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NAG-NAG link definition seems to have no effect
by Benjamin Stauch 11 Jun '14

11 Jun '14

Hi Phenix, apologies for the beginner question, and I do realise that there are some related threads already but nothing so far has helped me to solve this problem. I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI), apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname ASN and resid 74" } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname NAG and resid 402" } when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG. There might be some clues in the refine.log file: Build ligand and use monomer library to name atoms : NAG Using monomer library entry NAG as template which I guess looks good, and then something like this which could be where things are going wrong: Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) Furthermore there's still a HO4 attached to the O4 of NAG ... while the BETA1-4 should care to delete it .. however the mon_lib reads BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_beta1-4 which doesn't seem entirely relevant for my case? Any help would be appreciated Thanks! Ben

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Using .fcf file with Phenix
by Rex Palmer 10 Jun '14

10 Jun '14

Can I run Phenix with a .fcf file and a .pdb file? If not how can I convert .fcf to the correct format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Run PHENIX commands on GUI verison?
by 李翔 09 Jun '14

09 Jun '14

Hi, I currently can only access to PHENIX with my laptop which has a Windows system (GUI). I want to run some commands for generating restraints for my models such as: iotbx.show_distances MR.1.pdb > contacts.distances, phenix.secondary_structure_restraints model.pdb Is there a way I can run commands in GUI version or can I run the above commands in the GUI version? Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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B-factors for some sidechains were not refined well
by Zhou, Tongqing (NIH/VRC) [E] 08 Jun '14

08 Jun '14

Dear colleagues, I am refining one structure at 1.94 A with phenix.refine with individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 19.8%. But when inspecting the maps, I noticed that the sidechain tip of some residues showed positive density and the b-factor for those atoms were very high while those for the other atoms of the same residues were normal; The b-factors for newly added ligands were also not refined well showing high b-value and positive density at the same time; the disulfide bonds also show positive density and high B. The occupancy were all set to 1. Please give suggestions. Thanks! Best regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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launching MR jobs from the command line.
by Francis Reyes 04 Jun '14

04 Jun '14

Hi all, For the moment (1.9-1692) phenix.automr still works from the command line but I received a note that it's a 'Deprecated program' . ************************************************************************ WARNING - DEPRECATED PROGRAM Please note: the command-line AutoMR tool and associated GUI have been deprecated and will be removed in future releases. We recommend that you use phenix.mrage or phenix.phaser, both of which are available in the GUI. The program will resume execution in 5 seconds. ************************************************************************ phenix.mrage doesn't resolve to anything, and phenix.phaser runs the phaser binary. Is there a new way to launch MR jobs from the command line (which had all the PHIL friendly goodies that automr had?) ? Thanks, F

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difference map peak in coot not showing all peaks?
by Murpholino Peligro 04 Jun '14

04 Jun '14

In coot I have set the map contour level to 5.0 rmsd and I do Validate -> Difference Map Peaks ... and the new window shows me where the peaks are...but not all of them. For example, see screenshot attached. (there are peaks above sg cys80 and sg cy64, both appear in the visual window in coot but only one of them, cys80, in the listing. If I understand clearly, they should both appear in the visual window and in the listing because I have the same filter (5.0 rmsd). Right? Now...the peaks values are from Phenix doing a Isomorphous Difference Map ... So I do not know if this is from Coot or from Phenix.

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software update
by Edna Patricia Matta, Ms 04 Jun '14

04 Jun '14

Hello everybody, Quick question, do I have to uninstall the old version of the software If I want to have the new one? Thanks a lot, E Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 [http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275 [http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 02 Jun '14

02 Jun '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2014 issue is 16 June 2014 (with some leeway if you are still working on the text). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Autosol and sequence file
by Stefan Knight 02 Jun '14

02 Jun '14

I don’t seem to have much luck with Phenix these days… Trying to run Autosol from the GUI but the process aborts immediately complaining that a sequence file is required to run Autosol. I have given it a sequence file in fasta format that is recognised as such when added. I’ve also tried instead pasting the sequence into the Crystal info window but that didn’t help. Grateful for any tip on how to convince Phenix it has all it needs to get going ;-). Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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How to add difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map?
by Murpholino Peligro 01 Jun '14

01 Jun '14

Hi all. How to add a difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map? Because what I get (after Phenix Isomorphous Difference Map) is a pdb with the peaks (chain A) and holes (chain B) with their positions given by UNKnown atoms, 1 for occupancy and in the B-column their peak-or-hole value. I would be happy if I could get the actual atoms with positions and the peak-or-hole value in the B-column. Thanks again and again.

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