[ccp4bb] Procheck fails to run on Mac OS X 10.5
Dear ccp4bb readers, when I'm trying to run Procheck in CCP4i or with procheck xxx.pdb 'resolution' , it starts, but remains running forever. In the log file, it says that it started (or tried to start) the Clean-up program CLEAN (interface) or Running clean-up on file: xxx.pdb (without interface), but then it stops and nothing happens, until I finally kill it. My ccp4 version is 6.0.2., I still have the older check version (Procheck and Sfcheck) without Rampage; Mac OS X 10.5.2. Other ccp4 programs work fine (pdbset, even sfcheck), so I assume it's not a problem with paths, permissions or writing .ps files (I didn't try Amore or Refmac yet). Python is version 2.5, Tcl/Tk 8.4.16. Any help would be greatly appreciated! Eva
Re: [ccp4bb] Refmac and B factors
Hi Simon, you can't stop it - I asked the same question (with some more questions) some weeks ago. You can find the original email and the tips I got for not-so-good resolution B-factor refinement here: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. [EMAIL PROTECTED]: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the refine temperature factors box. However, when I look at the resulting pdb file my B factors vary from 2 to 90. Is Refmac just calculating my B factors or is it still refining them, and if the latter how can I stop it? Thanks, Simon
[ccp4bb] Summary - Stop Refmac from refining B factors?
Hi all, thanks for all your help so far, and as we ended up in a more general discussion about temperature factor refinement at not-so-great resolution, here is a quick summary of what I'll try out: 1.) Refine overall B's instead of isotropic B's. 2.) Use isotropic B's with the following (combinable) options: a) Isotropic in the beginning, grouped B's in the end. b) Use tight geometric restraints (I'm doing this anyways). c) Use tight B restraints rather than grouped CNS B's (not geometrically restrained, and most likely not restrained by NCS). 3.) Use not so tight B restraints, but tight geometric restraints with individual or grouped B's, plus TLSMD server and multi-group TLS refinement. 4.) Use CNS and try Mark White's tools, and simulated annealing. 5.) Use phenix with weighted nearest-neighbor restraint. ...and some remarks: * Of course I never wanted not to refine any B factors! I just wanted to see their contribution/influence on the refinement and explain their strange behaviour. * Luckily, I have NCS :o) Thanks for your good wishes, Mark. Eva 2007/4/18, Eva Kirchner [EMAIL PROTECTED]: Hi, I have a little problem with B-factor refinement. I'm using the CCP4i interface, Refmac 5.2.0019, a resolution of 30-3.2 A (I tried 8-3.2 A as well, it doesn't make a big difference for this problem), and a current Rfree of 30.4%. Refmac refines the B-factors so that they are nearly the same for main chain and side chain, and I don't like that (or could it make sense in any way?). Moreover, my structure is a protein complex, and Refmac is mainly doing this for one component of the complex. If I take the B-factors from the original uncomplexed protein (around 18, 1.75 A) and add 44 to them with moleman to get them in the range they are in the complex, Refmac flattens them remarkably in only 5 cycles of restricted refinement. Does anyone have an explanation for this? I am pretty sure that the complex components are in the right place, I see beautiful density and everything I should see at this resolution. Here is what I tried further: * I de-selected Refine isotropic temperature factors in the Refmac interface. There was no REFI BREF ISOT any more in the com file. But there was also no difference in the B-factors compared to when there _was_ REFI BREF ISOT in the com file... So does Refmac just _ignore_ my wish not to refine B-factors? (The REFI keywords were as follows: type REST - resi MLKF - meth CGMAT - is there any B-factor-thing hidden in this?) * I played around with the geometric parameters. If I select the B-factor values there (the keywords are TEMP|BFAC wbskalsigb1sigb2sigb3sigb4), it does not make _any_ difference, what values I fill in there, the resulting B-factors are always the same (but different from when I don't use the TEMP keyword, and even flatter). Default for WBSCAL is 1.0, I tried 10, 1.0, 0.1, 0.01, and the equivalent numbers for the sigbs. Thanks for any thoughts on this, Eva
Re: [ccp4bb] Stop Refmac from refining B factors?
Thank you Roberto, I saw that line in the log file, too. So it is as I feared: Refmac cannot be stopped from refining B-factors ;-) Maybe I'll use CNS... Eva 2007/4/18, Roberto Steiner [EMAIL PROTECTED]: On 18 Apr 2007, at 14:39, Eva Kirchner wrote: (But I'm still curious about the B-factor refinement when there is no REFI BREF ISOT in the com-file...) Eva, Refmac internal default is REFI BREF ISOT that's why even if you remove the above line from the com file (or deselect that option from the interface) it still does ISOT BREF refinement. It does tell you that though if you look at the log file there's a bit that says ... Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width:20 0.0080 Refinement of individual isotropic Bfactors .. what do you have there when you deselect the B fact option from the interface? I agree with Herman that at 3.2 A isotropic B values refinement can be useful. Roberto Eva 2007/4/18, Mischa Machius [EMAIL PROTECTED]: Like Harry said, it is not justified to do individual B factor refinement at that resolution. Well, you can do it, but you'll end up with funny results, such as what are observing right now. Still, from a pragmatic point of view, individual B factor refinement in cases like these can have a positive effect on the electron density. However, keep in mind that the resulting B factors may physically not be very meaningful. In the end, you'll have to switch to grouped B factor refinement, or you risk nasty comments from an attentive mentor or reviewer (and rightly so). Hope that helps. Best - MM On Apr 18, 2007, at 7:20 AM, Eva Kirchner wrote: Hi, I have a little problem with B-factor refinement. I'm using the CCP4i interface, Refmac 5.2.0019 , a resolution of 30-3.2 A (I tried 8-3.2 A as well, it doesn't make a big difference for this problem), and a current Rfree of 30.4%. Refmac refines the B-factors so that they are nearly the same for main chain and side chain, and I don't like that (or could it make sense in any way?). Moreover, my structure is a protein complex, and Refmac is mainly doing this for one component of the complex. If I take the B-factors from the original uncomplexed protein (around 18, 1.75 A) and add 44 to them with moleman to get them in the range they are in the complex, Refmac flattens them remarkably in only 5 cycles of restricted refinement. Does anyone have an explanation for this? I am pretty sure that the complex components are in the right place, I see beautiful density and everything I should see at this resolution. Here is what I tried further: * I de-selected Refine isotropic temperature factors in the Refmac interface. There was no REFI BREF ISOT any more in the com file. But there was also no difference in the B-factors compared to when there _was_ REFI BREF ISOT in the com file... So does Refmac just _ignore_ my wish not to refine B-factors? (The REFI keywords were as follows: type REST - resi MLKF - meth CGMAT - is there any B-factor-thing hidden in this?) * I played around with the geometric parameters. If I select the B-factor values there (the keywords are TEMP|BFAC wbskalsigb1sigb2sigb3sigb4), it does not make _any_ difference, what values I fill in there, the resulting B-factors are always the same (but different from when I don't use the TEMP keyword, and even flatter). Default for WBSCAL is 1.0, I tried 10, 1.0, 0.1, 0.01, and the equivalent numbers for the sigbs. Thanks for any thoughts on this, Eva Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]
