Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

[venkatareddy dadireddy]

Thank you very much Garib.

Venkat

On Sat, Apr 6, 2024 at 1:12 AM Garib Murshudov 
wrote:

> Unless you are confident that twin exists you should not use twin
> refinement (Occam’s razor)
>
>
>
> On 5 Apr 2024, at 17:24, venkatareddy dadireddy 
> wrote:
>
> CAUTION: This email originated from outside of the LMB:
> *.-owner-ccp...@jiscmail.ac.uk -.*
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> phish...@mrc-lmb.cam.ac.uk
>
>
> --
> Hi Kay and Garib,
>
> Thank you for your input.
> It is actually the twin refinement that gave rise to resolution
> discrepancy.
> For what reason I don't remember that I have turned the twin refinement ON
> and the same job was cloned again and again.
> With the twin refinement OFF, it gave rise to resolution present in the
> MTZ (2.0 A).
> From Xtriage: *the correlation between*
> *the intensities related by the twin law 1/2*h-3/2*k, -1/2*h-1/2*k,-l with
> an estimated twin*
> *fraction of 0.10 is most likely due to an NCS axis parallel to the twin
> axis*.
> The statistics independent of twin laws show no twinning (more close to
> untwinned than perfect twin).
> Please suggest to me on how I proceed with refinement (twin OFF or ON).
>
> Thank you,
> Venkat
>
>
>
>
>
>
>
> On Fri, Apr 5, 2024 at 1:00 AM Garib Murshudov 
> wrote:
>
>> Did you use twin refinement (is it really twin if you used that).
>> If twin refinement was used then twin related intensities might have
>> different resolution, in case when your crystal are pseudomerohedral
>> twinned.
>>
>> Regards
>> Garib
>>
>> On 4 Apr 2024, at 18:40, venkatareddy dadireddy 
>> wrote:
>>
>> CAUTION: This email originated from outside of the LMB:
>> *.-owner-ccp...@jiscmail.ac.uk -.*
>> Do not click links or open attachments unless you recognize the sender
>> and know the content is safe.
>> If you think this is a phishing email, please forward it to
>> phish...@mrc-lmb.cam.ac.uk
>>
>>
>> --
>> Hi Kay,
>>
>> Thank you very much for your insights.
>> Following are the cell parameters from mtz and pdb header.
>> *MTZ: 117.8560   66.1700   70.9040   90.   91.4240   90.000*
>>
>> *CRYST1  117.856   66.170   70.904  90.00  91.42  90.00 C 1 2 1*
>>
>> The only difference is in the 3rd decimal point.
>>
>>
>> Thank you,
>> Venkat
>>
>>
>>
>> On Tue, Apr 2, 2024 at 10:10 PM Kay Diederichs <
>> kay.diederi...@uni-konstanz.de> wrote:
>>
>>> Hi Venkatareddy Dadireddy,
>>>
>>> do the unit cell parameters of your MTZ file and PDB file agree exactly ?
>>>
>>> Take for example a cell of (100,110,120,90,90,90) in the header of the
>>> MTZ file,
>>> and (97,110,120,90,90,90) in the CRYST1 line of the PDB file.
>>>
>>> In this example, the (50,0,0) reflection would be at 2.0A resolution if
>>> using the cell from the MTZ file,
>>> but it would be at 1.94A resolution if calculating the resolution based
>>> on the cell from the PDB file.
>>>
>>> So perhaps REFMAC5 takes the cell from the PDB file, and phenix.refine
>>> takes the cell from the MTZ?
>>> I didn't check but it may be worth finding out.
>>>
>>> HTH,
>>> Kay
>>>
>>>
>>> On Tue, 2 Apr 2024 21:16:57 +0530, venkatareddy dadireddy <
>>> venkatda...@gmail.com> wrote:
>>>
>>> >Hi,
>>> >
>>> >The resolution range in my MTZ file is 70.88 - 2.0 A. When I refined my
>>> >structure using REFMAC5, the resolution that it gives is 70.88 - 1.94 A,
>>> >the difference of 0.04 A. I also used Phenix.refine which gives the
>>> >resolution output as it is in the MTZ file. Again, EDS (validation
>>> report)
>>> >gives the right resolution. What could be the possible reason for this
>>> >discrepancy? I have the structure deposited in the Protein Data Bank
>>> and it
>>> >is on hold. Thank you in advance for your help.
>>> >
>>> >Thank you,
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >*Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
>>> >Physics,IISc, Banglore.Cell: 07259492227*
>>> >
>>> >
>>> >
>>> >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
>>>
>>> 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/
>>>
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>> *Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
>> Physics,IISc, Banglore.Cell: 

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email: filip.vanpete...@gmail.com
Twitter: @FilipPetegem
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Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

[Garib Murshudov]

Unless you are confident that twin exists you should not use twin refinement 
(Occam’s razor)



> On 5 Apr 2024, at 17:24, venkatareddy dadireddy  wrote:
> 
> CAUTION: This email originated from outside of the LMB:
> .-owner-ccp...@jiscmail.ac.uk -.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> If you think this is a phishing email, please forward it to 
> phish...@mrc-lmb.cam.ac.uk 
> 
> --
> 
> Hi Kay and Garib,
> 
> Thank you for your input.
> It is actually the twin refinement that gave rise to resolution discrepancy.
> For what reason I don't remember that I have turned the twin refinement ON
> and the same job was cloned again and again. 
> With the twin refinement OFF, it gave rise to resolution present in the MTZ 
> (2.0 A).
> From Xtriage: the correlation between
> the intensities related by the twin law 1/2*h-3/2*k, -1/2*h-1/2*k,-l with an 
> estimated twin
> fraction of 0.10 is most likely due to an NCS axis parallel to the twin axis. 
> The statistics independent of twin laws show no twinning (more close to 
> untwinned than perfect twin).
> Please suggest to me on how I proceed with refinement (twin OFF or ON).
> 
> Thank you,
> Venkat
> 
>  
> 
>  
> 
> 
> 
> On Fri, Apr 5, 2024 at 1:00 AM Garib Murshudov  > wrote:
> Did you use twin refinement (is it really twin if you used that). 
> If twin refinement was used then twin related intensities might have 
> different resolution, in case when your crystal are pseudomerohedral twinned. 
> 
> Regards
> Garib
> 
>> On 4 Apr 2024, at 18:40, venkatareddy dadireddy > > wrote:
>> 
>> CAUTION: This email originated from outside of the LMB:
>> .-owner-ccp...@jiscmail.ac.uk -.
>> Do not click links or open attachments unless you recognize the sender and 
>> know the content is safe.
>> If you think this is a phishing email, please forward it to 
>> phish...@mrc-lmb.cam.ac.uk 
>> 
>> --
>> 
>> Hi Kay,
>> 
>> Thank you very much for your insights. 
>> Following are the cell parameters from mtz and pdb header.
>> MTZ: 117.8560   66.1700   70.9040   90.   91.4240   90.000
>> CRYST1  117.856   66.170   70.904  90.00  91.42  90.00 C 1 2 1
>> 
>> The only difference is in the 3rd decimal point.
>> 
>> 
>> Thank you,
>> Venkat
>> 
>> 
>> 
>> On Tue, Apr 2, 2024 at 10:10 PM Kay Diederichs 
>> mailto:kay.diederi...@uni-konstanz.de>> 
>> wrote:
>> Hi Venkatareddy Dadireddy,
>> 
>> do the unit cell parameters of your MTZ file and PDB file agree exactly ?
>> 
>> Take for example a cell of (100,110,120,90,90,90) in the header of the MTZ 
>> file, 
>> and (97,110,120,90,90,90) in the CRYST1 line of the PDB file.
>> 
>> In this example, the (50,0,0) reflection would be at 2.0A resolution if 
>> using the cell from the MTZ file, 
>> but it would be at 1.94A resolution if calculating the resolution based on 
>> the cell from the PDB file.
>> 
>> So perhaps REFMAC5 takes the cell from the PDB file, and phenix.refine takes 
>> the cell from the MTZ?
>> I didn't check but it may be worth finding out. 
>> 
>> HTH,
>> Kay
>> 
>> 
>> On Tue, 2 Apr 2024 21:16:57 +0530, venkatareddy dadireddy 
>> mailto:venkatda...@gmail.com>> wrote:
>> 
>> >Hi,
>> >
>> >The resolution range in my MTZ file is 70.88 - 2.0 A. When I refined my
>> >structure using REFMAC5, the resolution that it gives is 70.88 - 1.94 A,
>> >the difference of 0.04 A. I also used Phenix.refine which gives the
>> >resolution output as it is in the MTZ file. Again, EDS (validation report)
>> >gives the right resolution. What could be the possible reason for this
>> >discrepancy? I have the structure deposited in the Protein Data Bank and it
>> >is on hold. Thank you in advance for your help.
>> >
>> >Thank you,
>> >
>> >
>> >
>> >
>> >
>> >
>> >*Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
>> >Physics,IISc, Banglore.Cell: 07259492227*
>> >
>> >
>> >
>> >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/ 
>> >
>> >
>> 
>> 
>> 
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>> 

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Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

[venkatareddy dadireddy]

Hi Kay and Garib,

Thank you for your input.
It is actually the twin refinement that gave rise to resolution discrepancy.
For what reason I don't remember that I have turned the twin refinement ON
and the same job was cloned again and again.
With the twin refinement OFF, it gave rise to resolution present in the MTZ
(2.0 A).
>From Xtriage: *the correlation between*
*the intensities related by the twin law 1/2*h-3/2*k, -1/2*h-1/2*k,-l with
an estimated twin*
*fraction of 0.10 is most likely due to an NCS axis parallel to the twin
axis*.
The statistics independent of twin laws show no twinning (more close to
untwinned than perfect twin).
Please suggest to me on how I proceed with refinement (twin OFF or ON).

Thank you,
Venkat







On Fri, Apr 5, 2024 at 1:00 AM Garib Murshudov 
wrote:

> Did you use twin refinement (is it really twin if you used that).
> If twin refinement was used then twin related intensities might have
> different resolution, in case when your crystal are pseudomerohedral
> twinned.
>
> Regards
> Garib
>
> On 4 Apr 2024, at 18:40, venkatareddy dadireddy 
> wrote:
>
> CAUTION: This email originated from outside of the LMB:
> *.-owner-ccp...@jiscmail.ac.uk -.*
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> phish...@mrc-lmb.cam.ac.uk
>
>
> --
> Hi Kay,
>
> Thank you very much for your insights.
> Following are the cell parameters from mtz and pdb header.
> *MTZ: 117.8560   66.1700   70.9040   90.   91.4240   90.000*
>
> *CRYST1  117.856   66.170   70.904  90.00  91.42  90.00 C 1 2 1*
>
> The only difference is in the 3rd decimal point.
>
>
> Thank you,
> Venkat
>
>
>
> On Tue, Apr 2, 2024 at 10:10 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Hi Venkatareddy Dadireddy,
>>
>> do the unit cell parameters of your MTZ file and PDB file agree exactly ?
>>
>> Take for example a cell of (100,110,120,90,90,90) in the header of the
>> MTZ file,
>> and (97,110,120,90,90,90) in the CRYST1 line of the PDB file.
>>
>> In this example, the (50,0,0) reflection would be at 2.0A resolution if
>> using the cell from the MTZ file,
>> but it would be at 1.94A resolution if calculating the resolution based
>> on the cell from the PDB file.
>>
>> So perhaps REFMAC5 takes the cell from the PDB file, and phenix.refine
>> takes the cell from the MTZ?
>> I didn't check but it may be worth finding out.
>>
>> HTH,
>> Kay
>>
>>
>> On Tue, 2 Apr 2024 21:16:57 +0530, venkatareddy dadireddy <
>> venkatda...@gmail.com> wrote:
>>
>> >Hi,
>> >
>> >The resolution range in my MTZ file is 70.88 - 2.0 A. When I refined my
>> >structure using REFMAC5, the resolution that it gives is 70.88 - 1.94 A,
>> >the difference of 0.04 A. I also used Phenix.refine which gives the
>> >resolution output as it is in the MTZ file. Again, EDS (validation
>> report)
>> >gives the right resolution. What could be the possible reason for this
>> >discrepancy? I have the structure deposited in the Protein Data Bank and
>> it
>> >is on hold. Thank you in advance for your help.
>> >
>> >Thank you,
>> >
>> >
>> >
>> >
>> >
>> >
>> >*Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
>> >Physics,IISc, Banglore.Cell: 07259492227*
>> >
>> >
>> >
>> >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:
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>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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>>
>
>
> --
>
>
>
>
>
>
> *Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
> Physics,IISc, Banglore.Cell: 07259492227*
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>

-- 






*Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of
Physics,IISc, Banglore.Cell: 07259492227*



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[ccp4bb] Instruct-ERIC Structure Meets Function Webinar 32

[ccp4mail]

Register now for the 32nd edition of the Instruct-ERIC Structure Meets Function 
webinar 
series,
 taking place on Zoom, 17 April at 11:00 CEST.





Register 
Here





The latest webinar will have two speakers who have accessed the Instruct-ERIC 
facilities, expertise, and machinery via the ISIDORe project.



Talk 1: Nikitas Georgiou - National and Kapodistrian University of Athens
Title: Potential anti-inflammatory drugs



Talk 2: Séverine Padiolleau - Université de Technologie de Compiègne
Title: Identification of aptamers interacting with a protein target involved in 
lyme disease


Read the full talk abstracts and register for the webinar 
here.





[https://instruct-eric.org/upload/bPEETiDbLkqAYuMtVkEgCUz85k143gkA.jpg]



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Re: [ccp4bb] Refmac problem: Validation and Analysis

[Jon Agirre]

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  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(12701)]
> [.WebGL-0x23e9d90]GL ERROR :GL_INVALID_VALUE : glVertexAttrib4f: index out
> of range
>
> <--- Last few GCs --->
>
> [4500:0xc37]   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
> [4500:0xc37]   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
> [4500:0xc37]   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(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=1
>


-- 
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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[ccp4bb] Refmac problem: Validation and Analysis

[Marian Oliva]

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 
(12701)] [.WebGL-0x23e9d90]GL ERROR 
:GL_INVALID_VALUE : glVertexAttrib4f: index out of range

<--- Last few GCs --->

[4500:0xc37]   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
[4500:0xc37]   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
[4500:0xc37]   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 (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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