Search results for "look through"

Re: [phenixbb] sequence independent model building possible?

by Kaushik Hatti

Dear All, Thanks for all the valuable inputs. I was able to build side chains for the core of the protein. Using this sequence information, I was able to identify sequence family from Pfam. It seems like it has phosphate-binding domain (I could also see a blob which looks like a phosphate). I am using Multiple sequence alignment from the closest Pfam hits to built sidechains for the rest of the protein. The latest scores are, R/Rfree: 28/37; LLG=3681; TFZ=39.2 I hope to solve it very soon. Thanks, Kaushik P.S: 1) I had searched Dali too. These hits (with less than 2 A RMSD), when used as phasing model in Phaser failed to yield a solution. The top hits probably belong to the same fold but seems to have internal domain movements. However, the core was conserved (which I recognise now as phosphate-binding domain). 2) Had also searched PDB for unit cell with similar dimensions without much help. Will checkout Nearest-Cell v2.0. Thanks for the this. 3) ~20% of the structure is loop for which backbone isn't built. I hope to model this soon. Thanks again for all the help. On Sat, Feb 6, 2016 at 3:01 AM, Jon Agirre <jon.agirre(a)york.ac.uk> wrote: > Dear Kaushik, > > if you're suspecting you've crystallised something else, perhaps you could > try running your crystal parameters through the nearest-cell server ( > http://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi), which will > scan the PDB for crystals that match the input one. > > Good luck, > > Jon > > On 5 February 2016 at 20:06, Christian Roth <christianroth034(a)gmail.com> > wrote: > >> Hi, besides the already excellent suggestions, you might want to try if >> density modification (NCs, solvent flattening, histogram matching) improves >> your map a bit further. If you can assign enough residues you improve your >> maps than even further step by step. On top your stretches are than >> definitely long enough for a blast search. >> >> Christian >> On 5 Feb 2016 06:02, "Kaushik Hatti" <hskaushik(a)gmail.com> wrote: >> >>> Hello, >>> >>> Is abinitio model building possible for a map with poly alanine model at >>> 1.9A resolution? >>> >>> We thought we had crystallised our protein of interest X, collected data >>> at 1.9 A and all attempts to solve protein X (which has many homologs) >>> through MR failed. All attempts to re-crystallise the same protein also >>> failed. >>> >>> Now, we think the initial protein which got crystallised could be a >>> contaminant (we don't have any crystals left from this batch to check for >>> the sequence of the crystallised protein). Through various methods (and a >>> bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 >>> and R/Rfree : 37/41 (for a poly alanine model). >>> >>> I believe these scores indicate right fold. As I still don't know the >>> sequence information, is it possible to build sidechains directly from the >>> map (I could only identify a couple of residues and the model largely >>> remains PolyAla)? Autobuild with Rebuild-in-place didn't help in >>> identifying any more residues. >>> >>> I have also searched PDB database for similar structures. But, none of >>> those are either from our expression system (E. coli) or organism of our >>> protein of interest. Neither did I find any similar sequences from E. coli >>> or our organism of interest. >>> >>> Any leads/suggestions would be helpful. >>> Thanks, >>> Kaushik, >>> MRN Murthy lab, >>> MBU, >>> IISc, India >>> >>> -- >>> Stupidity is everyone’s birthright. However, only the learned exercise >>> it! >>> --Kaushik (28Oct2014) >>> >>> _______________________________________________ >>> 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 >> > > > > -- > Dr Jon Agirre > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, YO10 5DD, York, England > http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ > +44 (0) 1904 32 8253 > -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

9 years, 4 months

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

by Martin Uhrin

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

13 years, 3 months

[phenixbb] Re: Simulate map from model

by Pavel Afonine

Hi, additionally: - If you want an exact map (not a finite-resolution Fourier map), use: phenix.model_map model.pdb scattering_table=electron - We are close to making a multipolar model available for density calculations, which—if I understand correctly—is what you need to simulate Coulomb potential maps. This feature is not yet available to general Phenix users, but if you send me the model off-list, I can generate and send the map back to you. Pavel On 4/2/25 10:52, James Holton wrote: > Ostensibly, all you need to do is run phenix.fmodel with > scattering_table=electron . And perhaps try to come up with what > k_sol should be for the bulk solvent density. There are caveats, of > course, not the least of which is that, last I checked, the modified > scattering from formal charges like ions vs neutral groups is not > implemented. I don't actually know of a program that handles things > like charges. I've heard rumors that someone was working on full QM > calculations of electrons moving through matter to try and get this > "right", but I have not heard about any progress for some time. > > Sorry can't be more helpful, > > -James > > > On 4/2/2025 4:52 AM, Ricardo Righetto wrote: >> Hi, >> >> Apologies if I'm missing something obvious, but I was not able to >> find this in the documentation: is there a PHENIX tool for simulating >> Coulomb potential maps (aka "cryo-EM maps") from atomic models? >> >> I'm looking for something like the molmap >> <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> >> command in ChimeraX, but more accurate. One such alternative is the >> simulate program from cisTEM, but I figured PHENIX might also have >> something? >> >> Thank you! >> >> -- >> Ricardo Diogo Righetto >> >> _______________________________________________ >> phenixbb mailing list --phenixbb(a)phenix-online.org >> To unsubscribe send an email tophenixbb-leave(a)phenix-online.org >> Unsubscribe: phenixbb-leave@%(host_name)s > > > _______________________________________________ > phenixbb mailing list --phenixbb(a)phenix-online.org > To unsubscribe send an email tophenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

3 months

Re: [phenixbb] How to locate and refine a ligand using anomalousscattering

by Schubert, Carsten [PRDUS]

Just a quick note from somebody who does this for a living.... -If the compound in question retains its bromine it will practically scream at you when you look at the fofc maps. No need for elaborate anomalous difference maps, unless you like to go through the motions, which is commendable. -Beware that if the part of the compound were the bromine is bound is dangling, i.e. not well ordered, you will lose the anomalous signal, so use common sense to decide if the compound is bound or not. -Always good to collect an intrinsic control to make sure that you have the procedure under control or experiment with a high redundancy (>10x) lysozyme dataset collected at home to get comfortable with the procedure. The sulfurs in the lysozyme dataset light up in an anomalous map, when the collection was done right. -I usually only use anomalous maps in the context of sulfur containing compounds, since it allows me to determine the orientation of thiazole rings and such. Everything with more electrons is usually easily detected in the fofc maps. -Make sure you collect a high redundancy dataset (> x6) on or a bit beyond the Br edge. Don't overkill it, radiation damage is you enemy. Good luck. Carsten From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Jason Sent: Tuesday, February 08, 2011 1:14 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] How to locate and refine a ligand using anomalousscattering Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: * Using phenix.hyss to locate the anomalous scatterers * Using phenix.autobuild to build the protein model (which data set to use?) * Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) * Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

14 years, 4 months

Re: [cctbxbb] Git

by luis.fuentes-montero＠diamond.ac.uk

Hi fellows, I believe it is not a bad idea to move to https://github.com (the servers) and later on decide if move to use git (the CLI tool). This can an incremental way to do transition. And will allow really old fashion developers (those who refuse to learn git) or conservative policies to survive and still move to a new more reliable code repository. Just my thoughts, Greetings, Luiso From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of markus.gerstel(a)diamond.ac.uk Sent: 12 January 2016 09:56 To: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] Git Dear Luc, We actually had a look at the quality of the Github svn interface when we prepared for the DIALS move. My verdict was that it is surprisingly useful. All the possible git operations are mapped rather well onto a linear SVN history. All the branches and tags are accessible either by checking out the root of the repository, ie. svn co https://github.com/dials/dials.git (not recommended, as, say, any new branch/tag will probably result in a huge update operation for you) or by checking them out directly, ie. svn co https://github.com/dials/dials.git/branches/fix_export or svn co https://github.com/dials/dials.git/tags/1.0 Forks by other people are, as is the case when using git, simply not visible. I agree that looking at the project history through SVN may not be as clear as the git history. I wonder how relevant this is though, as you can explore the history, without running any commands, on the Github website, eg. https://github.com/dials/dials/network, https://github.com/dials/dials/commits/master, etc. Creating new branches and tags and merging stuff via SVN would be a major operation. However, that has always been the case with SVN, and for that reason one generally just does not do these things in SVN. But for an SVN user group those operations would not be important – you every only need to merge stuff if you create branches – so I don’t really see the problem. If you want to tag releases you can do that on the Github website as well as with a git command. In summary, I do recognize that SVN users will have difficulties participating in branched development, and in particular will not be able to quickly switch between branches. But I don’t think that this will be a problem, or that there is a need for a policy to keep the history linear. Best wishes -Markus From: cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Luc Bourhis Sent: 11 January 2016 16:45 To: cctbx mailing list Subject: Re: [cctbxbb] Gi, Hi Graeme, Can we revisit the idea of moving to git for cctbx? This brings to mind a question I have been asking myself since the subject has been brought forth. The idea Paul wrote about on this list was a move to Github. I guess some, perhaps many, developers will keep interacting with the repository using subversion. I am worried this would clash with the workflow of those of us who would go the native git way. By that I mean creating many branches and merge points, which one would merge into the official repository when ready. I am worried the history would look very opaque for the subversion users. I would even probably create a fork on Github, making it even more opaque for a tool like subversion. Has anybody thought about such issues? My preferred solution would be for everybody to move to git but I don’t think that’s realistic. At the other end of the spectrum, there is putting in place a policy to keep the history linear. Best wishes, Luc -- 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

9 years, 5 months

Re: [cctbxbb] reflection conditions for non-standard settings

by David Waterman

Thanks for the suggestions. The application is for selection of rows in a table of reflections where particular reflections are systematically absent. The catch is that this is in a language (R) that is "vector oriented" and is much more efficient at applying a single subset condition (derived from the ITvA reflection condition) over the entire table in a vectorised operation rather than explicitly looping through and checking each hkl. Variety is the spice of life, etc. So, I would need absence conditions for every setting. I have all the standard conditions already. As was suggested, it does seem like it would be a manageable amount of work to use the change of basis operations in syminfo.lib to figure out the mapping between h, k and l in the standard setting with h, k, and l in other settings and adapt the absence conditions accordingly. I had a quick look through absences.py, but as I'm just starting out with cctbx I need a strong coffee and a bit more time to achieve familiarity. Best wishes -- David On 4 June 2011 21:12, Petrus Zwart <phzwart(a)lbl.gov> wrote: > This could be of use perhaps: > > http://cci.lbl.gov/cctbx_sources/mmtbx/scaling/absences.py > > I use it in xtriage for spacegroup determination. I'm not sure what your > application is you have in mind, it might nit be suitable of course. > > Hth > P > > > > Verstuurd vanaf mijn iPhone > > Op Jun 4, 2011 om 13:04 heeft "Ralf W. Grosse-Kunstleve" <rwgk(a)yahoo.com> > het volgende geschreven: > > Hi David, > > cctbx does not include lists of reflection conditions as you find them in > the International Tables. > > It is very easy and fast to derive the reflection condition for a given hkl > directly from the symmetry operations. See the code near the top of > cctbx/sgtbx/miller.cpp. This is what we use for all practical applications. > For example: > > from cctbx import sgtbx > sg = sgtbx.space_group_info("19").group() > print sg.is_sys_absent((1,2,3)) > print sg.is_sys_absent((0,0,3)) > > I have C code given to me by Maxim Larine and Slava Klimkovich in 1997 > which computes the conditions, but it involves inefficient grid searches. > > I think a good solution would be to tabulate the conditions for the 230 > reference settings and figure out the transformation law to obtain the > conditions for arbitrary settings via a change of basis. But I yet have > to find a practical motivation for spending the effort implementing this. > > If you find that Phil has a solution, it would be nice to move it into > cctbx. > > Ralf > > ------------------------------ > *From:* David Waterman <dgwaterman(a)gmail.com> > *To:* <cctbxbb(a)phenix-online.org>cctbxbb(a)phenix-online.org > *Sent:* Saturday, June 4, 2011 3:28 AM > *Subject:* [cctbxbb] reflection conditions for non-standard settings > > Hi, > > I'm new to cctbx and to this mailing list, so please let me first apologise > if the answer to this question should be obvious, or lies in the archive. > > I want a list of general reflection conditions for all space groups and > settings listed in the CCP4 file syminfo.lib. At first I thought I could get > this information from the online version of ITC vol A, but I soon realised > that only certain standard settings are included. To avoid deriving them all > by hand from the symop and cenop lines, I wonder if there is a foolproof way > I can get this information from cctbx, but I don't know where to begin. > Perhaps something in sgtbx? > > Many thanks > > -- David > > _______________________________________________ > cctbxbb mailing list > <cctbxbb(a)phenix-online.org>cctbxbb(a)phenix-online.org > <http://phenix-online.org/mailman/listinfo/cctbxbb> > 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 > >

14 years

Re: [cctbxbb] iotbx newbie question

by Richard Gildea

Hi Wolfram, The build_crystal_structures() method is aimed at extracting a cctbx xray.structure object from a small molecule cif file, and isn't aimed at mmcif-format files, so in your case it looks through all the data blocks in the provided CIF, can't find any suitable xray.structures, so returns an empty dictionary. If you simply want to access the raw CIF items from the file, then this code snippet shows how you can extract (e.g.) the Rwork from the 1NXC cif block: import iotbx.cif reader = iotbx.cif.reader(file_path="1NXC.cif") cif = reader.model() cif_block = cif["1NXC"] # get a single item from cif_block print cif_block["_refine.ls_R_factor_R_work"] # get a looped item from cif_block print list(cif_block["_citation_author.name"]) If you want to extract the model for your crystal structure, then probably the most useful thing to do is extract a pdb.hierarchy object (the cctbx's internal representation of a PDB/mmCIF structure file). This functionality can accept both PDB and mmCIF files as input: import iotbx.pdb # this works exactly the same for pdb files pdb_input = iotbx.pdb.input(file_name="1NXC.cif") pdb_hierarchy = pdb_input.construct_hierarchy() Alternatively, if you are only reading mmCIF files, need access to both the raw cif items and the pdb_hierarchy, and are concerned about overhead of reading mmCIF twice (only really relevant for extremely large files), then you can pass the cif object created above to the iotbx.pdb.mmcif.cif_input function: import iotbx.pdb.mmcif pdb_input = iotbx.pdb.mmcif.cif_input(cif_object=cif) pdb_hierarchy = pdb_input.construct_hierarchy() Please let me know if you have any more questions about using iotbx.cif! Cheers, Richard On 6 November 2013 11:38, wtempel <wtempel(a)gmail.com> wrote: > Hello all, > please consider the scenario of a manuscript that, among other things, > describes 20 crystal structures. > Suppose the journal editor requires a Table 1. > I now looking for a tool to prepare such table with high accuracy and > little effort. > My PDB deposition workflow includes the preparation of mmcif coordinates > with pdb_extract. The mmcif file is complete in the sense that after upload > to RCSB-ADIT, virtually no additional information is required for > deposition. > My intuition was to combine CSV and IOTBX python modules and produce the > table via input of a list of mmcif files. > The current phenix table_1 tool provides some, but not all of that > functionality, and I thought once familiar with the python modules, I would > quickly write the script. > After confirming that the example at > http://cctbx.sourceforge.net/iotbx_cif/ > works with my cctbx installation, > I attempted to transform that code to read in PDB mmcif coordinates: > <code> > test_structure = iotbx.cif.reader( > file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] > </code> > which throws an exception: > <output> > Traceback (most recent call last): > File "1NXC.py", line 3, in <module> > test_structure = > iotbx.cif.reader(file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] > KeyError: '1NXC' > </output> > How do I need to write the code so that it returns a python object with > access to all the cif items? > Thank you, > Wolfram Tempel > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

11 years, 7 months

[phenixbb] IBA2025 - discounted registration ending soon

by Chip Lesburg

Discounted registration for the upcoming IBA conference ends on April 1. Register soon to secure your place before the price increases. We're looking forward to seeing you at the MassBioHub in Cambridge MA on May 5 & 6, 2025! Conference information and registration is available at https://industrialbiostructuresamerica.org [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZ…> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender. From: Chip Lesburg Sent: Monday, February 24, 2025 8:19 PM To: phenixbb(a)phenix-online.org Subject: IBA2025 - May 5&6 2025 - Cambridge MA The Industrial Biostructures America conference will take place on May 5 & 6, 2025 at the MassBioHub in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Stephen K. Burley, Director RCSB Protein Data Bank and Rutgers University Professor * Dr. James Fraser, Professor and Chair Department of Bioengineering and Therapeutics Sciences at UCSF * Dr. Stephen Harrison, Professor Harvard Medical School/Investigator Howard Hughes Medical Institute * Dr. Mark Murcko, Founding CSO/Board Member at Dewpoint Therapeutics and Relay Therapeutics Conference information is available at https://industrialbiostructuresamerica.org along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Structural Biology of Targeted Protein Degradation: Glues, TCs & DUBs * Developing Fragments to Drugs: Challenges & Victories * Molecular Dynamics and Allostery - Bridging Experimental and Computational Drug Discovery * Membrane Protein Structure Guided Design * CryoEM Synergies with Molecular Modeling and Computational Models * Biologics (Antibody Design & ADCs) * AI/ML in Structural Biology and Drug Discovery * Hot Topics (SBDD, Kinases, RNA) The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for information regarding Exhibitor and Sponsor opportunities

3 months

Re: [phenixbb] command line molprobity tools

by Pavel Afonine

Hi Engin, that's right, it outputs only global figures... Tools that Nat listed output detailed lists. Pavel On 5/1/13 12:26 PM, Engin Özkan wrote: > Thanks Pavel. This does half the job by reporting the overall values, > but does not list detail. For example, it tells you the Ramachandran > outlier percentage, but does not list the outlier residues. Or the > bond and angle outliers. I would like to see those output as well. > These are all done beautifully in the GUI, but apparently not output > as human-readable text files. > > I looked at full parameter list, but could not see a longer output > switch. > > Engin > > On 5/1/13 12:19 PM, Pavel Afonine wrote: >> Hi Engin, >> >> try: >> >> phenix.pdbtools model_stat=true model.pdb >> >> If this doesn't do what you want then please let me know. >> >> Pavel >> >> On 5/1/13 12:15 PM, Engin Özkan wrote: >>> Hi everybody, >>> >>> I want to create a comprehensive, human-readable log file by running >>> validation using molprobity tools within phenix command-line. I do >>> not have structure factors/maps. Apparently, the GUI runs validation >>> through phenix.model_vs_data (according to the .eff file), but in >>> command-line, I cannot get phenix.model_vs_data to run without an >>> mtz/hkl. I guess I could provide it a fake data file, and then set >>> the comprehensive flag to "True"? BTW, the log file produced by the >>> GUI is not comprehensive at all. >>> >>> I could not find a related mmtbx or cctbx function either. Another >>> mentioned tool, phenix.validate, does not even exist in my >>> installation (dev 1361). >>> >>> Thanks, >>> Engin >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > >

12 years, 2 months

Re: [phenixbb] How do I turn off sidechain rotamer fitting?

by Pavel Afonine

Hi Owen, local real-space refinement will not fit a side-chain into a rotamer outlier: it uses both, map and rotamer library, and also it uses a quite complex logic that aims to find best density fit and at the same time keep good geometry (no outliers of any sort). That's why I wanted to look at the files because to me what you described is an indicator of a problem somewhere else or a bug.. Pavel On 7/15/13 11:56 AM, Owen Pornillos wrote: > Hi Pavel - > > Thanks for the reply. > > I have a 2.6 A data set that has a dimer in the asymmetric unit, and > so I'm using NCS. Some of the big sidechain densities (LYS, ARG, etc.) > are not well-defined so I'd like to just restrain them to the other > chain. The auto rotamer fitting of course tries to fit them, and the > result is a list of half a dozen or so rotamer violations. I'm going > through the list to see if the density truly defines different > conformations. I think this is just a general run of the mill problem > with fitting/refinement with NCS. > > Thanks, > > Owen > > On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote: > >> Hi Owen, >> >> you can disable it by turning of real-space refinement off. >> >> I'm interested to know what exactly is not going well: could you please >> explain this to me off list and send files so I can reproduce the >> problem? >> >> Pavel >> >> >> On 7/15/13 10:46 AM, Owen Pornillos wrote: >>> I'm using one of the nightlies - dev 1427. It's not doing very well >>> in combination with NCS. Or what is the most recent nightly that does >>> not have this feature? >>> >>> Many thanks, >>> >>> Owen >> >> _______________________________________________ >> 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

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