- phenixbb - phenix-online.org

OpenMP incompatible with Phenix GUI?
by Donnie Berkholz 07 Apr '10

07 Apr '10

Dear developers, I would really like to use OpenMP parallelization and also use the Phenix GUI. When I attempted a source build with OpenMP support, I was informed that the two were incompatible. My understanding is that this used to work fine with the old wizards. Would it be possible to fix this? -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 612-991-1321

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Re: [phenixbb] phenixbb posting
by Leonid Flaks 07 Apr '10

07 Apr '10

Nathaniel Echols wrote: > The server bounced your message - are you subscribed to the list? > FYI, I'm not sure why firefox won't start here; sometimes it gets > confused by Phenix's copy of GTK, but that's not what the error > message looks like. You can try opening the Preferences in Phenix, > select the "File handling" parameters, and check "Reset > LD_LIBRARY_PATH for external apps". Let me know if that doesn't fix > the problem. > > thanks, > Nat > > ---------- Forwarded message ---------- > From: Leonid Flaks <flaks(a)bnl.gov <mailto:[email protected]>> > To: phenixbb(a)phenix-online.org <mailto:[email protected]> > Date: Wed, 07 Apr 2010 15:51:11 -0400 > Subject: problem with firefox and phenix-1.6.1-357 > I installed phenix-1.6.1-357 on Fedora-12. If I click on the question > mark in the GUI, I see the following: > > Using browser /usr/bin/firefox > /usr/lib/firefox-3.5.9/firefox: symbol lookup error: > /usr/lib/libgnome-2.so.0: undefined symbol: g_dgettext > > > and firefox would not start. I saw similar errors reported more then a > year ago, but that is a new fedora-12 installation. > > Any ideas? > > > Thanks, > > Leon > > Yes, I realized that I need to subscribe first, which I did after sending my message ;-) I tried to follow your advice - checked the box, but nothing changed. Same error message. -- Leon

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individual_sites_real_space?
by Francis E Reyes 07 Apr '10

07 Apr '10

Phenixer's I just upgraded from 1.4-87 and noticed that there's individual_sites_real_space now. The documentation (http://www.phenix-online.org/documentation/refinement.htm ) just shows that it's a parameter phenix.refine. What is this and when is it helpful (bad resolution/ bad model? or high resolution/ good model? or high resolution/bad model?) Thx F --------------------------------------------- Francis 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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LSTc refinement in phenix.refine
by JXQI 07 Apr '10

07 Apr '10

Dear all, I am refining a structure complexed with LSTc (alpha 2,6-linked galactose,i.e. SIA-GAL-NAG-GAL).I know that the BETA1-4 or BETA1-3 in the mon-lib could restrain the bond distance,but I could not find the links between the SIA and GAL......any suggestions are appreciated. Best regards Janxon

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polygon and membrane proteins
by Pascal Egea 06 Apr '10

06 Apr '10

Dear Developers, I wonder if there would be a simple way to get the Polygon program implemented in Phenix to use only membrane protein deposited structures as the reference data set. I understand that the reference set is much smaller than the whole menagerie of available structures but it represents an homogenous class of protein (crystallized in detergent). Do you think that this would be meaningful and useful? Thanks in advance, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Re Double stranded DNA restraints?
by Thomas C. Terwilliger 06 Apr '10

06 Apr '10

Hi Sena, I would add this command helices_strands_only=True to force autobuild to just try and build helical segments. This probably won't fix the lack of connectivity however. All the best, Tom T Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena

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PPC binaries?
by Marcelo Carlos Sousa 05 Apr '10

05 Apr '10

Is Phenix no longer supported on Mac PPC? ____________________________________________ Marcelo C. Sousa, Ph.D. Department of Chemistry and Biochemistry Cristol Chemistry Building. Room 100 215 UCB University of Colorado at Boulder Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 5894

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(no subject)
by Prof Jennifer Martin (IMB) 04 Apr '10

04 Apr '10

The protein crystal structure I am refining has a redox modification: cysteine sulfenic acid (S-hydroxy cysteine). How do I go about including parameters for this modification in phenix refine? I have found parameters on HIC-UP (under CSO) but these are for XPLOR/ CNS. Many thanks in advance for suggestions, Jenny Martin University of Queensland

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Torsion angels refinement question
by Peter Grey 04 Apr '10

04 Apr '10

Dear Phenix users, I try to refine a big complex at low resolution. I am a little confused about the syntax of using torsion angels gradient-driven refinement. Is it now the default for individual sites refinement instead of cartesian ? If not, should I add : sites.Torsion_angles=all for example ? Could you shed some light on this, Thank you, -- Peter

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Optimizing the Geometry Weight for a 2.76 A structure
by Sam Stampfer 03 Apr '10

03 Apr '10

Hi, I'm refining a 2.76 A structure and need help optimizing the refinement weight on geometry. When I refine at the default refinement weight (wxc = 0.5), phenix seems to generate a much poorer structure (both geometrically AND by Rfree value) relative to lower wxc values which put a stronger weight on geometry. I am trying to pick the best structure to use for my next round of rebuilding. The R-stats and condensed molprobity stats are listed below (at the end of this email). I have a few questions regarding this structure and those stats: 1. What is the relevance of having a LOW difference between Rfree and Rwork? My structure seems to have a higher than expected Rwork value relative to Rfree (aren't they supposed to differ by 0.05 or so, instead of the 0.03 observed in my structure?) Additionally, as I refine at lower wxc values (more weight on geometry) I get an increased Rwork value with an equal or decreased Rfree (relative to the refinement at a higher wxc value). Does that mean my structure is better or worse? 2. How can I judge the output from my refinement? I have looked at Rwork, Rfree, and the molprobity clashscore and overall score values. I included them below, at the end of this email. How do I tell which the best refinement is? Which one would you suggest? I thought the best was wxc = 0.1 since the R-work and Rfree aren't changed much from the start values but the geometry is far better. 3. How do I optimize the weight on geometry in refinement? My PI said that phenix can do it but not for twinned structures (my structure is twinned). Can the new version of phenix do weight optimization for twinned structures? How? If not, what's the best way for me to do it manually? As always, thanks immensely for all your help! -Sam All have the same values for: Start R-work = 0.2002, R-free = 0.2376 *wxc = 0.01 *Final R-work = 0.2104, R-free = 0.2378 Molprobity Clashscore: 19.46 Molprobity Score: 2.29 *wxc = 0.05 *Final R-work = 0.2049, R-free = 0.2377 Molprobity Clashscore: 20.96 Molprobity Score: 2.38 *wxc = 0.1 *Final R-work = 0.2010, R-free = 0.2388 Molprobity Clashscore: 23.50 Molprobity Score: 2.54 *wxc = 0.2 *Final R-work = 0.1969, R-free = 0.2399 Molprobity Clashscore: 27.15 Molprobity Score: 2.79 *wxc = 0.3 *Final R-work = 0.1945, R-free = 0.2411 Molprobity Clashscore: 30.76 Molprobity Score: 2.97 *wxc = 0.4 *Final R-work = 0.1930, R-free = 0.2420 Molprobity Clashscore: 34.54 Molprobity Score: 3.11 *wxc = default (0.5) *Final R-work = 0.1918, R-free = 0.2429 Molprobity Clashscore: 37.73 Molprobity Score: 3.22

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