Dear Marian,
This issue regarding validation report in refmac task has been fixed in
the latest update 8.0.019. Please let us know if the problem persists.
Best wishes,
Martin
On 05/04/2024 13:19, Jon Agirre wrote:
Dear Marian,
Thanks for your report. I'm sorry you're having to deal with this
problem. There is nothing wrong with your machine; this is an
identified bug and we're working towards fixing it. In the meantime,
the only workaround I can think of is to roll CCP4 back to a previous
update, e.g. 015.
I will keep you posted,
Jon
On Fri, 5 Apr 2024 at 12:54, Marian Oliva <mar...@cib.csic.es> wrote:
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
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--
Dr Jon Agirre (He/Him)
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology
Communications
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
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