip > installer. What stopped me is the exact conclusion you reached too: the > user would not have the pip experience he expects. You are right that it is > a lot of effort but is it worth it? Considering that remark, I don’t think > so. Now, Conda was created specifically to go beyond pip pure-python-only > support. Since cctbx has garnered support for Conda, the best avenue imho > is to go the extra length to have a package on Anaconda.org< > http://anaconda.org/>, and then to advertise it hard to every potential > user out there. > > Best wishes, > > Luc > > > On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto: > asbrewster(a)lbl.gov>> wrote: > > Hi, to avoid clouding Dorothee's documentation email thread, which I think > is a highly useful enterprise, here's some thoughts about putting cctbx > into pip. Pip doesn't install non-python dependencies well. I don't think > boost is available as a package on pip (at least the package version we > use). wxPython4 isn't portable through pip ( > https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). > MPI libraries are system dependent. If cctbx were a pure python package, > pip would be fine, but cctbx is not. > > All that said, we could build a manylinux1 version of cctbx and upload it > to PyPi (I'm just learning about this). For a pip package to be portable > (which is a requirement for cctbx), it needs to conform to PEP513, the > manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For > example, numpy is built according to this standard (see > https://pypi.org/project/numpy/#files, where you'll see the manylinux1 > wheel). Note, the manylinux1 standard is built with Centos 5.11 which we > no longer support. > > There is also a manylinux2010 standard, which is based on Centos 6 ( > https://www.python.org/dev/peps/pep-0571/). This is likely a more > attainable target (note though by default C++11 is not supported on Centos > 6). > > If we built a manylinuxX version of cctbx and uploaded it to PyPi, the > user would need all the non-python dependencies. There's no way to specify > these in pip. For example, cctbx requires boost 1.63 or better. The user > will need to have it in a place their python can find it, or we could > package it ourselves and supply it, similar to how the pip h5py package now > comes with an hd5f library, or how the pip numpy package includes an > openblas library. We'd have to do the same for any packages we depend on > that aren't on pip using the manylinux standards, such as wxPython4. > > Further, we need to think about how dials and other cctbx-based packages > interact. If pip install cctbx is set up, how does pip install dials work, > such that any dials shared libraries can find the cctbx libraries? Can > shared libraries from one pip package link against libraries in another pip > package? Would each package need to supply its own boost? Possibly this > is well understood in the pip field, but not by me :) > > Finally, there's the option of providing a source pip package. This would > require the full compiler toolchain for any given platform (macOS, linux, > windows). These are likely available for developers, but not for general > users. > > Anyway, these are some of the obstacles. Not saying it isn't possible, > it's just a lot of effort. > > Thanks, > -Aaron > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

6 years, 5 months

Re: [phenixbb] Command line phenix.sculpt_ensemble

by Randy John Read

Dear Matthew, Sorry, I somehow missed this for a few days. The first thing I would say is that I’m not sure there’s much of a use case for sculptor and ensembler (or the combined application you were using) in these days of AlphaFold. Sculpted ensembles were a really powerful way to combine information from a collection of distant homologues to make a better model for molecular replacement. However, since AlphaFold became available I think the current best approach in this scenario is to take the AlphaFold model (which will integrate everything known structurally about the class of proteins far better than ensembler), run it through process_predicted_model (to downweight or trim off the less reliable parts of the model) and use that single model as your molecular replacement model. I haven’t yet seen a counter-example where the experimental structures of the distant homologues are better. Of course, if someone has a counter-example that would be very interesting to learn about! In terms of this bug, I’m wondering whether it’s a Python compatibility issue. I’m guessing that your Mac might be one of the newer ones with ARM (M1 or M2) chips. If so, are you using a build for the older Intel processors, or the native ARM build? In any case, if you’re using the ARM build then this will be built with Python 3. The easiest way to tell is to go to a terminal window with Phenix set up and type: phenix.python --version This will report whether or not you’re using Python 2.7 or Python 3.7. The sculpt_ensemble procedure has a lot of options, and I would need to know exactly which options you had set in order to try to reproduce the problem. Could you look in the project directory for a file with a name like .phenix/project_data/sculpt_ensemble_NN.eff, where “NN” is the job number? If you could send me that file, that would help. Best wishes, Randy Read > From: Whitley, Matthew (NIH/NCI) [C] <matthew.whitley(a)nih.gov> > Date: Thu, Sep 7, 2023 at 10:54 PM > Subject: [phenixbb] Command line phenix.sculpt_ensemble > To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > > > Hello all, > I am trying to use the command line tool phenix.sculpt_ensemble to process a series of PDB files in preparation for molecular replacement. > However, when I run the following on the command line: > phenix.sculpt_ensemble 2*.pdb input.target_sequence=RRAS2.fasta > I get the following errors: > Traceback (most recent call last): > File "/Applications/phenix-1.21rc1-5015/build/../modules/phaser/phaser/command_line/sculpt_ensemble.py", line 84, in <module> > sculpt_ensemble.run( phil = params.phil, logger = logger ) > File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 610, in run > logger = logger, > File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 259, in read_in_target_sequence_files > for ( fname, i ) in itertools.zip_longest( filenames, range( 1, nchains + 1 ) ): > AttributeError: 'module' object has no attribute 'zip_longest' > I am running phenix 1.21rc1-5015-000 on Mac OS 13.5.1. > Any ideas? > Thanks, > Matthew > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

2 years, 5 months

[phenixbb] Fwd: Phenix installation on macOS 14 Sonoma

by Billy Poon

Sorry if this is a duplicate, but I'm not sure if my response got sent to the bulletin board correctly. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Sun, Dec 31, 2023 at 6:29 PM Subject: Re: [phenixbb] Phenix installation on macOS 14 Sonoma To: Klureza, Maggie <mklureza(a)g.harvard.edu> Cc: <phenixbb(a)phenix-online.org> Hi Maggie, Can you run the script from inside the sonoma_fix directory? That is, 1) Extract sonoma_fix.tar.gz 2) cd sonoma_fix 3) sudo ./fix_wxpython.sh /Applications/phenix-1.19.2-4158 Inside the sonoma_fix directory, there should be a "bin" directory with conda.exe. The installed versions of Phenix do not come with conda. The fix comes with a standalone version of conda that can modify the Phenix environment with the dependencies. Let us know if it's still not working. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza(a)g.harvard.edu> wrote: > Hi all, > > Reviving this thread (or trying to, anyway - TBD if I can successfully > reply to a thread begun before I'd joined the phenixbb list!), I recently > updated my Mac OS to 14/Sonoma, and am now also having issues getting > Phenix to work. > > As directed on the installers page > <https://phenix-online.org/download/phenix/release/>, I downloaded the > supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, > extracted the tarball, and ran that code as `sudo > Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. > This was the resulting output/error I got: > > Password: > Removing old version of wxPython > ================================ > Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such > file or directory > > Installing new version of wxPython > ================================== > Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such > file or directory > > The wxPython package has been updated in /Applications/phenix-1.20.1-4487. > > > Sure enough, when I went to my phenix installation and looked in > conda_base/bin, there was no file named `conda.exe` present. This was true > for both my prior installation (phenix-1.19.2-4158) and when I tried a > newly downloaded version (phenix-1.20.1-4487). > > Can anyone tell me how I get that conda.exe file included with the Phenix > download/how else I might be able to run Phenix with this OS? > > (I sent an email about this to help(a)phenix-online.org before thinking to > hunt through the phenixbb archive, so apologies to whoever checks that > email and is getting this message twice!) > > Many thanks, > Maggie > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

2 years, 1 month

Re: [phenixbb] Joint X-ray / neutron refinement

by Tim Gruene

Hello Kristoffer, maybe this is related to the first paragraph at the link that you provide ("The paradigm and implementation of the joint X-ray and neutron refinement were changed in the fall of 2023, as documented here: https://pubmed.ncbi.nlm.nih.gov/37942718/"): It is better to use the information from an X-ray dataset via geometric restraints and refine against neutron data only (cf. DOI 10.1107/S1600576713027659), so that you focus on the information from the neutron data. Cheers, TIm On Fri, 23 Feb 2024 10:58:17 +0000 Kristoffer Lundgren <kristoffer.lundgren(a)compchem.lu.se> wrote: > Hello phenixbb, > > When trying to do joint refinement in phenix.refine 1.21-5207 using > the suggested joint_xn.eff file found at > https://phenix-online.org/documentation/reference/refinement.html#neutron-a… > as a template I get some error messages (running phenix.refine from > the command line): > > Unrecognized PHIL parameters: > ----------------------------- > xray.refinement.refine.strategy (file "joint_xn.eff", line 33) > xray.refinement.main.simulated_annealing (file "joint_xn.eff", > line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", > line 37) xray.refinement.main.number_of_macro_cycles (file > "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file > "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing > (file "joint_xn.eff", line 48) > neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line > 49) neutron.refinement.main.number_of_macro_cycles (file > "joint_xn.eff", line 50) > > Can you please advice on how to proceed? It looks like the options > supplied are not recognized at all by phenix.refine. > > Best regards > Kristoffer > > > From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan > <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at > 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" > <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / > neutron refinement > > Hi phenixbb, > > I'm trying to understand the current status of joint X-ray/neutron > refinement in phenix.refine. The announcement of the latest release > mentions a change in the algorithm as described in the recent > publication. In the documentation: > > Structure refinement in > PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> > phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> > > [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> > > > > it's described how you can run joint refinement using a parameter > file. Does this mean that it is *only* possible in this way and not > through the GUI? The GUI was very useful in the past as it > automatically opened Coot with the maps for both X-rays and neutrons, > and the refinement statistics for both were displayed in the GUI. As > far as I can see joint refinement via the GUI last worked in version > 1.19.2-4148 from 2021. > > Best regards > Derek -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

1 year, 11 months

Re: [phenixbb] parallel phenix.phaser on SGE cluster

by Jon Schuermann

Lionel, It's not quite as easy as one would hope, and it has nothing to do with Phenix or Phaser. We make use of extensive multiprocessing across our cluster in our RAPD software used at the beamline to speed up the results for the user. I set this up a while ago, but from what I remember, you first have to setup a 'parallel environment' (PE) in SGE. The options maybe different depending on your version of SGE. We use 6.2u4. There are probably default PE's setup already but they might not have the correct parameters. I created a new one called 'smp' with the number of 'slots' set to the number of cores of your cluster, or some other lower limit. (If you set 'slots' to 12 and you submit 5 jobs requiring 4 slots each, only three will run, until one has finished and the resources are free.) The 'allocation rules' are set to '$pe_slots' so that the job can use only the cores on a single node. There are other rules that might be better for what you want to do. In our case, I setup different queues with different priorities that have access to specific PE's depending on the jobs that are getting submitted at the beamline. Your setup may not need this complexity. I would read through the huge manual for SGE for details or do a search on Oracle's website. When you submit the job, make sure you add 'qsub ... -pe smp 1-4 ...' which will tell SGE that your job will need 1-4 cores on a single node. You could also just specify a single integer (4 instead of 1-4) to request 4 slots. Obviously, you can modify these to your needs. After you submit the job, run 'qstat' and look at the last column labeled 'slots' to see how many slots are saved for the job. In your Phaser command include 'JOBS 4' to match your requested number of slots. I am not sure how much this speeds up a single Phaser job because there isn't a whole lot of code to parallelize in MR. Randy Read mentioned (either to me or the BB, I don't remember) that everything that could be parallelized in Phaser is done. On a side note, if you write code in Python, and you start a new multiprocessing.Process() it will automatically launch it on another core on the same node. You have to account for this when you request a specific number of slots during job submission, otherwise you could overload your cluster pretty quickly. Many programs will have an optimized number of slots to request and requesting more slots will not make it run any faster, but it will limit resources available for other jobs on the cluster. I assume Phaser is one of these programs. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist, NE-CAT Argonne National Laboratory, 436E 9700 S. Cass Ave. Argonne, IL 60439 Email: schuerjp(a)anl.gov Tel: (630) 252-0682 On 07/10/2013 09:16 AM, L. Costenaro (IBB) wrote: > Hello, > > I am trying to run phaser in a SGE cluster (qsub) using multiple proc > (either phenix.phaser from the command line or phaser-MR from the > GUI), but the jobs do not parallelize. When I run the phaser-MR > locally (same executable) it does parallelize (multiple python threads). > > Any help , advice would be welcome. > > Best regards, > Lionel > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 7 months

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