- phenixbb - phenix-online.org

real_space_correlation
by Jianghai Zhu 28 Feb '13

28 Feb '13

Hi All, I was trying to use "phenix.real_space_correlation *.pdb resolve_composite_map.mtz" to get some real space cc for my ligand against the SA composite omit map. But I am not sure that the map used here was the SA composite omit map. Will phenix use the omit map I provided or will it just simply calculate a sigmaA weighted 2Fo-Fc map based on the pdb? Thanks. --Jianghai

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mr_rosetta: two proteins, one chain placed, build second chain
by Tobias Beck 28 Feb '13

28 Feb '13

Dear phenixbb, I would like to use mr_rosetta to build a second protein chain. For the first protein, I have a search model with known structure. The search model can be placed with Phaser (TFZ 10). For the second protein, the structure of a homologue has been determined. The second protein accounts for about 2/3 of the residues in the ASU. I would like to fix the first protein chain and build the second protein chain with mr_rosetta. I have obtained fragment files for both proteins from robetta. What input parameters are required to tell mr_rosetta to build the second chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option. Here is an excerpt of my parameter file with the input files: run a) search_models = "path/chainA.pdb" (from Phaser) search_models = "path/chainB.pdb" (homologue structure) fixed_ensembles { fixed_ensembleID_list = ensemble1 fixed_euler_list = 0.0 0.0 0.0 fixed_frac_list = 0.0 0.0 0.0 fixed_frac_list_is_fractional = True } alignment_files = "path/chainA.dat" alignment_files = "path/chainB.dat" with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment. I have set fragment files with chain_list for both chains. I get this error when running phenix.mr_rosetta (running from command line with .eff file) "Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? This could indicate a problem with sequence alignment in rebuilding. It could be that there are near-duplicate sequences in your sequence file ...if this is the case then you may need to artificially rename your duplicated chains and renumber residues to make a single chain containing a duplication" This error also occurs run b) Without any alignment files run c) Without any alignment files and with just chainA.pdb as search model. An alignment of the sequences from chainA and chainB gives low identity (no duplicate regions), so I suspect the problem is located somewhere else? I have seen a post by Tom Terwilliger, explaining how to deal with two identical chains with different conformations where no alignment files are required. However, I would like to use the information from the homologue structure, that is why I specified the alignment file. By inputting chainB.pdb as search model, mr_rosetta also tries to use this model as a search model for molecular replacement, but I think this is not necessary (and gives a warning that the space group of the search model and the data file do not match). I just want to provide the structural information from structure chainB.pdb to mr_rosetta for building. ----- So in summary this is what I would like to do: chain A: keep fixed - use chainA.pdb as fixed model chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain What is the best strategy to do this? What input parameters are required so that I do not get the error described above? ----- Thanks a lot in advance, Tobias.

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phaser output and packing
by Ursula Schulze-Gahmen 26 Feb '13

26 Feb '13

Could somebody explain to me how phaser decides if there is a solution. When I look at the log file there are a few solutions in the translation function that have fewer than the allowed clashes, but they are still not recognized as potential solutions. Why is that. Is there another parameter that I should be looking at? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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WCPCW 21
by Williams, John Charles 22 Feb '13

22 Feb '13

All, We will be finalizing the program for the workshop on Monday, Feb 25th. The Monterey Plaza and Spa has confirmed that we can accommodate a few more people. So, if you are interested in attending and would like to be considered for an oral presentation or would like to present a poster, please register and submit an abstract no later than Monday, 12 noon (PST). The meeting will be March 17th-20th with Wayne Hendrickson as the Keystone speaker! Best, John wcpcw.org --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

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Maximum Entropy Maps
by Morten Groftehauge 22 Feb '13

22 Feb '13

Hi guys, I see that phenix.maximum_entropy_map is now a command in Phenix. Some quick questions: Where is this likely to be must useful and does it take ridiculously long to run? From the Nishibori 2008 paper in Acta D it seems like this would mainly be useful for very high resolution structures that you would normally call complete - and that it would take a very long time to compute. I love trying out new methods but I need a bit more to go on with this one. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Building sugars
by Folmer Fredslund 21 Feb '13

21 Feb '13

Dear all, What's the "correct" way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar "ligands" in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund

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phenix.table_one citation
by Alexander Batyuk 20 Feb '13

20 Feb '13

Dear developers, How to cite phenix.table_one? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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cut out density vs FFT
by Yunji Wu 19 Feb '13

19 Feb '13

Hi all-- I'm trying to make a 2Fo-Fc map with density wrapped around my asymmetric unit to make a figure showing density for my sub-8Å structure. I am not building into this map or doing MR. My model was refined in Phenix.refine (R's in the high 30's), and so I have the output model .pdb and the output map coefficients .mtz. When I input these into cut_out_density, the only "map labels" input options it gives me are 2FOFCWT, PH2FOFCWT, which seem fine. Using either box, sphere, or model for the cutout type, I get a VERY nice looking map that looks extremely solvent flattened and tight around my model, albeit still to 8Å. Suspicious of anything that looks good, I went to try the same thing in FFT (CCP4). There I generated a simple map (using the same .mtz) to cover all atoms in a pdb file- the same model I put into cut_out_density. For the input I selected 2FOFCWT and PH2FOFCWT, leaving Sigma and Weight unassigned. The map that comes out of this looks terrible, with a lot of noise and little density corresponding to the model aside from what one might expect from a very poor resolution experimental map. I've also tried using FFT in Phenix to do the same thing, and it gives like better maps than CCP4 FFT but worse than cut_out_density. It almost appears as if there is some additional solvent flattening going on, which I know happens at the beginning of refinement, but that should be intrinsic to the map coefficients file which is common to everything I've tried. My questions are (1) what should I use for what I am trying to do (just display 2Fo-Fc density around asymmetric unit for a figure) and (2) what is the difference between what these three programs (cut_out, FFT-CCP4, FFT-Phenix) are calculating? The inputs are exactly the same -- mtz (2FOFCWT and PH2FOFCWT) and pdb output from refinement. Thanks for the help, Yunji

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Problems placing second component in Phaser
by Morten Groftehauge 19 Feb '13

19 Feb '13

Hi guys, So I have a solution that covers some of target and I ran it through phenix.mr_rosetta and I am actually kinda happy with the output from there. However, while I can place both (NCS=2) with the original model I only seem to be able to place one of the rosetta models, even with 'packing function' set to 'all' or 'allow'. Original model - Refinement after placing component 1: LLG 175 Refinement after placing component 2: LLG 620 Rosetta model (packing 'all') - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 390 Rosetta model (packing standard) - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 350 More notably there is little to no increase in TFZ with the placement of the second component... There are more residues in the Rosetta model and I would expect more clashes but this looks weird. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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where is brute rotation output
by Ursula Schulze-Gahmen 18 Feb '13

18 Feb '13

Hi, Has anybody experience with the output from the brute rotation function. I ran this and it finished without complaints, but there are no output files ***.rlist or ***.sol in the directory. I cannot figure out why and how to continue now with the translation function. From the log file it seemed that there were peaks that could have been written out. Thanks for any help Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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