- phenixbb - phenix-online.org

cif files
by Shya Biswas 23 Jan '12

23 Jan '12

Hi all, It appears that the cif file generated from prodrg (REFMAC format) is not recognised by phenix during refinement. Did anyone have similar issues or i am doing something wrong? somehow the geometries obtained from elbow are not right for my ligand so had to use prodrg to generate cif files. thanks, Shya

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Refinement of two co-factors/ligands at the same position
by Kornelius Zeth 23 Jan '12

23 Jan '12

Dear all, how can I refine two different co-factors/ligands ('XXX and YYY', with differing occupancy and cif-Files) located at the same position within an enzyme? What about the chain IDs, segment IDs etc? Thanks and best wishes Kornelius -- Kornelius Zeth ZMBP, Uni-Tuebingen Auf der Morgenstelle 1 72076 Tübingen Germany

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There's BARELY A WEEK left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 20 Jan '12

20 Jan '12

Half of the seats are still available for RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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phosphate stereochemistry
by Luca Pellegrini 20 Jan '12

20 Jan '12

Hi, I have noticed that Phenix mangles O-P bond lengths and angles in the phosphate groups of my DNA chain (example in pict attached). This only happens to 3 out of 28 phosphates. The refined protein-DNA structure does not present any other unusual stereochemistry issues and refinement runs normally. Could anybody advice on what is going on and how to fix this, please? I am using Phenix-1.7.3-928. Refinement is with default target weights, hydrogens on and does not include simulated annealing. I could make the stereochemistry targets more stringent, but the default values seem strict enough (bond and angle rmsd is 0.005 and 1.225). Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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phenix.refine is auto selecting an old .pdb file for refinement
by Andrews, Forest Hoyt 20 Jan '12

20 Jan '12

I'm having a bit of an issue with phenix.refine. I was receiving the following error "number of groups of duplicate atom labels: 4789 total number of affected atoms: 9578" However when I looked inside my .pdb file there where only 4789 atoms total....No duplicates. I discovered that phenix.refine is auto selecting a .pdb from a previous run. I found this out by not selecting any .pdb file and found phenix.refine refining my data with an older model I use to refine a previous round. How can I stop phenix.refine from auto selecting a .pdb during refinement? __________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Pavel Afonine [pafonine(a)lbl.gov] Sent: Friday, January 20, 2012 12:20 PM To: PHENIX user mailing list Subject: Re: [phenixbb] phosphate stereochemistry Hi Luca, what kind of NCS restraints did you use: torsion or Cartesian? I wonder if torsion NCS would naturally avoid this problem? I hope Jeff comments on this. Pavel On 1/14/12 10:51 AM, Luca Pellegrini wrote: > I think I discovered what was happening to my DNA molecule during > refinement, that caused distortion of the phosphate groups. It was > something along the lines of what Dale suggested, I mention it here so > that it might be useful to others. > > I have two DNA molecules in the ASU and I didn't realised that I had > accidentally swapped OP1 and OP2 in 3 out of 28 phosphates (so that, > if the two DNA molecules were superimposed, OP1 ended on top of OP2). > Because I had NCS restraints on during refinement, I guess phenix was > trying to move OP1 in one DNA molecule towards the NCS-equivalent > position of OP1 in the second molecule, hence the altered geometry. > > I have fixed the atom nomenclature problem and now the geometry of my > DNA is ok. I appreciate that most people tend to avoid such mistakes > ;-) but perhaps it would be good if phenix could flag situations such > as these. > > Luca > > On 6 Jan 2012, at 16:15, Pavel Afonine wrote: > >> Hi Luca, >> >> phenix.refine always generates a *.geo file that lists all the >> geometry restraints (bonds, angles, planarities, chiralities, >> dihedral, non-bonded, ncs(if any)) used in refinement for all atoms. >> For each restraint it list current model value, target (library) >> value, etc. >> >> Can you have a look at *.geo file for O-P bonds in question? May be >> this gives a hint about what's going on? >> >> Pavel >> >> On 1/6/12 4:31 AM, Luca Pellegrini wrote: >>> >>> Hi, >>> >>> I have noticed that Phenix mangles O-P bond lengths and angles in >>> the phosphate groups of my DNA chain (example in pict attached). >>> This only happens to 3 out of 28 phosphates. The refined protein-DNA >>> structure does not present any other unusual stereochemistry issues >>> and refinement runs normally. Could anybody advice on what is going >>> on and how to fix this, please? >>> >>> I am using Phenix-1.7.3-928. Refinement is with default target >>> weights, hydrogens on and does not include simulated annealing. I >>> could make the stereochemistry targets more stringent, but the >>> default values seem strict enough (bond and angle rmsd is 0.005 and >>> 1.225). >>> >>> Thanks, >>> Luca _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version.

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version. Fulvio Saccoccia, PhD student Dept. of Biochemical Sciences Sapienza University of Rome

1 0

problem converting PDB file to mmcif for deposition
by Salameh, Mohd A., Ph.D. 19 Jan '12

19 Jan '12

Hi Everybody, I encountered a problem recently in converting my PDB file to mmcif using the pdb_extract tool in rcsb. It simply writes out an empty file!! I wonder if any of you have faced such a problem before and know the solution!! I carefully examined the PDB file header and I couldn't really find a reason why this PDB failed to be converted. I only use PHENIX for molecular replacement and refinement. I used the default TLS refinement so I assume the whole structure will be refined as a group. I hope somebody is familiar with this can help me out. Thank you very much, Mohd

2 1

real space correlation
by Jerome Nwachukwu 19 Jan '12

19 Jan '12

Hi: I am trying to run phenix.real_space_correlation from the command line and received the following error message. Is there a specific syntax i should use? Thank you, -Jerome Syntax error: expected "=", found "Date" (file "3_refine_001.pdb", line 1) Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 9, in <module> command_name = "phenix.real_space_correlation") File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/real_space_correlation.py", line 332, in cmd_run track_unused_definitions = True) File "/usr/local/phenix-1.7.1-743/cctbx_project/libtbx/phil/__init__.py", line 1718, in fetch assert source.name == self.name AttributeError: 'NoneType' object has no attribute 'name'

2 2

noisy sa-omit maps in solvent region.
by Francis E Reyes 19 Jan '12

19 Jan '12

Hi phenixers I'm calculating a composite sa-omit map for my entire molecule at 4 A. While my molecule more or less has density (very good for backbone, not so much for sidechains), the solvent region seems to be particularly noisy. Is this the normal experience for composite sa-omit maps at this resolution? I'm particularly interested in what autobuild does when it 'stitches' the individual maps together, is it a direct stitch of the 2fo-fc's after refinement or is there some kind of real space density modification involved? Or a combination of both? Any suggestions appreciated, F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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adding exchangeable H to a perdeuterated structure with ready set?
by Maxime Cuypers 19 Jan '12

19 Jan '12

hello, how can i add exchangeable H to a perdeuterated structure with readyset? (other than manualy editing the file please) i see readyset does the opposite. thanks in advance Maxime

2 1

an error in the operation of SF-Tool
by Dialing Pretty 18 Jan '12

18 Jan '12

Dear All, By the RCSB SF-Tool I have tried to convert my PDB file and the corresponding mtz file into mmCIF for the purpose of RCSB depositation, by the Automatic (default) mode. I got the following message: "Converting structure factor to mmCIF format.... Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file" Obviously there is an error message, although the conversion is succesful. As for I intend to deposit the structure including the mmCIF file into RCSB, I am afraid I have lost some message in the MTZ file and mmCIF file. Will you please tell me how can I add the labels, which have been lost I think, to the mtz file, so that the labels message will also be included into the mmCIF file if it was necessary? Cheers, Dialing

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tool for dispersive difference fourier ?
by Francis E Reyes 17 Jan '12

17 Jan '12

I'd like to make a dispersive difference fourier using phases from a model. Is there a tool to do so? phenix.maps doesn't seem to have the 'map_type' to do this.. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

1 0

Rosetta rebuilding...
by Francis E Reyes 16 Jan '12

16 Jan '12

Phenixers, I'm curious about using rosetta to rebuild an existing model (phenix.mr_rosetta it seems) [0] What is being rebuilt in rosetta? The whole model? Or is the model divided into chunks and each chunk sent to rosetta? [1] Can a specific region be chosen to be rebuilt? (In the case where most of the model is correct) [2] How are the rosetta models scored ? Specifically, "(d) refine Rosetta models, average density from top 20%, continue rebuilding each Rosetta model using averaged density". What's the scoring function (mapCC, R-Free, LLG??) How's the top 20% obtained? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

3 2

Only two weeks left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 13 Jan '12

13 Jan '12

Many seats are still available for RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Simulated annealing omit maps
by SEKHAR1＠pitt.edu 12 Jan '12

12 Jan '12

Hello friends, I have a couple of questions regarding simulated annealing composite map calculations. (1) Is there a way of specifying the percentage of residue co-ordinates to be omitted each time as we move through the asymmetric unit? I have found, when using CNS earlier, that depending on the structure, the map quality often varies if you change this from the usual 5% to 4% or even 3%, sometimes getting clearer. (2) Does the 'number of boxes' you can specify in the GUI only affect the fine structure/grid spacing of the map? The map probably does not get better all the time as we keep on increasing the number of boxes; when do we reach the point of diminishing returns and what would be the best way to estimate it? Thank you very much and wish you all a Very Happy 2012. K. Chandrasekhar

2 1

phenix.find_ncs
by Ursula Schulze-Gahmen 11 Jan '12

11 Jan '12

I am working with a complex of 3 different proteins, and there are 3 complexes in the asymmetric unit. During phenix.refine I used automatic NCS and it worked fine. I now wanted to determine the NCS parameters with phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with 3 chains, and 1 group with 2 chains.I cannot figure out why one chain is not included. I tried to run it with only pdb input, or pdb anf map coefficients, same result. Any suggestions hat else to try? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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brainpool research associate position
by intekhab alam 11 Jan '12

11 Jan '12

Dear members Have a look on the advertisement for the position of research associate in structural biology. Interested candidates please reply to khkim(a)korea.ac.kr. Informal enquiries can also be made. Structural Bioinformatics Lab, Department of Biotechnology & Bioinformatics, Korea University, Seoul KoreaBrainpool Research Associate – Full time, fixed term appointment for up to two years The Structural Bioinformatics Lab is seeking a Brainpool Research Associate to carry out structural analysis (x-ray crystallography) and biophysical studies of complexes related to virus-host interaction. The group is led by Professor Kyung Hyun Kim and has over the years produced good results (PNAS, NAR, JGV). The research programme is funded by a grant from the Korean Federation of Science and technology Societies (www.brainpool.or.kr) to which both the applicant and our team apply together. Further details on the research group can be found at http://sbl.korea.ac.kr/. Applicants should have a PhD in Structural Biology, Biophysics or a related area, with at least 5 years of research experience after Ph.D., or high profile publications in the highest impact journals. Salary range will be from $45,000-$55,000 per annum plus plane ticket, moving expense and medical insurance. Initial salary for possibly the two months will be dependent on the skills and experience of the successful applicant. Closing date for completed applications: 5 February 2012. To apply for this position please send emails to khkim(a)korea.ac.kr with your resume. Korea U is an equal opportunities employer and encourages applications from all candidates irrespective of gender, race, disability, sexual orientation, age, religion and belief or another protected characteristic. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Re: [phenixbb] phenix.find_ncs
by Thomas C. Terwilliger 11 Jan '12

11 Jan '12

Hi Ursula, In that case...sounds like something I need to fix! Would it be possible to send me (off-list, terwilliger(a)lanl.gov) the entire PDB file and I'll have a look? In the meantime, I guess if you run each group separately you have the information that you are looking for... All the best, Tom T >> I just did waht you suggested. I ran phenix.find_ncs on the problem group >> only. This time it found all 3 chains in the group. >> >> Ursula >> >> On Wed, Jan 11, 2012 at 10:16 AM, Thomas C. Terwilliger < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Ursula, >>> >>> I am not sure why find_ncs did not get the 3rd chain for the third >>> group. >>> I think that when you run phenix.refine it is (for the moment) actually >>> just calling find_ncs to get the NCS groups, so the groups found there >>> should (if everything is working the way I think it should) be identical >>> to the ones you would find with phenix.find_ncs. >>> >>> Here is something to try: Split your model into just protein #3 (you can >>> use phenix.pdbtools and keep="chain C or chain F or chain I" to do >>> this), >>> and also just protein #1 and #2. Then run find_ncs separately on these. >>> Can find_ncs get the ncs for your 3 copies of protein #3 all by >>> themselves? >>> >>> If not...then it indicates that perhaps one of the chains is actually >>> different (maybe very different conformation, maybe mostly missing, >>> maybe >>> different sequence...?) >>> >>> All the best, >>> Tom T >>> >>> >>> >> I am working with a complex of 3 different proteins, and there are 3 >>> >> complexes in the asymmetric unit. During phenix.refine I used >>> automatic >>> >> NCS >>> >> and it worked fine. I now wanted to determine the NCS parameters with >>> >> phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with >>> 3 >>> >> chains, and 1 group with 2 chains.I cannot figure out why one chain >>> is >>> not >>> >> included. I tried to run it with only pdb input, or pdb anf map >>> >> coefficients, same result. Any suggestions hat else to try? >>> >> >>> >> Thanks >>> >> >>> >> Ursula >>> >> >>> >> -- >>> >> Ursula Schulze-Gahmen, Ph.D. >>> >> Assistant Researcher >>> >> UC Berkeley, QB3 >>> >> 356 Stanley Hall #3220 >>> >> Berkeley, CA 94720-3220 >>> >> _______________________________________________ >>> >> phenixbb mailing list >>> >> phenixbb(a)phenix-online.org >>> >> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> >> -- >> Ursula Schulze-Gahmen, Ph.D. >> Assistant Researcher >> UC Berkeley, QB3 >> 356 Stanley Hall #3220 >> Berkeley, CA 94720-3220 >>

1 0

Phenix for CUDA?
by Schubert, Carsten [JRDUS] 10 Jan '12

10 Jan '12

Hi, are there any development plans for phenix in the works to take advantage of NVIDIA's CUDA platform? Cheers, Carsten

3 2

Question about unrestrained refinement
by Louis Lazar 10 Jan '12

10 Jan '12

Hello all, I had a question about unrestrained refinement. I have several data sets (right near 1 A resolution) that are nearly fully refined, but to finish I would like to run one round of unrestrained refinement. At this point, I want to focus on unrestrained refinement of just the protein, and not any waters. How would the syntax for refining just the chains of the protein (and not water) look in the command line? I also want to include anisotropic refinement of B-factors in this last refinement run. Should it look something like: strategy=individual_sites+occupanices+individual_adp \ adp.individual.anisotropic="not water and not element H" wc=0 wu=0 Then what should I add after this to include just my protein chains and omit waters from the unrestrained refinement? Also, if I wanted to not refine the waters at all in this round of refinement, what should I add to the command line to make that happen? Thank you in advance as always. Regards, Louis

2 1

zn anomalous
by Pengfei Fang 10 Jan '12

10 Jan '12

Dear All, I collected a dataset at 0.9774 angstrom. the structure is already by MR. Can you please teach me how to tell a specific site has Zn-atom anomalous signal or not using phenix? thank you! Pengfei

2 1

phenix.refine request: output den restraints to a file...
by Francis E Reyes 10 Jan '12

10 Jan '12

Hi phenixbb (Jeff probably), I wanted to try a few different protocols with the den refinement. It occurred to me that phenix.refine won't take den restraints as an external file, instead it seems to be generating them on the fly. Can I have an option to output (and also read in) den restraints? I'd like to generate them once and use the same restraints to test a different refinement params. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

Output for den optimization runs
by Francis E Reyes 09 Jan '12

09 Jan '12

Is there a refine.log for each den (gamma, weight) optimization? I can't seem to find one anywhere and I'm curious to see how it's doing. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Chirality of Ribityl chain of FMN inverted
by Yuri 09 Jan '12

09 Jan '12

Hello Developers, When I built Ligand restraints using eLBOW, my resulting .pdb had an inverted chiral center in the ribityl chain of the flavin mononucleotide particularly C4'. In the database the ligand had an S configuration (correct), but after minimization and restraint generation the output had R configuration at that particular center. I wonder if there is a way to enforce the configuration for each center, although I suspect it could be a little bug, because I noticed my restraints have that center annotated as S eventhough it is R in the actual .pdb Cheers, -- Yuri Pompeu

4 4

molecular replacement of protein/DNA complex
by Wei Shi 07 Jan '12

07 Jan '12

Hi all, I have been trying to solve a protein-DNA complex structure using molecular replacement. I suspect two copies of protein bind one piece of the DNA, and the angle between the two copies of protein is somewhere between 130 to 180 degrees. I could get molecular replacement solution using a search model of protein/DNA complex I made with deletion in part of the protein and with the angle between the two proteins about 145 degrees. Only 1 copy of this two-protein/one-DNA complex is expected in the ASU. Below is the statistics for the solution. RFZ=2.9 TFZ=6.9 PAK=0 LLG=111 TFZ==14.6 LLG=111 And when I open the pdb file and generate symmetry mates, no clashes and I could see contacts between the end of DNA, but space instead of contacts between layers of the protein/DNA complex. I suspect that the angle between the two proteins I use in the search model is not quite right. No solution if I search with DNA and protein separately. I am trying to find a way to move the protein a little bit around the original solution and see whether that can help me make the solution better. I just read that “ROTate AROUnd option of the brute rotation serch” and “NMAPdb” might do this? Does anyone have any suggestions about what I could try? Thank you so much! Best, Wei

2 2

Only three weeks left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '12

06 Jan '12

We are offering RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

CCI-Apps - Cygwin incompatibility after upgrade
by Schubert, Carsten [JRDUS] 05 Jan '12

05 Jan '12

Hi, After upgrading my cci_apps install on Windows from 1.7-718 to 1.7.3-928 the interoperability with cygwin is gone. Calling phenix.refine just gives a 'Command not found' error. Turns out that the little .exe files for each subprogram were replaced by .bat files. That is fine if one just wants to use the DOS CLI, but cygwin is not able to call programs via .bat files as far as I know. Is there a workaround for this problem besides working in the DOS CLI (yuk)? Thanks Carsten

2 2

phenix.metal_coordination
by Young-Jin Cho 03 Jan '12

03 Jan '12

Hi everyone and wish your happy new year. I have a question regarding phenix.metal_coordination. when I typed my pdb file that has two alternative conformations of different species including metal such as a metal(B) and a water(A). It seems like, in this case, phenix.metal_coordination doesn't read the metal. Otherwise, is there other way I can let make .edits file for this pdb file? Thanks always in advance, Young-Jin

3 2

whether my following data are acceptable
by Dialing Pretty 02 Jan '12

02 Jan '12

Dear All, Following is the data range of my x-ray statistics by resolution bin: FOM between 0.84 to 0.86 Phase error between 17.90 to 24.14 scale factor from 0.88 to 1.07 SigmaA from 0.85 to 0.95 #work from 2688 to 2922 #test from 133 to 157 Do these data are within the acceptable range? Cheers, Dialing

4 10

reference model restraints
by Ursula Schulze-Gahmen 24 Dec '11

24 Dec '11

I am refining a 3.1 A structure and are trying to use model restraints for this. There are 3 molecules in the asymmetric unit of my structure. I input the high resolution structure of one molecule of the reference structure to create restraints during the refinement. From looking at the log file, it seems to me that the reference structure is aligned to only one of my molecules, but not the other 2. How can I make sure the restraints are valid for all 3 molecules. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

4 3

eLBOW generates Mogul geometries
by Nigel Moriarty 23 Dec '11

23 Dec '11

Folks For a few weeks now eLBOW has been able to generate Mogul geometries. If you have CCDC's mogul installed and accessible at the command-line, eLBOW can request Mogul provide an experimentally accurate geometry. Simply use the --mogul option at the command-line and eLBOW will query Mogul for the geometry to use to generate a restraints file and a PDB file. Stay tuned for more details in the Computational Crystallography Newsletter. Happy Holidays, Merry Christmas and Happy New Year Nigel -- Nigel W. Moriarty, PhD 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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partial model in autobuild?
by Yarrow Madrona 21 Dec '11

21 Dec '11

Hello, I would like to use autobuild to start from a partial model. I have done Phaser EP with phases from MR. I can see the fourth molecule but it is not well defined and I am not exactly sure where to place it. Is it possible to run autobuild from the partial model to fill in the fourth model? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 20 Dec '11

20 Dec '11

Robbie, Yes, the thought that the anomalous R free flags could have something to do with it occurred to me as well, so I checked. As far as I can see, the test reflections are evenly distributed between the + and - sets; they were not selected from the + or - set only. For the vast majority of the test reflections, both Bijvoet mates were measured and both were flagged properly. For some, however, only one Bijvoet mate was measured and flagged. It probably wouldn't do any harm to consolidate the test flags, discarding the few with only one measured Bijvoet mate, but I really don't see why it should be necessary to do so. For now, I have converted the reflection file into the CNS format and sent to the PDB, hoping that they will be able to deal with that one properly. Bit surprised though that no one has run into that problem before. Thanks for your suggestion. MM On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten wrote: > Hi Mischa, > > Your mtz file seems to contain 'anomalous' free R-flags (that is what I gather from Pavel's post). This is kind of weird. Do you really want I+ in the work set and I- in the test set? That would bias your R-free. If the two flags match (which I really hope), then you can leave one column out before you (re)deposit your data. This will hopefully solves the problem. > > Cheers, > Robbie Joosten > > Netherlands Cancer Institute > > On 12/15/2011 05:40 PM, Machius, Mischa Christian wrote: >> Y'all, >> >> While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. >> >> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. >> >> Indeed, using this file in CCP4 fails with the message: >> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" >> >> The file contains anomalous data. I have no problems with files that do not contain anomalous data. >> >> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. >> >> When I use iotbx.reflection_file_reader, I cannot detect any anomalies. >> >> I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. >> >> Anybody ran into this issue before? Any ideas for how to resolve it? >> >> Many thanks in advance! >> >> MM >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

4 4

Failure in installing Phenix-1.7.3
by arka chakraborty 20 Dec '11

20 Dec '11

Hi all I am facing a problem while installing phenix 1.7.3 on Redhat Enterprise 5 OS. I have tried with fedora 3 binary as instructed in the download page and also with others but nothing works. I have tried installing from the root. Every time the error log is states that GLIB 2.4 is unavailable which is required by user/local/.. Please help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

3 2

SF-Tool check
by Dialing Pretty 19 Dec '11

19 Dec '11

Dear All, I have done the SF-Tool check for my protein crystal structure, and the result is as following. My 3 questions are (1) What does the following mean and how to solve the problem "Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done?" (2)Where there is no "Calculated phenix R_factor(all data)"? (3) Where there is no "Correlation (Fo-Fc)"? I am looking forward to getting your reply. Dialing Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file Checking Xray Data by PHENIX (model_vs_data) ... PHENIX (model_vs_data) is done. Checking structure factor quality ... PHENIX.xtriage is done. Summary of Results (XXXX : ) Reported PHENIX Calculated phenix High resolution 2.829 2.83 Low resolution 50.937 50.94 Number of Reflection17446 17446 Completeness 99.98 100.0 R_factor (all data) 0.2134 ? R_factor (work set) 0.2106 0.2093 R_free 0.2668 0.2667 Correlation (Fo-Fc) ? ?

2 1

Prevent MacPyMOL from registering as a valid pdb/pml/etc viewer.
by Francis E Reyes 19 Dec '11

19 Dec '11

Hi phenix developers I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working. Can future builds keep the internally distributed pymol as walled in as possible? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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fwd: Annual CCP4 summer school in USA, at APS, June 19-26
by Nathaniel Echols 19 Dec '11

19 Dec '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Date: Mon, 19 Dec 2011 11:39:28 -0600 Subject: Annual CCP4 summer school in USA, at APS, June 19-26 Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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phenix.refine and ligands
by AFL 19 Dec '11

19 Dec '11

Hi, I'm facing an extremely annoying 'problem' when refining structures with ligands. When I try to refine a structure with a ligand inserted in coot from what I believe is refmac dictionary I'm getting following error: Number of atoms with unknown nonbonded energy type symbols: 13 "HETATM 3279 OG2 FLC B 1 .*. O " "HETATM 3280 CGC FLC B 1 .*. C " "HETATM 3281 OG1 FLC B 1 .*. O " "HETATM 3282 CG FLC B 1 .*. C " "HETATM 3283 CB FLC B 1 .*. C " "HETATM 3284 OHB FLC B 1 .*. O " "HETATM 3285 CBC FLC B 1 .*. C " "HETATM 3286 OB2 FLC B 1 .*. O " "HETATM 3287 OB1 FLC B 1 .*. O " "HETATM 3288 CA FLC B 1 .*. C " ... (remaining 3 not shown) When FLC (citrate anion) is exported via libcheck and cif file is generated with phenix.elbow everything works fine. Why is the phenix.refine not compatible with the refmac dictionary definitions? Or maybe I am doing something wrong? Cheers, Andrzej -- alnyds(a)gmail.com e-mail

2 1

High B-factors after Phenix restrained refinement
by Da Duan 18 Dec '11

18 Dec '11

Hi all I am rather new to the crystallography so please bear with me, :-). I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of rigidbody refinement with Phenix Refine I proceeded to restrained refinement. The R/Rfree from the refinement decreased nicely as expected but the B average is at ~100 (using Group B factor refinement option). I took the same model and mtz through Refmac and the B average is about ~40. Has anyone experienced this before? I am almost positive it maybe a setting issue in Phenix Refine that i should be looking at to get the B factors to refine correctly. Thanks in advance for your help! Da Duan

7 12

Phaser problems
by Yarrow Madrona 18 Dec '11

18 Dec '11

Hello, Lately I have been having some trouble with phaser MR. For some reason even if I get a complete solution, it involves molecules from two different unit cells and it one case it picked up a symmetry related molecule as a crystallagraphic dimer. Recently I re-ran jobs from a sucessful run (over a year ago) in Phaser 2.1.4 where I get 4 molecules in the asymetric unit with plausable contacts that refined very well. Recently, however, I have re-run the job with the same search molecule and settings (all default). Although I get a solution, it involves molecules apparently from two asymetric units. The dimers formed are not the same contacts as what was seen in the earlier phaser run with Phaser 2.1.4. However if you turn on the symetry related molecues the tight crystallagraphic dimer seen previously shows up between one molecule and a symmetry mate. Has anyone had experiences like these recently with phaser? BTW my search model is 99% identical to my molecule (only one residue difference). Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 1

Re: [phenixbb] GUI MR_Rosetta without explicit search model?
by Gohlke, Ulrich 16 Dec '11

16 Dec '11

Dear Nat, I changed the .py file as you suggested, and for the moment, it seems to work. Thanks! Cheers, Uli --------------------------------------------------------------------------- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.gohlke(a)mdc-berlin.de <mailto:[email protected]> http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur… <http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur…>

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Re: [phenixbb] WAS High B-factors after Phenix restrained refinement
by Bryan Lepore 16 Dec '11

16 Dec '11

This classic essay has excellent tips that are worth reviewing from time to time : http://catb.org/~esr/faqs/smart-questions.html -Bryan

1 0

GUI MR_Rosetta without explicit search model?
by Gohlke, Ulrich 16 Dec '11

16 Dec '11

Dear colleagues, I am trying to set up an MR_Rosetta run using the GUI of Phenix 1.7.3. Unlike the command line version, it doesn't seem to accept either Robetta fragment files or alignment files from the hhpred server as the sole input but it keeps on asking for a pdb-file as search model. Is this behaviour intended or am I missing something? Best regards, Uli Gohlke --------------------------------------------------------------------------- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.gohlke(a)mdc-berlin.de <mailto:[email protected]> http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur… <http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur…>

2 1

Compilation problem rosetta MR on Fedora 10
by Martin Moche 15 Dec '11

15 Dec '11

Dear Phenix Users, I am trying to compile rosetta mr on my fedora 10 computer: http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35 Compared to the instructions % tar xzf rosetta3.2_Bundles.tgz did not work for me, instead I run % tar xvf rosetta3.2_Bundles.tgz and subsequently % tar xvf BioTools-3.3.tgz % tar xvf protocol_capture-3.3.tgz etc etc >From the rosetta_source directory as an ordinary user (not root) I run: % python scons.py -j2 bin mode=release The compilation runs for a while but finally I got the termination message below. What should I try next? Best regards, Martin #################### my computer info ################## daffy-mochma 183% scons --version SCons by Steven Knight et al.: script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on scons-dev engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on scons-dev Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons Foundation daffy-mochma 104% uname -a Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST 2009 i686 i686 i386 GNU/Linux daffy-mochma 105% python --version Python 2.5.2 ############# termination message ############################# g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/ -shared build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os build/src/release/linux/2.6/32/x86/gcc/utility/heap.os build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os build/src/release/linux/2.6/32/x86/gcc/utility/exit.os build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3 /usr/bin/ld: cannot find -lz collect2: ld returned 1 exit status scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1 scons: building terminated because of errors. Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 15 Dec '11

15 Dec '11

Y'all, While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. Indeed, using this file in CCP4 fails with the message: "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" The file contains anomalous data. I have no problems with files that do not contain anomalous data. Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. When I use iotbx.reflection_file_reader, I cannot detect any anomalies. I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. Anybody ran into this issue before? Any ideas for how to resolve it? Many thanks in advance! MM

5 7

Dec 16, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 Dec '11

15 Dec '11

Dear Users, > > The deadline for Feb/April 2012 Collaborative > Crystallography proposals will be *Dec 16, 2011. * > > ---------------------------------------------------------------------------------------- > Through the Collaborative Crystallography Program (CC) at the > Advanced Light Source (ALS), scientists can send protein crystals > to Berkeley Center for Structural Biology (BCSB) staff researchers > for data collection and analysis. The CC Program can provide a > number of benefits to researchers: > > * Obtain high quality data and analysis through collaborating with > expert beamline > researchers; > * Rapid turn around on projects; and > * Reduced travel costs. > > To apply, please submit a proposal through the ALS General User > proposal review process for beamtime allocation. Proposals are > reviewed and ranked by the Proposal Study Panel, and beamtime is > allocated accordingly. BCSB staff schedule the CC projects on > Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only > non-proprietary projects will be accepted. As a condition of > participation, BCSB staff researchers who participate in data > collection and/or analysis must be appropriately acknowledged - > typically being included as authors on publications and in PDB > depositions. Please consult the website for additional information at: > > http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography > > ----------------------------------------------------------------------------------------- > How To Apply: > > To learn more, go to: > > http://www.als.lbl.gov/als/quickguide/becomealsuser.html > > To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll > down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information, with > attention to the following details: > > * For question 3/First choice, select "5.0.1 > (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." > * Check box (yes) in response to question (7) "Do you want collaborative > crystallography > (beamline 5.0.1 or 5.0.2 only) > * In question 4, please describe a specific research project with a > clear end point. > > In order to request CC time for Feb/April 2012 allocation period, > proposals must be submitted by *Dec 16, 2011.* > > The deadline for CC proposals for the time period May/June 2012 will be > Mar 15, 2012. > > Regards, > Banumathi Sankaran > >

1 0

Re: [phenixbb] Compilation problem rosetta MR on Fedora 10
by Eugene Valkov 15 Dec '11

15 Dec '11

Hi Martin, I had encountered an issue with building Rosetta 3.2.1 on Ubuntu 11.04, specifically that SCons could not compile it because it used gcc 4.1 libraries, whereas there was gcc 4.4 installed. Could you check what version of gcc you have installed on your Fedora box? If it is the compiler issue then there are some workarounds documented on Rosetta forums: https://www.rosettacommons.org/node/2274 These worked for me, but you have to hack around in code a bit to make it happen. HTH, Eugene > On 15 December 2011 13:08, Martin Moche <Martin.Moche(a)ki.se> wrote: >> Dear Phenix Users, >> >> I am trying to compile rosetta mr on my fedora 10 computer: >> http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35 >> >> Compared to the instructions >> % tar xzf rosetta3.2_Bundles.tgz >> >> did not work for me, instead I run >> % tar xvf rosetta3.2_Bundles.tgz >> >> and subsequently >> % tar xvf BioTools-3.3.tgz >> % tar xvf protocol_capture-3.3.tgz >> etc etc >> >> From the rosetta_source directory as an ordinary user (not root) I run: >> % python scons.py -j2 bin mode=release >> >> The compilation runs for a while but finally I got the termination message >> below. >> >> What should I try next? >> >> Best regards, >> Martin >> >> #################### my computer info ################## >> >> daffy-mochma 183% scons --version >> SCons by Steven Knight et al.: >> script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons >> Foundation >> >> daffy-mochma 104% uname -a >> Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST >> 2009 i686 i686 i386 GNU/Linux >> >> daffy-mochma 105% python --version >> Python 2.5.2 >> >> >> >> ############# termination message ############################# >> >> g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so >> -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/ >> -shared >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os >> build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os >> build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os >> build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os >> build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/heap.os >> build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os >> build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/exit.os >> build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os >> -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc >> -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib >> -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3 >> /usr/bin/ld: cannot find -lz >> collect2: ld returned 1 exit status >> scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1 >> scons: building terminated because of errors. >> >> >> Martin Moche, Ph.D. >> Head of Protein Crystallography >> Karolinska Institutet >> MBB/PSF >> Scheeles väg 2 >> 171 77 Stockholm >> Sweden >> phone: +46-8-524 868 43 >> mobile: +46-73-322 93 27 >> fax: +46-8-524 868 68 >> email: Martin.Moche(a)ki.se >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> -- Eugene Valkov, D.Phil. MRC Career Development Fellow Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH email: evalkov(a)mrc-lmb.cam.ac.uk tel: +44 (0)1223 402261

1 0

loosening constraints on water addition
by Crystal VanderZanden 15 Dec '11

15 Dec '11

I'm trying to adjust the parameters on the water picking to allow for more waters to be found. I tried creating a solvent.params file with the code below, then I increased and decreased the primary map cutoff. When I ran the water picking command with the solvent.params file, it actually decreased the number of waters found, both at the high and low primary map cutoff. Does anyone know what I can do to relax the water finding criteria so more waters will be found? Thanks, Crystal refinement { ordered_solvent { low_resolution = 2.8 b_iso_min = 1.0 b_iso_max = 50.0 b_iso = 25.0 primary_map_type = mFobs-DFmodel primary_map_cutoff = 3.0 secondary_map_and_map_cc_filter { cc_map_2_type = 2mFobs-DFmodel } } peak_search { map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 } } }

2 1

how to get the sf.ent file
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, Will you please tell me how can I get the sf.ent file from a PDB enty? Cheers, Dialing

3 2