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modify the helices
by xinghua qin 19 Jul '10

19 Jul '10

hi everyone: Thanks for all the response! what I said last time may be chinglish and lead to some misunderstanding, the word I said fix a helix means that the model quality of the helix is not very good, I want to modify it manually.It is so hard to do this in low resolution.I modified the helix according to the electron density map, after refinement, large red areas appear in the difference map. That made me crazy! Are there any suggestions or any reviews about this point? I am new beginner to structural biology, any suggestions are welcomed ! Best regards Xinghua Qin Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District?Beijing?China?100094 Tel: +86-10-62732672 > > > Message: 2 > Date: Fri, 16 Jul 2010 22:10:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] sum(occ)<1? > Message-ID: <4C413B48.305(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, > > > Reset occupancies that are outside the [0,1] range at every step of > > minimization. > > this simply will not work: this will invalidate the internal memory of > LBFGS minimizer that we use in phenix.refine and as result it will drive > it crazy. > > Pavel. > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 22:24:35 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? > Message-ID: <4C413E93.6010002(a)lbl.gov> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Xinghua, > > you can use secondary structure restrains that are available in > phenix.refine. It will automatically figure out secondary structure and > apply proper restrains. This should preserve your helix geometry and > still refine it. > > Example: > > phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true > > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > If you still prefer not refining that helix over applying > secondary-structure restrains, then you can do that too: > > phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A > and resseq 123:156)" > > where atom selection > > chain A and resseq 123:156 > > selects your helix, and prefix "not" means you exclude it from refinement. > > Of course you can do all this from PHENIX GUI. > > Let me know if you have any questions. > > Pavel. > > > ------------------------------ > > Message: 4 > Date: Fri, 16 Jul 2010 22:48:52 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? - P.S. > Message-ID: <4C414444.8080208(a)lbl.gov> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > By the way, more information about secondary structure restraints in > phenix.refine you can find in recent PHENIX Newsletter (pages 12-17): > > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf > > Pavel. > > > On 7/16/10 5:52 PM, xinghua qin wrote: > > Hi phenixers: > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > > > Best regards > > > > Xinghua Qin > > > > -- > > Xinghua Qin > > College of Biological Sciences > > No.2, Yuan Ming Yuan West Road > > Haidian District?Beijing?China?100094 > > Tel: +86-10-62732672 > > > > > > ------------------------------ > > >

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sum(occ)<1?
by Ed Pozharski 18 Jul '10

18 Jul '10

Let's say there are two orientations of a ligand for which occupancies need to be refined. By default, the sum of the two will be fixed at 1.0. From quick look at the manual, the only way to have the sum(occ) at lower level is to reset main.occupancy_max. However, this will probably affect all the atoms for which occupancies are refined, which is undesirable (while ligand may have total occupancy of <1, alternate conformers for protein residues should always add up to 1). Am I missing something or the only way to get this done is to refine twice - once only for ligand occupancy, and then for the rest of the model. And what if total occupancy of the ligand is unknown? Is there a way to allow sum(occ) to be anywhere between 0 and 1? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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how to fix a secondary structure?
by xinghua qin 17 Jul '10

17 Jul '10

Hi phenixers: Recently I am trying to fix a helice, but found that it is so hard for me because of the poor resolution(3.2A) and also a unvisible loop near it, so is there any way to just fix a helice ? can I get it out of the whole structure to refine it? Best regards Xinghua Qin -- Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District，Beijing，China，100094 Tel: +86-10-62732672

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How to manually define NCS group for phenix.autobuild?
by J J 16 Jul '10

16 Jul '10

Hello everyone, It is easy to manually define NCS group in phenix.refine, but how to manually define it in phenix.autobuild? phenix.simple_ncs_from_pdb will generate an .ncs_spec file which can be used in autobuild, but what if I want to define ncs group myself, say removing some residues from the automatically detected one. I can manually remove them from the .ncs_spec file, but the operations defined in the .ncs_spec is no longer valid? Thanks in advance Jason U Pitt

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How to define multiple rebuilding region?
by J J 16 Jul '10

16 Jul '10

Dear All, I am trying to use phenix.autobuild to rebuild some poor regions in my model. Since I know which part should be rebuilt, I was thinking using rebuild_chain_list in combination with rebuild_res_end_list and rebuild_res_start_list. The manual suggested: " You can specify more than one region by using the Parameter Group Options button to add lines." What is this Parameter Group Options button? I am running through an .eff file. I have tried something like this: rebuild_chain_list= " 'A, 'B' " rebuild_res_end_list= 50 rebuild_res_start_list=10 However, it does not work. It becomes more obscure to me what if I want to rebuild more than one region in a single chain? Thanks in advance. Jason ------------------------------------------------ University of Pittsburgh School of Medicine 3501 Fifth Avenue Pittsburgh, PA 15261 ------------------------------------------------

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Rwork/Rfree and aniso ADPs
by Roberto Battistutta 15 Jul '10

15 Jul '10

Dear All, I have noticed a (too much?) increment in the difference between Rwork and Rfree upon introduction of anisotropic ADPs, from 18.6/21.6 (isotropic ADPs) to 14.5/20.0. The max resolution is 1.6 A with good statistics. What could be the reason for that? Is 1.6 A too low for anisotropic ADPs in phenix? I would like to keep Rwork/Rfree values nearer, how could I do? Thank you. Bye, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.8275265/67 fax. +39.049.8275239 roberto.battistutta(a)unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it

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Selecting ellipsoid of data
by Frank von Delft 15 Jul '10

15 Jul '10

Hi, is there a tool in phenix that allows me to select an ellipsoid of data -- specified e.g. by the highest resolutions in three reciprocal lattice directions. (Yes, I'm playing with anisotropy, "playing" being the operative word.) phx

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Interpreting new ligands
by Monique Gangloff 13 Jul '10

13 Jul '10

Hi, I have not managed to refine glycans such as beta-L-fucose (FUL) that are not listed in the PHENIX library. I am not sure what the problem is. eLBOW works fine and creates a cif file for FUL. elbow.ligand_linking file.pdb crashes with the following error message: "Fatal problems interpreting PDB file". The refinement works fine when I remove FUL from my pdb file. Any suggestion would be very welcome. Cheers, Monique

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Re: [phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 13 Jul '10

13 Jul '10

Hi Ralf and Pavel, Thanks so much for the quick response and advice. I have tried both of your suggestions: To assign different altloc identifiers, with the same res ID, chain ID and different resnames (Ralf) and with the same resname (Pavel). I had thought of this but was afraid it would cause confusion with the associated .cif files. Unfortunately, this appears to be the case. For your strategy Ralf, the .cif and .pdb files created by "phenix.ready_set modified.pdb" and the .cif file created by "phenix.elbow modified.pdb" were all accepted by phenix.refine, however the two molecules were still driven away from each other =( For your strategy Pavel, I could not get phenix.refine to run with either the pehnix.ready_set, or the phenix.elbow outputs. It consistently gives the following .cif file error: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 52 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). I will send to you the appropriate sections of both modified pdb files off list and the associated .cif files. Thanks so much again to both of you for all of your help. Cheers, Joe. _________________________________________________________________ View photos of singles in your area! Looking for a hot date? http://clk.atdmt.com/NMN/go/150855801/direct/01/

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Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 13 Jul '10

13 Jul '10

Dear Phenix community, I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this? This is a 1.6Å structure using Phenix version 1.6.1-353. Many thanks for all your help in advance, Joe. _________________________________________________________________ Browse profiles for FREE! Meet local singles online. http://clk.atdmt.com/NMN/go/150855801/direct/01/

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