[ccp4bb] crashes of CCP4i2
Dear all, sudden crashes occur while using CCP4i2 (CCP4 v. 8.0.008) and a Mac machine either with BigSur or Ventura. Here below the termination reason reported by the log: Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [9790] Do you have any advice or suggestion? Thanks in advance, Best regards Luca Mazzei Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] H atoms in refined structure
Hello, just to clarify, I do not use H atoms for refinement, but as idealised riding H atoms. In the old-style GI of Refmac one could use riding hydrogens during refinement without adding them in the output coordinate file. I do not find this option in the new GI of the CCP4i2 window. As a result from a a REFMAC job, the ouput PDB file does not contain H atoms, while the mmcif output file does. At the end of the story, I ran pdbx/mmcif to convert the PDB in a mmcif file that does not contain H atoms anymore. It seems to work. Best regards Luca Mazzei Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 > Il giorno 16 mag 2022, alle ore 15:43, Luca Mazzei ha > scritto: > > Dear CCP4 people, > > Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens > during refinements by generating riding hydrogens I obtain a PDB file that > does not contain H atoms. However, the corresponding mmcif file that I should > use for deposition contains their coordinates and give them either full or > zero occupancy. Do you know how I can safely delete H atoms from the mmcif > file prior deposition? Would this affect Rwork and Rfree calculated upon > validation on the wwPDB? > > Thanks in advance, > > Luca Mazzei > > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] H atoms in refined structure
Dear CCP4 people, Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens during refinements by generating riding hydrogens I obtain a PDB file that does not contain H atoms. However, the corresponding mmcif file that I should use for deposition contains their coordinates and give them either full or zero occupancy. Do you know how I can safely delete H atoms from the mmcif file prior deposition? Would this affect Rwork and Rfree calculated upon validation on the wwPDB? Thanks in advance, Luca Mazzei Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] weight matrix selection
Thanks Tim and Jon. It is a Macc laptop, the font size was too big and “manual” was not visible in the drop-down menù. Good to know. Best, Luca Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 > Il giorno 8 apr 2021, alle ore 23:09, Jon Cooper > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> ha scritto: > > Good point. It looks like a mac to me ;- > > Best wishes, Jon.C. > > Sent from ProtonMail mobile > > > > Original Message > On 8 Apr 2021, 19:52, Tim Gruene < tim.gru...@univie.ac.at> wrote: > > Dear Luca, did you click at the empty line below where it says 'automatic'? > Maybe the word 'manual' is just not visible for inappropriate colour > settings. Best wishes, Tim On Thu, 8 Apr 2021 18:14:35 +0200 Luca Mazzei > wrote: > Dear CCP4 people, > > I am trying to change manually the geometry > weight in Refmac, but > something funny is occurring. As you can see in the > snapshot I can > not switch from auto to manual. Suggestions? > > Thanks in > advance, > > Luca > > > Luca Mazzei - PhD > Laboratory of Bioinorganic > Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater > Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna > - Italy > Tel: +39 0512096235 > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This > message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list > hosted by www.jiscmail.ac.uk, terms & conditions are > available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the > Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna > Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A > To > unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message > was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by > www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] possible solution with Phaser
Hi all, I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly suggests the presence of 4 mol per asym unit (space group P6222). The results after a search of 4 mol per asymmetric unit of my monomer are the following: ** SINGLE solution ** Solution written to SOL file: phaser_3f6v_A1_MOLREP.sol ** Solution written to PDB file: phaser_3f6v_A1_MOLREP.1.pdb ** Solution written to MTZ file: phaser_3f6v_A1_MOLREP.1.mtz Solution annotation (history): SOLU SET RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7) LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 SOLU SPAC P 62 2 2 SOLU 6DIM ENSE autoMR EULER 125.3 60.8 300.2 FRAC 0.17 -0.13 0.08 BFAC -9.34 #TFZ==10.0 SOLU 6DIM ENSE autoMR EULER 305.4 60.8 300.2 FRAC 0.27 -0.16 0.08 BFAC -5.29 #TFZ==29.8 SOLU 6DIM ENSE autoMR EULER 294.7 119.1 120.3 FRAC 0.45 0.01 0.26 BFAC 0.34 #TFZ==22.5 SOLU 6DIM ENSE autoMR EULER 305.5 61.6 300.1 FRAC 0.11 -0.16 0.08 BFAC 29.19 #TFZ==5.4 SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD 0.93 #VRMS 0.79 It seems (also looking at the maps) that it correctly places three monomers out of four. How can I use this information to improve the search of the fourth monomer using the same template model? Thanks in advance for your help, Best regards Luca Mazzei Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Refmac use - water addition
Dear Jon, thanks for your answer. Maybe I have been too quick in writing my last message. The point is that with the old CCP4 interface, I would have been able to run Coot-findwaters to automatically add and remove water molecules at certain DELFWT and FWT rmsd tresholds, respectively, through REFMAC interface. Now, with the new interface, Coot-findwaters is not made explicit anywhere, and DELFWT and FWT rmsd tresholds seem not to be changeable. There’s only "R lower than” that is surely what you say = Rfactor (%) lower than 30%. I would not want to create misunderstandings, I am just asking for things which are not clear to me (maybe given my limited experience), starting from the assumption that my knowledge in refinement, model building and, more in general, protein crystallography, can always improve. Thanks for the precious help, Luca Mazzei Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy > Il giorno 12 set 2020, alle ore 17:55, Jon Cooper > ha scritto: > > Hello, I'm not totally up-to-the minute with this but I didn't know that > refmac itself added waters so maybe it's another program in an i2 pipeline, > or something. However, I know another excellent refinement program that does > ;-) and an excellent graphics program that does, too ;-0 > > In the past, we have added well-defined water molecule when the R-factor goes > into the mid-to-low thirties, or lower. > > Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to > be real but you can lower that cutoff a bit (~1.5) if your resolution is not > brilliant. > > Glad to be corrected on this. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > > > Original Message > On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote: > > Dear CCP4 people, > > I am approaching in these days to the new CCP4i2 interface and, in > particular, to REFMAC. Can anyone quickly explain what the factor R, that > must be chosen in order to automatically add water molecules, is? How can I > relate this value with the previous DELFWT and FWT map values? > > Thanks, > > Luca > > Luca Mazzei - PhD > Department of Pharmacy and Biotechnology > University of Bologna > Viale Giuseppe Fanin, 40 - 40127 > Bologna - Italy > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > <https://www.jiscmail.ac.uk/policyandsecurity/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Refmac use - water addition
Dear CCP4 people, I am approaching in these days to the new CCP4i2 interface and, in particular, to REFMAC. Can anyone quickly explain what the factor R, that must be chosen in order to automatically add water molecules, is? How can I relate this value with the previous DELFWT and FWT map values? Thanks, Luca Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] unable to launch ccp4 old interface on mac
Dear CCP4 people, Can you help me with this? At the end of installation of CCP4 7.1 on Mac with OS Mojave, CCP4 folder contains ccp4i2 icon, whereas ccp4 icon is not present. This way I can not launch the old interface, neither by clicking on the invisible icon nor using the terminal. I just fixed the problem by a copy-and-paste of the ccp4 icon coming from another Mac on which CCP4-7.0 is installed and It seems to work well (I ran Refmac, Coot and Molrep with success usingthe old interface)! Do you have any suggestion on why this occurs and how to overcome this problem in a more efficient way? Thanks in advance, Luca Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] unable to launch ccp4 old interface on mac
Dear CCP4 people, At the end of installation of CCP4 7.1 on mac OS Mojave, CCP4 folder contains ccp4i2 icon, whereas ccp4 icon is not present. This way I can not launch the old interface, neither by clicking on the invisible icon nor using the terminal. I just fixed the problem by a copy-and-paste of the ccp4 icon coming from another Mac on which CCP4-7.0 is installed and It seems to work well (I ran Refmac, Coot and Molrep with success usingthe old interface)! Do you have any suggestion on why this occurs and how to overcome this problem in a more efficient way? Thanks in advance, Luca Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] COOT crashes when I merge molecules
Dear CPP4 people, COOT (0.8.9.2 EL) crashes everytime I merge my model with the monomer EDO (1,2-Ethanediol, cryoprotectant). The same issue does not occur with other monomers. I tried to replace EDO.cif in a new monomer (EDQ.cif) and COOT works fine. Any suggestion? Thanks in advance, Luca Mazzei Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy Il giorno 4 giu 2019, alle ore 09:02, Darren Hart mailto:darren.h...@ibs.fr>> ha scritto: You have to start it via the menu item, not the command line. Darren On 03/06/2019 14:31, Pedro Matias wrote: Well, I can't get it to work in FC30 - I installed FC30 on a virtual machine and managed to install both snapd and pymol-oss but pymol does not run as a command. Am I missing something rather obvious? Pedro Às 12:46 de 03/06/2019, Matic Kisovec escreveu: Hi, thank you very much for this. Work fine on Ubuntu 19.04. Kind regrds, Matic On 17. 05. 19 20:04, Arunabh Athreya wrote: Thanks for sharing this. Get Outlook for Android<https://aka.ms/ghei36> From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of David Schuller <mailto:schul...@cornell.edu> Sent: Thursday, May 16, 2019 11:41:19 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] PyMOL now packaged as a snap on Linux It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should also work on RHEL7 and Centos 7) Thank you. On 5/16/19 10:47 AM, Darren Hart wrote: Some more info: https://snapcraft.io/pymol-oss It seems to work exactly as expected. Darren On 16/05/2019 16:05, Folmer Fredslund wrote: Hi Darren, That's brilliant! I'll give it a spin and see how it works. Best regards Folmer tor. 16. maj 2019 13.02 skrev Darren Hart mailto:darren.h...@ibs.fr>>: Since yesterday, PyMOL (open source version v2.3) has been packaged as a distro-independent "snap" that can be installed easily on linux platforms - no more cloning from gitlab and compiling after installing the dependencies. On Ubuntu, install from software centre or: sudo snap install pymol-oss Many distros have the snap architecture already installed. If not, you just need to install snapd in the regular way first (e.g. on Debian: sudo apt install snapd). Hope this is useful for some folks. Best regards, Darren To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu<mailto:schul...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt<mailto:mat...@itqb.unl.pt> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Darren J. Hart, CNRS Research Director, Institut de Biologie Structurale (IBS) Unité Mixte de Recherche UMR5075 (CEA-CNRS-UGA) Director, Integrated Structural Biology Grenoble (ISBG) Unité Mixte de Service UMS3518 (CNRS-UGA-CEA-EMBL) *
[ccp4bb] weight term and geometry
Dear all, I have a question about how PBDREDO and REFMAC treat the geometry weight (gw). In particular, I have a structure with a N-terminal CXM bound to a HIS as a second residue. After complete refinement, I run PDBREDO to choose the most appropriate gw. Let’s say best results are found using gw = 0.1. I run REFMAC using that value, but the carbonyl carbon of CXM detaches from the amidic N of HIS (distance 1.84 A). If i run the same job using a gw of 0.2, 0.3 and so on, that distance decreases and the C-N bond is restored. By the way, increasing the gw Rfree increases as well as the difference between Rfactor and Rfree. Any idea on how to solve the problem? Should I keep higher Rfree and worse stats with still having a peptide bond there? Thank you, Luca Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
