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Molecular replacement at low resolution
by mohamed noor 09 May '15

09 May '15

Dear developers I have a dataset to about 4 A in point group P 4 2 2 (Pointless suggests P 41 21 2). The protein is about 11 kDa and has an identity of about 50 % to my search model. Phaser calculated the eLLG to be about 5, and maybe not surprisingly, it failed even after using Sculptor to prepare the model. It also says that solutions with Z-scores more than 8 were rejected for failing the packing test. Are there any suggestions on getting a solution? Solvent content calculation from Xtriage suggests about 8 copies in the asu. Would this be of any help in MR? Thanks.

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Raw diffraction images required
by mohamed noor 09 May '15

09 May '15

Dear all I am looking for diffraction images that were collected to a resolution of 3 A or so (by visual inspection), highly redundant and the I/sigma at the outermost resolution should be low (not more than 1). Maybe there is something already in the JCSG database but I don't know exactly which one. I want to show that high redundancy can provide a background average to extract weak but useful spots and that this relationship increases to a certain limit. Thanks.

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How to fix atoms in refinement
by Rajeshwer Sankhala 07 May '15

07 May '15

Hi, I have flexible a flexible loop in my structure and every time i refine it derange ramachandrans. Can anyone suggest how can i fix these flexible residues in phenix refinement so basically i don't wanna refine them. Can i do this in GUI? Thanks Raj The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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feature request: update project
by Sebastiano Pasqualato 07 May '15

07 May '15

Dear Phenix developers, it happened to me recently to go from one Mac to another, working on the same Phenix projects. I have the directory synchronised via Google Drive, with the same absolute path. Importing a project is not a problem, at all. The problem is that, if I modify one project on one computer, the changes are not “seen” by the other computer, and there is no way to “update” the project, forcing it to read the info on the .phenix directory. Would that be difficult to implement? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

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on phenix.real_space_refine
by Smith Liu 06 May '15

06 May '15

Dear All, If I only want to refine resi 30-50 in Chain A by phenix.real_space_refine, and my protein contains A, B, C chains of a identical sequence of 800 aas, will you please let me know how can I specify "residue 30-50 of Chain A" in the phenix.real_space_refine command? Smith

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neutron refinement of protonated Glu and residues with alternate conformation
by crystallogrphy 05 May '15

05 May '15

Hi, I am doing joint X-ray and neutron refinement for my structure. I found a few residues with two alternate conformations. After I generated alternation conformations, I used phenix.readyset to generate hydrogen and deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms for exchangable H atoms, such as the amide H atoms. The reason is that A and B letters have been assigned for the alternate conformation, not for the D/H atoms for particular conformations. Could anyone know how to solve this problem? The second question is that I found one Glu residue is protonated at OE1 atom of its carboxylate side chain. How could I generate protonated Glu? Do I need a strain file for this? Thanks! Qun

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SA
by Irina PROKHOROVA 01 May '15

01 May '15

Hello, I am trying to run coordinate refinement 5 cycles with first cycle of simulated annealing (torsion) via command line. Here is a part of my params file that I adapted from my colleges: refinement.main { number_of_macro_cycles = 5 target = *ml mlhl ml_sad ls simulated_annealing_torsion = True } simulated_annealing { mode = every_macro_cycle second_and_before_last once *first first_half } refinement.refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = segid *A individual = segid *B } As a result I get the Error Unused parameter definitions: simulated_annealing.mode (file "refine.params", line 26) Could you help me with the syntax, please. Should I include sites definition for simulated annealing? Irina

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Phenix.real_space_refine and B-factor
by Smith Liu 30 Apr '15

30 Apr '15

Dear All, By Phenix.real_space_refine if is very nic to fit a PDB into an EM map, and we can get a fitted PDB. However no matter what is the run strategy (default, morphing, local grid search, etc), in the got PDB the B-factors for each atom in the coordinates were always those from the original input PDB, which may make the B-factors in refined PDB meaningless. As finally we need to deposit the refined PDB and EM to the database, will you please explain how to settle the B-factor issues in the refined PDB related to Phenix.real_space_refine? Smith

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on B-factor refine
by Smith Liu 29 Apr '15

29 Apr '15

Dear All， If in the Phenix refine GUI, I only want to refine based on individual B-factors, can I only click "individual B-factors" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options"? Further, if I only click "XYZ cordinates" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options", what the Phenix refine realy do? Smith

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extra density for phosphorylated Thr
by Ursula Schulze-Gahmen 29 Apr '15

29 Apr '15

I have a structure with a phosphorylated Thr (TPO). As far as I can see, phenix recognizes the TPO residue, but the electron density maps have a large positive density around the side chain of this residue. Any suggestion what is wrong? Do I need a special definition file for the TPO? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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