[ccp4bb] Monomer Library Sketcher
Another problem we encountered with the newly installed CCP4 6.3.0 on a 64-bit Linux computer: The graphic window of Monomer Library Sketcher can't pop up, giving the following error: Can not run Monomer Library Sketcher with the BLT extension to Tcl/Tk installed. See your system manager or the CCP4i installation documentation Appreciate any help to fix the problem. Regards, Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] can't creat new project directory in CCP4i
A postdoc in the lab ran into problem creating new project directory in CCP4i GUI in his computer account. When he tried to add project the following error popped up: Can't read array 'CCP4_DATABASE How to fix this problem? Thanks for your help. Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] Problem running shelxC/D/E
Thanks, Boaz, That was the problem. Once programs were moved to $CBIN directory they worked fine through either ccp4i or hkl2map GUI. Thanks also George and Tim for useful hints. Huiying On Tue, 21 Jun 2011, Boaz Shaanan wrote: They should reside in the $CBIN directory for the gui to see them, is that where you have them installed? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Huiying Li [h...@crystal.bio.uci.edu] Sent: Tuesday, June 21, 2011 9:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem running shelxC/D/E We had trouble running shelxC/D/E through ccp4i (CCP4 Suite 6.1.13 CCP4Interface 2.0.6). The log file gave the following error: shelxC: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory We do have the shelx programs installed in the system. Any help to trouble shoot this problem is appreciated. Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] Problem running shelxC/D/E
We had trouble running shelxC/D/E through ccp4i (CCP4 Suite 6.1.13 CCP4Interface 2.0.6). The log file gave the following error: shelxC: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory We do have the shelx programs installed in the system. Any help to trouble shoot this problem is appreciated. Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] merge and scale high-res and low-res scans with SCALA
I have collected two sets of data, high-res and low-res, with the same crystal and integrated them separately with imosflm. Now I want to merge and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how to input 2 MTZ files through the Scala input GUI window (under Data Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] Can LSQKAB calculate RMSTAB for two pre-superposed structures?
Thanks for your reply, Eleanor. The problem I had with LSQKAB is that it ONLY outputs the RMSD for the residue range the superpose calculation based upon. What I wanted is to superpose the two structures with the N-terminal 100 residues, but calculate the RMSD for the entire structure (400 residues). Can LSQKAB do that? Best regards, Huiying Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu On Wed, 24 Nov 2010, Eleanor Dodson wrote: Yes - I think there is a button on the GUI to click? Eleanor On 11/24/2010 01:58 AM, Huiying Li wrote: Another question on RMSD: I have two structures of the same protein superposed with the LSQ Superpose in Coot by matching the first ~100 residues of the N-terminal domain. Now I'd like to calculate the pair-wise RMSD for the entire pre-superposed structures (~400 residues). Can LSQKAB output RMSTAB for the two input PDB files without doing its own FIT/MATCH calculation? Thanks, Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] Can LSQKAB calculate RMSTAB for two pre-superposed structures?
Another question on RMSD: I have two structures of the same protein superposed with the LSQ Superpose in Coot by matching the first ~100 residues of the N-terminal domain. Now I'd like to calculate the pair-wise RMSD for the entire pre-superposed structures (~400 residues). Can LSQKAB output RMSTAB for the two input PDB files without doing its own FIT/MATCH calculation? Thanks, Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] iMosflm can't read images
I had trouble adding image files into iMosflm (1.0.4) GUI running on our in-house Linux machine (64-bit, Fedoro). It complained about the filenames: * FATAL ERROR * Image filenames must be of the form ABCDE_###.ext or ABCDE-###.ext where the initial string can be up to 40 characters long and must be separated from a 3 digit number by a _ or -, and the extension (ext) can be up to 8 characters long. The filenames are actually following the convention Mosflm required. The same image files were readable by iMosflm on Linux machine at the synchrotron station. Is anything wrong with our iMosflm installation, configuration...? Thanks for your help. Huiying _ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] Coot:findwaters in REFMAC
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters to the refined structure. Often for the well ordered water sites the routine added two water molecules in single water site, with their distance (~1 Angs) way shorter than allowed hydrogen bonding distance. I have to remove the extra water molecules manually. Is this a intended feature? It seems to only create extra work to the user. What is the purpose of having different chain IDs for waters output from this routine? Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] tortion angle restraints in REFMAC
Acturally, I want to find a way to keep the OH tilted out of the neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC refinement tends to refine it into the plane even though I have included torsion angle restraint in the library for the ligand. I thought I could play with the weight or the esd of the target value but having trouble to achieve it. In CNS, adjusting the force constant of the target value is a way to tighten or loosen the restrain. I would like to know how to enforce a geometry effectively in REFMAC. Thanks for any comments. Huiying On Wed, 3 Dec 2008, Abhinav Kumar wrote: If you want to restrain the OH group to a plane, you need to include it in the plane definition, and not the torsion definition. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
[ccp4bb] tortion angle restraints in REFMAC
I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
[ccp4bb] scale data with multiple MTZ files
I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
Re: [ccp4bb] GUI problem with SIGMAA
Hi Eleanor, Thanks for doing the test. I did the same thing through run view com option as Chris Rife suggested. SIGMMA did wonderful job once I was able to provide the second run with the correct FOM from the first round of MAD phase combination. The density quality (after SOLOMON) calculated with correct FOM is much better than the one with the FOMmad (the one I could only select through the GUI). With the much improved density we were able to fit in most of the side chains. Thanks again for everyone who offered help. Huiying On Fri, 20 Apr 2007, Eleanor Dodson wrote: I cant find any test data - will have to create it to test properly.. Eleanor Have done so.. things are exactly asd you describe them I ran the first job with 2 sets oF PHI and HL coeffs Output PHCMBtest1 WCMBtest1 HLACMBtest1 etc Then tried second and as you said there was no FOM allowed for the input experimental phase PHCMBtest1 It runs OK if I use the option run and view com file and insert the extra info into the LABI line LABI FP= PHIBP=PHCMBtest1 etc and then I add WP=WCMBtest1 But that shouldnt be necessary as you say.. The only peculiarity I can see in the first SigmaA output is that the combined phases are in data set 0, but changing that doesnt help. Any ideas GUI experts??? Eleanor Huiying Li wrote: Thank Eleanor and others for making suggestions. We have tested SIGMAA in CCP4i(1.4.4.1) again carefully. In the first run, we used combine two sets of MIR phases mode to combine 2 sets of MAD phases, and output column labels changed to PHCMBtest and WCMBtest. The second run was in combine isomorphous phase with partial structure mode. We had no problem assigning other column labels such as FP, PHIBP, ... because the pull-down menu of each label includes list all labels option. But FOM pull-down menu had no list all labels option, we could not select the label WCMBtest generated from the previous run. It seems to me there is a bug in the GUI that limits the option in FOM pull-down menu. It only occurs in the combine isomorphous phase with partial structure running mode of SIGMAA. This is the run we really wanted to combine the model phases with the MAD phases before going through further density modifications with SOLOMON or DM. Regards, Huiying On Thu, 19 Apr 2007, Eleanor Dodson wrote: Sorry about that It is ages since I have used SIGMAA The MAD recombnation gives you PHCMB WCMB HLAC HLBC etc In that run I would make sure I renamed PHCMB WCMB PHCMBmadsWCMBmads or something You might have to use the option Run and view com file, then edit in a line: LABOUT PHCMB=PHCMBmads WCMB= etc Then I think you may be able to do what you want - I suspect the poor program is getting lost between what is a default output label, and something already in the header. Can you try that? Or you use the Clipper utility to combine phases.. it is more mindless but you do have to convert your PHIC FOM to HLA HLB (HLC HLD ==0) using another clipper utility first Eleanor Huiying Li wrote: My previous posting did not get answer, it might be a bit confusing. My questions is if I want to conbine phases from three different sources, 2 MAD data sets and a partial model, can I run SIGMAA twice? Combining MAD phases first, and then add in the model phases to the pre-combined MAD phases. When I run SIGMAA the second time CCP4i GUI allows me to choose labels PHCMB, HLAC, HLBC, HLCC, HLDC, but doesn't let me use WCMB as the input FOM. Is this a bug in the GUI or SIGMAA simply does not allow to use WCMB as an input FOM? Thanks in advance. Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] -- -- - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] --
Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)
Hi Pete, The sigmaa-weighing scheme implemented in SigmaA routine is the very means to remove the potential model bias. Also, the model phases we used in the phase combination were simply from a backbone poly-Ala model generated from the best parts of the MAD-phased density (some of them from an ARP/wARP run) leaving out the surface regions where the map quality is marginal. Combining partial model phases with the experimental phases has been used as a way to improve the map quality while the partial model is still far from complete and most of the side chains are not yet filled in. Once enough scattering mass has been built into the model and a reciprocal space refinement with CNS or REFMAC is warranted, the resulting 2Fo-Fc and Fo-Fc maps are often having much suprior quality for the further model building. One drawback of combining partial model phases with the density-modified experimental phases is that one cannot run the density modification second time after the combination. I have not tested whether combining model phases with the density modified MAD phases produces good quality map (experts in the field can make comments). I did get significant improvement in the map quality with the combine-then-modify procedure. HTH, Huiying On Fri, 20 Apr 2007, Peter Adrian Meyer wrote: structure running mode of SIGMAA. This is the run we really wanted to combine the model phases with the MAD phases before going through further density modifications with SOLOMON or DM. I would have thought that you'd want to do this the other way around (density modification on MAD before model phase combination) in order to reduce possible model bias. I'm curious...what's the reasoning for doing the model phase combination first? Pete Pete Meyer Fu Lab BMCB grad student Cornell University -- - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] --
[ccp4bb] How to run SIGMAA twice in a row?
My previous posting did not get answer, it might be a bit confusing. My questions is if I want to conbine phases from three different sources, 2 MAD data sets and a partial model, can I run SIGMAA twice? Combining MAD phases first, and then add in the model phases to the pre-combined MAD phases. When I run SIGMAA the second time CCP4i GUI allows me to choose labels PHCMB, HLAC, HLBC, HLCC, HLDC, but doesn't let me use WCMB as the input FOM. Is this a bug in the GUI or SIGMAA simply does not allow to use WCMB as an input FOM? Thanks in advance. Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] --
[ccp4bb] FOM label in SigmaA
We need to run phase combination twice with SigmaA via CCP4i and encountered some confusion in FOM column label assignment. First, two sets of MAD phases are combined, we have output figure of merit, WCMB, from the input FOM_mad1 and FOM_mad2. Second time, we wanted to combine the Fc and PHIC obtained from a partial helical model with the combined MAD phases. This time the GUI would not let us choose WCMB as the input FOM label, rather only FOM_mad1 and FOM_mad2 were allowed. Is this a feature in SigmaA trying to avoid potential confusion between the same FOM label for input and output, or a bug in the GUI? Thanks for any help. Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] --
