- phenixbb - phenix-online.org

Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 11 Mar '11

11 Mar '11

(was posted on CCP4 bb also) Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/[email protected]/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.

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automr renumbered all residues to 0 for final solution in dev-674
by Francis E Reyes 11 Mar '11

11 Mar '11

Is this fixed in a later version? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hi Pavel, What I meant it was just that the 2mFo-2DFc map looks really great and corroborates experimental data as far as the stereochemistry. But I dont understand ehy the carbonyl moiety of the ligand would be where it is now, no "driving force to be here". And when I look at my averaged kick and SA omit map it looks ambiguous. Any help?

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hello everyone, I have this strucuture I solved by Molecular replacement. It is a single mutant of previously solved enzyme. I started refining it and fit the ligand in a way that gives me the experimental stereochemistry. The final map 2mFo-2DFc looks great. After further examination I noticed, I have a carbonyl that does not seem to be bound to anything !!! I started looking at my average kick and SA composit omit-map prior to modeling in the ligand and now I am really lost. Could anyone help? Thank you

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Important change in phenix.refine output: MTZ file with data and map coefficients
by Pavel Afonine 04 Mar '11

04 Mar '11

Hi Everyone, starting development version dev-686: http://www.phenix-online.org/download/nightly_builds.cgi phenix.refine does not output *map_coeffs.mtz file. Instead, it creates prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections: - section 1: Original input data (Iobs or Fobs, and HL coefficients if provided) and flags (as supplied in input); - section 2: Experimental data used in refinement (labels: F-obs-filtered, SIGF-obs-filtered). This can be different from "Original data" due to Iobs->Fobs conversion (if input data are intensities) and outliers filtering; - section 3: Contains total model structure factors (labels: F-model, PHIF-model) used everywhere in refinement (for the formula, see: http://www.phenix-online.org/documentation/fmodel.htm). In the future, this section might be extended to explicitly list all contributions to Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk solvent contribution), and so on. - section 4: Fourier map coefficients (exactly the same as used to be in *map_coeffs.mtz file). This change is meant to reduce the confusion when people tended to use *map_coeffs.mtz file for refinement and PDB deposition, and facilitates the reproduction of refinement statistics (R-factors, for example). Also, thanks to Jeff Headd, by default phenix.refine now converts input intensities (Iobs) to amplitudes (Fobs) using French & Wilson method (Acta Cryst A34, 517, 1978), so no need to run a specific program (Truncate, for example) to do this. To see the content of a MTZ file use phenix.mtz.dump command: phenix.mtz.dump data.mtz Pavel.

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Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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Re: [phenixbb] number of cycles
by Maia Cherney 02 Mar '11

02 Mar '11

Hi, I am using now the latest phenix version and I am curious how to understand these lines: Flipped N/Q/H residues before refinement: A 28 HIS A 72 HIS A 141 GLN A 202 GLN A 296 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 388 HIS Maia

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[Fwd: Re: number of cycles]
by Maia Cherney 02 Mar '11

02 Mar '11

-------- Original Message -------- Subject: Re: [phenixbb] number of cycles Date: Tue, 01 Mar 2011 19:50:57 -0700 From: Maia Cherney <chern(a)ualberta.ca> To: Jeff Headd <jjheadd(a)lbl.gov> References: <40FBFA09-3C52-460A-A6A1-7D08F6496AD2(a)umich.edu> <AANLkTin=8_ddvihNSDyLp9k1iSpV9fVj6A2ndvoUTJ6O(a)mail.gmail.com> <0171D39299ABC14AAAA75ABABDD0BBB63868BF23AA(a)NIHMLBX12.nih.gov> <A8FA87FE-7DF1-48BE-AA44-E19BB7D0E6E0(a)crystal.harvard.edu> <4CAC89B8.9090909(a)lbl.gov> <4D12B58C.1030604(a)ualberta.ca> <4D12E866.9070602(a)lbl.gov> <4D138B20.5050001(a)ualberta.ca> <4D14E51F.2040305(a)lbl.gov> <4D164065.3050709(a)ualberta.ca> <4D165AE5.8090905(a)lbl.gov> <4D6C0DB1.5040003(a)ualberta.ca> <4D6C9271.6000301(a)lbl.gov> <4D6DA14C.6060806(a)ualberta.ca> <AANLkTi=GXvoGWsB+3+NNBNFvVtzc0Q0ag1Ln_U6FqHqO(a)mail.gmail.com> Thanks, Jeff. Though I don't see any clashes for any orientations. But this feature is really great. Jeff Headd wrote: > Hi Maia, > > Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle > and determines which orientation is likely correct given the local > environment of the sidechain. The best orientation will have no steric > clashes and satisfy local H-bond donors/acceptors. In cases where > there are other model errors in the region of the sidechain and both > orientations clash significantly, you'll see the **PLEASE CHECK > MANUALLY** warning which indicates that there are likely multiple > misfit sidechains that need to be corrected, and refinement alone is > not powerful enough to escape the false minimum. > > If you want to turn this feature off, you can add main.nqh_flips=False > to your refinement call or > > main { > nqh_flips=False > } > > to your param file. However, we highly recommend leaving this option > on as it is an excellent diagnostic of model errors. > > If you have any further questions please let me know. > > Thanks, > Jeff > > On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney <chern(a)ualberta.ca> wrote: > >> Hi, >> >> I am using now the latest phenix version and I am curious how to understand >> these lines: >> >> >> Flipped N/Q/H residues before refinement: >> A 28 HIS >> A 72 HIS >> A 141 GLN >> A 202 GLN >> A 296 ASN >> ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** >> ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** >> A 353 ASN >> A 388 HIS >> >> Maia >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >

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Glycan Links/Restraints
by Damian Ekiert 02 Mar '11

02 Mar '11

Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question. I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to >2 A. No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) ) Any suggestions would be appreciated! Thanks, Damian Ekiert >From my .eff file: apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 }

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