Dear list, I have a problem running the Validation and Analysis in Refmac and I would really appreciate any feed-back from your side. I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4). Last time I was using Refmac was in November 2023. At the time, I posted in the list an error with the CCP4i2 interface (no responding) that I solved by turning off the 3D picture in the reports (as kindly suggested by Stuart McNicholas). Now, despite the 3D picture in the reports is off, I still experience ‘some delays’ on the interface response, though this is not a major issue. The real problem I’m experiencing is that after a (apparent) normal termination of Refmac (no sign of warnings or error messages), I find no results from the Multimeric validation. Navigating through the jobs folders I have found that in job2 (which I guess correspond to the validation) there is: - no prosmart related files (.out, .pdb, .py). - the tables_as_csv_files folder is empty. - there is no molprobity.log file. Instead, there is a log_mtzjoin.txt file but it does not highlight any warning or error either. - the program.xml file only contains the heather but otherwise, it is blank (which I guess this is the reason it is not running). - also, in the param.xml file I found that there are 2 sets of input data (instead of one and I don’t know why), where: - There is no dbFileID for the input F-SIGF data (in any of them) - In the first one the XYZIN is the XYZIN-coordinated.pdb (instead of the xyzout_prosmart_refmac.pdb) and in the second it is the xyzout_prosmart_refmac.pdb) Checking the terminal while running refmac I saw the following error message that appears just after refmac window state ‘The job is finished’. This error repeats multiple times, with variations in the .WebGL-alphanumerical code, from time to time and ends as follows. [3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc <http://gles2_cmd_decoder.cc/>(12701)] [.WebGL-0x23e9d90]GL ERROR :GL_INVALID_VALUE : glVertexAttrib4f: index out of range
<--- Last few GCs ---> [4500:0xc3700000000] 177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) allocation failure [4500:0xc3700000000] 177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) allocation failure [4500:0xc3700000000] 177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) allocation failure <--- JS stacktrace ---> [4500:4500:0405/112334.605730:FATAL:memory.cc <http://memory.cc/>(38)] Out of memory. size=0 Because at the end there is an ‘out of memory’ message, I have increased the ram of my computer from 16GB to 32GB but the problem persists. Another piece of info is that my computer has 8 CPU but when running CCP4i2 it only uses one. Does anybody have an idea of which could be the problem? Best regards, Marian ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
