- phenixbb - phenix-online.org

Problems getting rigid and tls to run
by David Shin 19 Sep '14

19 Sep '14

Hi - Running versions: Version: 1.9.1692 mac-intel-osx-x86_64 osx-10.6.8 Version: 1.9.1692 intel-linux-2.6-x86_64 redhat-e5.10 In both cases, I can run an input model I used previously and get rigid and tls to work. With a newer model, I cannot get either to work (and yes, there was a reason I tested rigid on a model that was refined once). Weirder is I have gone from gui on mac to produce an .eff file to transfer to linux - in the .eff file I get: strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous despite having checked the rigid and tls boxes Weirder yet, is I hand edit the file to add *rigid *tls and run on the linux machine, and both still get turned off. I diff the input refine.eff files between using the older model and newer, and nothing appears very different. The only thing I can think of is that there could be some legacy .hidden files in the working directory that change something, but it makes no sense once I port everything to a different computer. Anyone have this trouble? Thanks, Dave

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Refining structure with overlapping conformations of different residues
by Igor Petrik 18 Sep '14

18 Sep '14

Hi, I am trying to refine a structure in which there are two sets of linked conformations of two residues. Around half of the occupancy (altloc A) corresponds to the sidechain of residue 29 pointing into the pocket and residue 65 pointing out and the other conformation (altloc B) has the side chain of residue 65 in the pocket (where residue 29 is in altloc A) and residue 29 pointing out of the pocket. I am refining them by using occupancy refinement groups in, but phenix refine seems to think that altloc A of residue 29 and altloc B of residue 65 may exist at the same time and pushes them apart to avoid clashes. Is there any way around this? - Igor

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calculate TLS contribution to total B-factor
by Michael Thompson 18 Sep '14

18 Sep '14

Hello All, I have a structure that was refined with phenix.refine using TLS, so my PDB file contains B-total in the isotropic B-factor column as well as ANISOU lines. For the sake of analysis, I am interested in determining the TLS contribution to these total B-factors. How can I split B-total into isotropic and TLS contributions? I'm fairly certain this is possible, as it is the inverse of what one would do after refining a structure with TLS in Refmac, which requires that the isotropic and TLS components be added together prior to deposition. I feel like perhaps there has been some discussion of this in the past, but I'm not able to dig anything up from the bb archives. Any help would be much appreciated. Thanks, Mike

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Problem finding and running iotbx.explore_metric_symmetry
by Arka Chakraborty 17 Sep '14

17 Sep '14

Dear BB members, I am having a problem finding and running the iotbx.explore_metric_symmetry program. I have tried accessing it from the phenix cctbx directory and also from a separate installation of cctbx but could not locate the program. Could anyone point out how exactly to access it?. Thanks a lot in advance, Best regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

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Immediately available: Postdoctoral position in Computational Structural Biology
by David Sivak 17 Sep '14

17 Sep '14

Dear colleagues, This fall I start my own research group in the Physics Department at Simon Fraser University in Vancouver, British Columbia. In the near future, I hope to hire an exceptional, highly-motivated postdoctoral fellow to work on computational structural biology. Please forward this announcement to any interested parties. My group combines approaches from physics, information theory, and statistics to study the fundamental principles of biomolecular function under strong fluctuations. The postdoctoral position will focus on the development of model comparison methods to understand the conformational heterogeneity revealed by structural biology experiments, especially X-ray crystallography. Within this broad research thrust there is ample freedom to pursue particular areas of personal scientific interest. Our theoretical flights of fancy are tethered to reality through a close collaboration with the experimental group of Jaime Fraser at UC San Francisco. Postdoctoral fellows in my group will work in the intellectually-stimulating and interactive biophysics community within SFU Physics, with close ties to the Molecular Biology/Biochemistry department, home to several top-notch structural biology groups. In my own (possibly biased) opinion, the endless all-season outdoors opportunities, mind-blowing food from all ethnicities, and mild weather make Vancouver an enviable place to call home; slightly more objectively, it makes every official top 5 list of most livable cities in the world. The ideal candidate would have experience with computer programming, biomolecular modeling and statistics, and a PhD in a relevant field (broadly construed: physics, biophysics, chemistry, bio- or chemical-engineering, molecular biology, or relevant areas of statistics, computer science, applied math, etc). But most important is intellectual curiosity, enthusiasm for research in this area, and an excellent track record in whatever field they have pursued. Interested candidates should send me a cover letter and CV (including publication list and contact information for 2-3 references). Further information is available at: http://davidsivak.com/ Thank you in advance! David -- David Sivak Asst. Prof., Dept. of Physics, Simon Fraser U david.sivak(a)gmail.com davidsivak.com 778-928-7995

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phenix.merging_statistics and resolution shells
by Murpholino Peligro 16 Sep '14

16 Sep '14

can I specify the ranges of the resolution shells in phenix.merging_statistics? (something like "XSCALE-word" RESOLUTION_SHELLS=) and how many resolution shells are ok? 10, 15, 20?

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LABELIT and MOSFLM version
by Ngoc Anh Thu Ho 15 Sep '14

15 Sep '14

Hello, labelit.index command cannot start Mosflm and gives an error, which reads: "MosflmVersionError: mosflm versions after 7.0.9 not supported” Other than that, indexing seems to be working fine. Can this be fixed or updated somehow? I’m using the latest Phenix 1.9-1692 and Mosflm 7.1.0 (with iMosflm 7.1.1). Best regards, Thu

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calculate CC*
by wei xia 15 Sep '14

15 Sep '14

Hi all:I have a set of data indexed with XDS (space group P222). When I use phaser, the MR solution was in space group P212121.I then changed the space group of mtz file to P212121 using phenix Reflection file editor and did the refinement. Now I use phenix to calculate CC*, in which I input unmerged data (from xds, P222) and merged data (mtz file, P212121) and final pdb file.It turned out to be "incompatible symmetry" error. Are there any easy ways to get the calculate CC* running?Thanks! Wei Xia

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Re: [phenixbb] [ccp4bb] Autobuild in specific area
by Terwilliger, Thomas Charles 14 Sep '14

14 Sep '14

Hi Foggy, This is a situation that autobuild does not address very well yet. Yes, you want rebuild_in_place=False. And yes, if you do that it will remove your model and rebuild it. It will also try to build into the remainder of the map. In practice, you already have pretty much the best that autobuild is going to produce. Delete the protein A chains that autobuild built, and put in your original protein A. Now you have your original model plus whatever autobuild was able to build. An alternative is: select "consider_main_chain_list=True" . This will take your input model A and at each step it will check to see if parts of that model are better than any other model that it has built. This can help for keeping the input model that you put in. All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Zhang Foggy [foggyccp4(a)GMAIL.COM] Sent: Saturday, September 13, 2014 10:40 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Autobuild in specific area Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Foggy

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Autobuild in specific area
by Zhang Foggy 13 Sep '14

13 Sep '14

Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. Foggy

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