April 2010 - phenixbb - phenix-online.org

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

3 2

Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

4 5

Can PHENIX write the peak list to a PDB file?
by Joe Krahn 03 Dec '10

03 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

5 7

Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

9 13

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 2

Defining planarity for Phenix.refine
by Peter Grey 22 Jun '10

22 Jun '10

Dear all, I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ? I am grateful for your advice, Peter

7 16

Improved refinement method for low resolution data
by Florian Nachon 14 May '10

14 May '10

Hi all, Axel Brunger just published a paper in Nature (http://www.nature.com/nature/journal/v464/n7292/abs/nature08892.html) about a new method to improve models despite low-resolution data. It is implemented in CNS 1.3. It might be a bit early, but is there any plan to implement that method in phenix? Florian.

10 21

Refinement with partial model - question
by Peter Grey 13 May '10

13 May '10

Dear Phenix Users, I have a partial model at low resolution. Is there a way let Phenix.refine know the model is not complete and that when a mask is calculated for bulk solvent correction it should take this fact into consideration ? Alternatively, can I use a solvent mask from density modification program in Phenix.refine somehow ? Alternatively, is there a program that will build dummy atoms (zero occupancy) automatically in a map in all peaks above a certain sigma (i.e. atoms just for mask calculation). Thank you in advance, Peter.

14 32

Phenix Ligand Identification error
by Rajan 13 May '10

13 May '10

Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX" but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click "OK" to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File "/home/programs/linux/phenix- 1.6.1-357/cctbx_project/libtbx/thread_utils.py", line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py", line 55, in __call__ result = self.target() File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 308, in __init__ ligand_identification.Run(self, params) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- ************************************************ Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014 Mob. +919417374197 Fax: +91-172-2625254 ************************************************

5 4

Rigid body refinement question
by Simon Kolstoe 06 May '10

06 May '10

Dear phenixbb, What do I need to change in my .def file if I want to refine chain A-E of a structure as per the defaults but specify a single chain (in my case chain L) for just rigid refinement in all cycles? I had a look at the manual page (http://www.phenix-online.org/documentation/refinement.htm ) but didn't find it too clear. Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek --------------------------------------------------------------

5 4