- phenixbb - phenix-online.org

Re: [phenixbb] Changing an amino acid to an unusual amino acid
by Schubert, Carsten [JRDUS] 03 Jun '15

03 Jun '15

Hi Nat, bonds in COOT do not mean much, as they do not translate into bonded interactions in the refinement programs. Phenix for instance tries to figure out the bonding by itself through some distance based heuristics. However in your case it looks as if the CRO residue may not be defined as a polymer, i.e. part of a protein chain in the monomer library you are using. In Windows the monomer library is located in C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The aminoacids or modified aminoacids considered part of the peptide chain have all 'peptide' in the header, CRO does not. That is probably the reason why coot does not make any bonds. This would probably cause problems later on with Phenix as well. You could pull out the CRO.cif into your directory, modify it to make it a peptide and read it into coot and phenix during refinement. I would also run it through REEL to make sure the definitions are kosher. HTH Carsten From: Natalia Ketaren [mailto:[email protected]] Sent: Tuesday, June 02, 2015 5:42 PM To: Schubert, Carsten [JRDUS] Subject: Re: Changing an amino acid to an unusual amino acid Hi Carsten, Th residue is a part of the correct chain. It just doesn't make an bonds with the residues on either side of it. Is this common for unusual amino acids when adding to the main chain? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/ On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] <CSCHUBER(a)its.jnj.com<mailto:[email protected]>> wrote: Hi Natalia, if the missing/wrong chain IDs are really the problem you can change them in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, since you probably have to use the correct residue range to change an individual residue into an existing chain. In your case I would write out the PDB file and use a text editor to change the chain ID and move the residue into its correct place in the file. HTH Carsten From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Natalia Ketaren Sent: Tuesday, June 02, 2015 5:17 PM To: phenixbb(a)phenix-online.org<mailto:[email protected]> Subject: [phenixbb] Changing an amino acid to an unusual amino acid Hello All, I'm working on a GFP structure and I'm trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling->Replace residues, where it's suppose to replace a Tyr residue. I type the 3 letter code, CRO, the residue appears, I'm able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I'm doing wrong? And possibly walk me through a solution? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

4 3

Negative density
by mohamed noor 03 Jun '15

03 Jun '15

Dear all After refinement, there is a single negative peak in my map where nothing is modeled. What does it mean? Thanks.

3 2

Changing an amino acid to an unusual amino acid
by Natalia Ketaren 02 Jun '15

02 Jun '15

Hello All, I’m working on a GFP structure and I’m trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr residue. I type the 3 letter code, CRO, the residue appears, I’m able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I’m doing wrong? And possibly walk me through a solution? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

2 1

Merging reflections
by mohamed noor 02 Jun '15

02 Jun '15

Dear all I have a few native datasets, one anomalous dataset with signal up to 10 A and two other datasets (also collected at the phasing wavelength but no anomalous signal seems to be present) and a sulfur SAD dataset with signal to about 7 A. All the datasets have a resolution of about 2-3 A and processed with xia2/XDS. I couldn't do fluorescence scan as the detector couldn't detect at such a high energy (20 keV). A few questions: 1. Why is there at least some signal from one dataset but not others? The signal should come from a covalently bound ligand, molybdopterin to be precise. 2. Since I(+) should not be equal to I(-) when there is anomalous signal, should I just merge the native dataset together with those collected at phasing wavelength that have no anomalous signal? Or do I merge everything together? 3. Will the anomalous signal to 10 A be useful to do MR-SAD? I could solve the structure with MR but I wanted to be sure my ligand is there. Thanks.

3 4

Allignment of multiple structures
by jens j birktoft 01 Jun '15

01 Jun '15

I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Structural DNA Nanotechnology Department of Chemistry New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

2 1

a question on phenix.real_space_refine
by Smith Liu 01 Jun '15

01 Jun '15

Dear Pavel, By phenix.real_space_refine, I fit a PDB with a 4.0 map. Most of the fitting were nice, but for the Ala residues, it indicates the o of the C=O occupies the density position which should be occupied by the CH3 side chain of the Ala, which also means the CH3 side chain of Ala cannot occupy the density position which clearly should be occupied by the CH3 side chain of Ala. Is any method or restraint to have the CH3 of Ala to ccupy its density position? Smith

1 0

alternate side chains conjugated with water molecules
by Jorge Iulek 31 May '15

31 May '15

Dear all, I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is: http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this. Jorge

2 2

Low resolution refinement - rotamers and Ramachandran
by mohamed noor 29 May '15

29 May '15

Dear developers I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier. Secondly, when I used phase_and_build to build my model, my R/Rfree is around 30/35 with atoms from some residues missing. When I fill them in with Coot, fix the outliers above and re-refine, R/Rfree jumps to 36/42 and the rmsd angles are too high (2.9). I have already used weight optimization and NCS. Am I doing something wrong? Thanks.

3 5

reference model restraints by segid
by jp d 28 May '15

28 May '15

Hi,I am having trouble getting phenix to used segid's in reference model restraints when my reference and target pdbs both don't use chain ID's.phenix quits with this message: *** Adding Reference Model Restraints *** Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains one or more errant TER cards. Please remove and try again. my definition file looks like this:refinement { main { reference_model_restraints = True } reference_model { file = two.pdb } } refinement.reference_model.reference_group { reference = segid A16S selection = segid A16S } (above about 50 more times) this was on versions 1.9-1692 , dev-2016 and dev-2056 any suggestions ?thanksjpd

4 4

riding hydrogen model
by Filip Qbukarski 27 May '15

27 May '15

Dear phenix community I am currently refining a 1.75A structure and wanted to usethe riding hydrogen model in pehnix.refine. From what I found in the manual andprevious discussions on the mailing list and if I understand well, using ridingHs is advised for every resolution and the way of doing this in phenix.refine is notRefmac-like but instead I should 1) put Hs using ReadySet, 2) select the‘riding’ option for Hs and 3) use the PDB containing the H coordinates fordeposition, even though they were not individually refined. In this case theircontribution to scattering is also taken into account (which makes sense),which is a different way of treating riding Hs compared to Refmac, if Iunderstand well. Would it be possible to comment on this and in case I got thingswrong, correct?In fact for my structure, after adding the Hs prior to refinement using ReadySet and using theriding option, I actually got Rfree dropping by 1% (from 19.5 to 18.5) and better clash score (~0.5 according to Molprobity). Thanks in advancebestFilip

2 1