[ccp4bb] (Computational) methods development in structural biology post-doc at DESY
Dear CCP4BB, The Protein Machinists lab is hiring ( https://www.hginn.co.uk/lab_website/index.php ) at DESY, Hamburg Germany! The Protein Machinists group specialises in establishing the basic fundamentals of computationally expressing protein movement. Our algorithms and concepts are applied to structure refinement against experimental data, and rational modification of proteins to modulate allosteric mechanisms. Our group collaborates closely with experimental groups in order to ensure that the theoretical work carried out provide meaningful benefit in the laboratory. Our approach to thinking about these problems are delivered in the form of implemented algorithms in a software package, which is written in C/C++. We pay care and attention to how these algorithms can be presented to third-party researchers. We are seeking a motivated post-doctoral research associate, who is keen on developing methods for the future of protein engineering and modulation of allosteric mechanisms. The full job advert is here: https://v22.desy.de/e67416/records197395/index_eng.html Best wishes Helen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] To Trim or Not to To Trim
Models for crystallography have two purposes: refinement and interpretation. Here these two purposes are in conflict. Neither case is handled well by either trim or not trim scenario, but trimming results in a deficit for refinement and not-trimming results in a deficit for interpretation. Our computational tools are not “fixed” in the same way that the standard amino acids are “fixed” or your government’s bureaucracy pathways are “fixed”. They are open for debate and for adjustments. This is a fine example where it may be more productive to discuss the options for making changes to the model itself or its representation, to better account for awkward situations such as these. Otherwise we are left figuring out the best imperfect way to use an imperfect tool (as all tools are, to varying degrees!), which isn’t satisfying for enough people, enough of the time. I now appreciate the hypocrisy in the argument “do not trim, but also don’t model disordered regions”, even though I’d be keen to avoid trimming. This discussion has therefore softened my own viewpoint. My refinement models (as implemented in Vagabond) do away with the concept of B factors precisely for the anguish it causes here, and refines a distribution of protein conformations which is sampled to generate an ensemble. By describing the conformations through the torsion angles that comprise the protein, modelling flexibility of a disordered lysine is comparatively trivial, and indeed modelling all possible conformations of a disordered loop becomes feasible. Lysines end up looking like a frayed end of a rope. Each conformation can produce its own solvent mask, which can be summed together to produce a blurring of density that matches what you would expect to see in the crystal. In my experience this doesn’t drop the R factors as much as you’d assume, because blurred out protein density does look very much like solvent, but it vastly improves the interpretability of the model. This also better models the boundary between the atoms you would trim and those you’d leave untrimmed, by avoiding such a binary distinction. No fear of trimming and pushing those errors unseen into the rest of the structure. No fear of leaving atoms in with an inadequate B factor model that cannot capture the nature of the disorder. Vagabond is undergoing a heavy rewrite though, and is not yet ready for human consumption. Its first iteration worked on single-dataset-single-model refinement, which handled disordered side chains well enough, with no need to decide to exclude atoms. The heart of the issue lies in main chain flexibility, and this must be handled correctly, for reasons of interpretability and elucidating the biological impact. This model isn’t perfect either, and necessitates its own compromises - but will provide another tool in the structural biology arsenal. —- Dr Helen Ginn Group leader, DESY Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR) Luruper Chaussee 149 22607 Hamburg To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Structural alignment and classification
Dear Armando, I have recently published a program which classifies/clusters protein structures on the internal torsion angles, RoPE (https://rope.hginn.co.uk). It is a GUI, in the form of a web application and a preferable Mac executable (faster & multi-threaded). I'm still working on setting up other binaries. The scientific write-up of the tool is here, and also contains a written tutorial for how to use the program: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4608 Additional instructions (particularly for loading your own PDB files or metadata for analysis) can be found here: https://rope.hginn.co.uk/index.php?page=dox One serious advantage of using the internal torsion angles is that you can skip the structural alignment (I would recommend using a different program for this explicitly), and it describes the conformation of the protein in the same parameter space as it naturally tends to flex. It can also highlight the 'hinge' regions within your structure (i.e. the backbone angles that vary the most). If you definitely want to cluster on RMSD alone, do ask (it's been implemented for comparison purposes in the paper, but is not the default option). I'd recommend it to anyone who is looking to classify/understand conformational changes across a range of related structures, regarding both large and subtle modes of motion. Best wishes Helen Dr Helen Ginn Group leader, DESY Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR) Luruper Chaussee 149 22607 Hamburg To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Fwd: Re: What refinement programs are fully Open Source?
Hi Pietro! As for free and open-source (GPLv3 license) refinement software, I am developing Vagabond. https://vagabond.hginn.co.uk It is based on refining bond torsion angles in an ensemble of related structures which also captures flexibility (no B factors!). There are no restraints, only constraints. This allows a significant side-step of the parametrisation problem and reduces the level of overfitting in the map (which is more widespread than I first realised). It is in the middle of development, very young and therefore not as polished or refined as other (atomistic) refinement software, and is currently best used as an intermediate tool, when you have confusing and muddy electron density, to create a less overfitting-biased map to build into and then continue with your favourite other refinement software. git clone https://www.github.com/helenginn/vagabond.git Typing this into a command line will demonstrate how open source it is! Helen --- On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote: Dear all, we are in the editorial stages of a manuscript that I submitted to Wellcome Open Research for publication. The journal/editor ask us to list fully Open Source alternatives to the pieces of software we used, for example for data processing and refinement. What refinement programs are fully Open Source? Thanks! Pietro Pietro Roversi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Error in data reduction!
Dear Mike and Andrew, I've since updated to a later version of ccp4 (7.0.076) and now have the XMLOUT tags specified automatically. Woops! Thanks for that error log Andrew - I had a look at the aimless.script file to see how that filename was generated, and looked up the command on the CCP4 developer's guide for programmers. Image hosted remotely to avoid mailbox indigestion: https://www.hginn.co.uk/ccp4bb/aimless_script.png Here, the variable `root` is set to [SetOutputFileRoot], defined in the bottom half of the image online, and is used to generate the Pointless XML file path. It is also used later and may cause similar problems for AIMLESS's output of .scales, graphs and other logs, so there is an underlying problem that ought to be solved for Mike. It seems that in order to have a filepath in the root of the filesystem itself (which is reassuringly non-writeable), judging from the definition, the project directory would have to be an empty string. None of the pointless GUI scripts rely on [SetOutputFileRoot], which would be consistent with the fact they work for Mike. So it might be worth Mike checking this: in the main window of the ccp4i interface, click Change Project and then Add/Edit Project. Find the project you are working on and confirm the directory path for your current project is a subdirectory in your home directory. Best wishes Helen On Thu, 11 Jul 2019 13:54:20 +0100 Andrew Leslie wrote: > Dear Mike and Helen, > > As I understand it, the XML is only written when POINTLESS/AIMLESS are run > through the CCP4 GUI and the command comes from the GUI script, so there is > no way you can turn this off from POINTLESS itself. > > However, if you use the “Run com file” option from CCP4i GUI, you will > see the XMLOUT command there (see attached figure). If you delete this (for > both POINTLESS and AIMLESS and CTRUNCATE) then the jobs will run and produce > an MTZ file, but it did give a "job failed" message: > > #CCP4I TERMINATION STATUS 0 Error from script > /Applications/ccp4-7.0/share/ccp4i/scripts/aimless.script: couldn't open > "/Users/andrew/g4/MOSFLM/camillo/camillo_1_pointless.xml": no such file or > directory > > However the MTZ file was there. > > Did your job produce a final MTZ file in spite of the warning? > > I’m afraid I don’t understand why the XML file was not written in your case, > are you sure the path shown in the “Command Line” output from the GUI is OK > for writing to? > > Best wishes, > > Andrew > > > >> On 11 Jul 2019, at 13:34, Helen Ginn wrote: >> >> Dear Mike, >> >> No problem! Happy to provide suggestions, though I'd prefer to be addressed >> directly on here. >> >> Here's another suggestion, no promises. If you can provide more detail on >> the GUI input and the output log files, it would be easier to know why this >> is happening in the first place. However, you can also click and hold "Run" >> in ccp4i and select "Run Com File". Then you will receive each >> program's command line input and you can edit them before you run them. I >> suggest removing or correcting any instances of `XMLOUT `. >> >> Thanks Andrew for confirming with Phil on the behaviour of pointless. I have >> looked at the ccp4i interface and cannot find any option for enabling XML >> output for pointless in the Symmetry/scale/merge pipeline. The option to >> output to XML in the standalone pointless does not seem to transfer this to >> the command line options, but Mike is probably using the former GUI input >> window anyway. As such I'm not sure where the XMLOUT command is coming from. >> >> Best wishes >> Helen >> >>> Dear Andrew, >>> >>> Thanks for your suggestion. Yes, you are right that the error is because >>> .xml file is not being written. but not able to find the reasons...I >>> checked...Disk space is free and have permission to write also. I could >>> able to run Pointless, but not Aimless. >>> >>> Any other reason?? >>> >>> Thanks >>> >>> Mike >>> >>> On Wed, Jul 10, 2019 at 5:37 PM Andrew Leslie <[log in to unmask]> wrote: >>> >>> I think Helen’s answer is absolutely right. I asked Phil Evans about this >>> when I saw him yesterday, and he said that error usually arises when it is >>> not possible to write the xml file, either because a disk is full, or >>> because you do not have permission to write to that area. >>> >>> Andrew >>> >>>> On 3 Jul 2019, at 15:09, Mike Xishan <[log in to unmask]> wrote: >>&
Re: [ccp4bb] Error in data reduction!
Dear Mike, No problem! Happy to provide suggestions, though I'd prefer to be addressed directly on here. Here's another suggestion, no promises. If you can provide more detail on the GUI input and the output log files, it would be easier to know why this is happening in the first place. However, you can also click and hold "Run" in ccp4i and select "Run Com File". Then you will receive each program's command line input and you can edit them before you run them. I suggest removing or correcting any instances of `XMLOUT `. Thanks Andrew for confirming with Phil on the behaviour of pointless. I have looked at the ccp4i interface and cannot find any option for enabling XML output for pointless in the Symmetry/scale/merge pipeline. The option to output to XML in the standalone pointless does not seem to transfer this to the command line options, but Mike is probably using the former GUI input window anyway. As such I'm not sure where the XMLOUT command is coming from. Best wishes Helen > Dear Andrew, > > Thanks for your suggestion. Yes, you are right that the error is because .xml > file is not being written. but not able to find the reasons...I > checked...Disk space is free and have permission to write also. I could able > to run Pointless, but not Aimless. > > Any other reason?? > > Thanks > > Mike > > On Wed, Jul 10, 2019 at 5:37 PM Andrew Leslie <[log in to unmask]> wrote: > >I think Helen’s answer is absolutely right. I asked Phil Evans about this > when I saw him yesterday, and he said that error usually arises when it is > not possible to write the xml file, either because a disk is full, or because > you do not have permission to write to that area. > >Andrew > >>On 3 Jul 2019, at 15:09, Mike Xishan <[log in to unmask]> wrote: >> >>Dear all, >> >>Sorry for asking for a very naive question that might be asked before. >> >>After integration, I am trying to do "data reduction" through Aimless, >> but task fails with an error message as >> >>#CCP4I TERMINATION STATUS 0 "FILEIO: cannot open file >> /Processing1_8_pointless.xml >> >>I really appreciate for your opinion and help to fix this problem. >> >>Thanks, >> >>Mike >> >> >>To unsubscribe from the CCP4BB list, click the following link: >>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Error in Aimless task!
Hello Mike, This is just a guess. From the error message it seems that it’s trying to write to the root directory of your filesystem. I am assuming you are using the old ccp4i interface. It might be because the ccp4i project directory you’re running it under has been set to / or is empty. If so, best set it to a user directory you can write to. Best wishes Helen Ginn > Date:Mon, 8 Jul 2019 12:21:39 +0530 > From:Mike Xishan > Subject: Error in Aimless task! > > Hello everyone, > > Data reduction with Aimless from (CCP4i) fails with error message as below > FILEIO: cannot open file /Processing1_8_pointless.xml > > How can this error be fixed? Comment please... > > Thanks > > Mike > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
