Re: [ccp4bb] pymol 2.5 GUI font size too small

[Xiao Lei]

Hi, Ursula,

I have the same problem on my Pymol version 2.5.1 on the Mac Mojave system,
I posted a solution from an old thread below that solved the problem.

"This looks like missing shader support, which is unexpected on modern Mac
hardware. Can you try to set the "use_shaders" setting?

PyMOL> set use_shaders, 1

If this fixes it, then please check your ~/.pymolrc file if the use_shaders
setting is wrongly disabled there (File > Edit pymolrc).

Cheers,

Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.  "

Best,

Xiao



On Tue, Jul 20, 2021 at 7:28 PM Ursula Schulze-Gahmen <
641349121f5f-dmarc-requ...@jiscmail.ac.uk> wrote:

> I just updated my pymol version to 2.5, which now displays a tiny font in
> the internal GUI. The settings in pymol don't have an option for the GUI
> font. Does anybody have a suggestion on how to change the font size in the
> pymol GUI in version 2.5?
>
> Thanks
>
> Ursula
>
> --
> Ursula Schulze-Gahmen, PhD
> Staff Research Scientist
> The J David Gladstone Institutes
> 1650 Owens St.
> San Francisco, CA 94158
> (415) 734 4835
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] generate symmetry mates of EM structures

[Xiao Lei]

Hi, Stefano,

Thanks. I use Pymol 2.4. I figured out that if I downloaded the PDB (5L93)
RCSB website (biological assembly 1 PDB file), Pymol would show each state
of the structure (3 chains) individually, if I execute the "set all_states,
on" command, I can see the assembly.

Best,

Xiao

On Fri, May 21, 2021 at 9:07 AM Stefano Trapani  wrote:

> Le 2021-05-21 13:54, Xiao Lei a écrit :
>
> Thank you for your help. It seems the problem is due to the Pymol program.
>
> Hi Xiao
> which version of PyMOL are you using ?
>
>
> I could only see 3 chains in Pymol from the assembly PDB downloaded from
> the RCSB website (biological assembly 1 PDB file).
>
> There is no *PDB* file for biological assembly 1 of that entry on the
> RCSB site. There is, instead, a *pdbx/mmCIF* file for the assembly (
> https://www.ebi.ac.uk/pdbe/static/entry/download/5l93-assembly-1.cif.gz).
>
> The assembly file is correctly displayed in PyMOL (at least the version I
> use : 2.2.0 Open-Source).
>
> Another way of displaying assemblies in PyMOL is:
>
> *set assembly, 1*
> *fetch 5l93*
>
> Best regards
>
> ---
> Stefano Trapani
>
> Maître de 
> Conférenceshttp://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
> -
> Centre de Biologie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
>
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
>
>
> --
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
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>



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Re: [ccp4bb] generate symmetry mates of EM structures

[Xiao Lei]

Dear David,

Thank you for your help. It seems the problem is due to the Pymol program.
I could only see 3 chains in Pymol from the assembly PDB downloaded from
the RCSB website (biological assembly 1 PDB file). If I use UCSF Chimera, I
can see 18 chains. With others' help, I can also use "sym" command in UCSF
Chimera to generate assembly in UCSF Chimera, but Pymol just could not do
the job.

Best,
Xiao

On Fri, May 21, 2021 at 6:50 AM David Armstrong  wrote:

> Dear Xiao,
>
> For public entries in the PDB archive, it is possible to download the
> coordinates of the assemblies defined in the PDB entry.
>
> If you visit the page for the entry at PDBe (pdbe.org/5l93) and select
> 'Downloads' you have the option to download various data, including mmCIF
> files containing the full assemblies. In this case, "Assembly 1 (mmCIF;
> gz)" would give you the full structure.
>
> Kind Regards,
> David Armstrong
>
> On 21/05/2021 11:33, Xiao Lei wrote:
>
> Dear Community,
>
> I wonder if there is a way to generate symmetry mates of EM structures?
> For example for PDB code 5L93, I tried PISA assembly server and Pymol to
> generate assembly (18 chains) but failed because it is not a crystal
> structure. I tried to download assembly directly from RCSB databank but
> after I opened the downloaded structure in Pymol, I can only see 3 chains,
> although the RCSB databank indicates the assembly should contain 18 chains.
>
> Best wishes and thank you in advance,
>
> Xiao
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
> David Armstrong
> Outreach and Training Coordinator
> PDBe
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD UK
> Tel: +44 1223 492544
>
>



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[ccp4bb] generate symmetry mates of EM structures

[Xiao Lei]

Dear Community,

I wonder if there is a way to generate symmetry mates of EM structures?
For example for PDB code 5L93, I tried PISA assembly server and Pymol to
generate assembly (18 chains) but failed because it is not a crystal
structure. I tried to download assembly directly from RCSB databank but
after I opened the downloaded structure in Pymol, I can only see 3 chains,
although the RCSB databank indicates the assembly should contain 18 chains.

Best wishes and thank you in advance,

Xiao



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Re: [ccp4bb] Lost extension bar in Coot

[Xiao Lei]

Hi, Kahkashan,

Does Coot 0.9 bundle with CCP4 7.1 installation?I install CCP4 7.1 and
I did not see Coot installed.

Best,

Xiao

On Thu, Jun 11, 2020 at 8:27 AM Firdous Tarique 
wrote:

> Hi
>
> Just downloaded the new CCP4-7.1. Wondering where the extension bar in
> Coot 0.9 has gone. Please help me to find it. I think it is hidden
> somewhere.
>
> Best
>
> Kahkashan
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

[Xiao Lei]

I used to use Ubuntu Mate OS to get 3D work for coot and pymol. I am not
sure if the latest version still works.

Regards

Xiao

On Fri, Nov 8, 2019, 7:19 AM Chris Richardson 
wrote:

> Apologies for the only slightly relevant question.
>
> Does anyone know the correct incantations to get nVidia 3D Vision glasses
> and emitter working with Ubuntu 18.04?
>
> None of the tricks that work with 16.04 are helping with the new release.
> In particular, disabling composite in the extensions makes the display
> blank while X11 restarts itself every few seconds.
>
> Thanks in advance,
>
> Chris
> --
> Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
>
>
>
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message
> from your computer and network.
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] Offtopic: Is there a way to search protein-protein interface structural similarity in database ?

[Xiao Lei]

Hi All,

I wonder if there is a way to search protein-protein interaction interface
similarities in PDB database?  For example, I have two proteins proA and
proB, part of proA and part of proB contact with each other in a crystal
structure, I want to search if there are similar interaction interfaces in
other protein structures in PDB database, I mean 3D structural similarities
of the interface, not amino acids identities similarities.

Thanks,

Xiao



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Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

[Xiao Lei]

Hi All,

Sorry to bring this old topic up again.  I planned to run tricine gels but
I found a possible error in table 2 (4% stacking gel formula) in Hermann
Schägger protocol (Nature Protocols volume 1, pages 16–22 (2006), the
author wrote 3ml 3X gel buffer in a total of 12 ml solution, it should be
4ml 3X gel buffer in a total of 12 ml solution right?

I tried to contact the author but unsuccessful, I do not know if anyone in
this forum has noticed if this is an error or not.

Xiao


On Thu, Jan 19, 2017 at 8:00 AM Didier Spittler 
wrote:

> Yes Tris-Tricine gel !
>
> Try to obtain this article from nature protocol.
>
> Best,
>
> Didier
>
>
> 2017-01-19 14:47 GMT+01:00 zeyaul islam :
>
>> Try Tricine gel. It is particularly suited for low molecular wt proteins
>> and it will give you very good resolution. Even you can run it overnight at
>> 30 V (16-18 hours).
>>
>> On Thu, Jan 19, 2017 at 9:33 AM, Walt  wrote:
>>
>>> Hi,
>>>
>>> I have a small protein (~9 kDa) with acidic pI (~4).
>>> When I run 18% native-PAGE, it appears my protein is in the dye front.
>>> How can I fix this problem? Changing the pH of separating gel
>>> might help? How about gradient native-PAGE? Thank you!
>>>
>>> Walt
>>>
>>
>>
>
>
> --
> Didier Spittler, PhD
> Phone number : +33658576481
>



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[ccp4bb] Postdoc position available

[Xiao Lei]

*Postdoctoral Scholar Position on Investigating CRISPR Mechanism at
University of Southern California, Los Angeles, California, USA*



The Qin Laboratory in the Chemistry Department of the University of
Southern California invites applications for postdoctoral scholar positions
supported by funding from NIH and NSF. The work centers on investigating
mechanisms of target recognition by the programmable CRISPR nucleases that
are revolutionizing genome engineering. The projects use a combination of
biophysical techniques, including spin-labeling and EPR (a specialty of the
Qin lab, seehttp://pzqin.usc.edu/pzqhome/), fluorescence, and structural
characterization. Candidates with prior experience on protein expression,
mutagenesis, structural analyses (e.g., X-ray, NMR), and protein-nucleic
acid interaction are particularly welcome. Strong writing and communication
skills, as evidenced by first author publications, are highly desirable.



The appointment is available initially for three years contingent on
satisfactory research progress. Funding starts in Fall 2018, and salary
will commensurate with qualifications. To Apply, please email a cover
letter, CV and contact information for three references to Professor Peter
Qin, p...@usc.edu

*(PS.  Please do not reply to this email, I post this job for Dr. Peter
Qin, please directly contact with Dr. Peter Qin)*



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[ccp4bb] Postdoc Position available at Dr. Peter Qin lab at University of Southern California

[Xiao Lei]

*Postdoctoral Scholar Position on Investigating CRISPR Mechanism at
University of Southern California, Los Angeles, California, USA*



The Qin Laboratory in the Chemistry Department of the University of
Southern California invites applications for postdoctoral scholar positions
supported by funding from NIH and NSF. The work centers on investigating
mechanisms of target recognition by the programmable CRISPR nucleases that
are revolutionizing genome engineering. The projects use a combination of
biophysical techniques, including spin-labeling and EPR (a specialty of the
Qin lab, see http://pzqin.usc.edu/pzqhome/), fluorescence, and structural
characterization. Candidates with prior experience on protein expression,
mutagenesis, structural analyses (e.g., X-ray, NMR), and protein-nucleic
acid interaction are particularly welcome. Strong writing and communication
skills, as evidenced by first author publications, are highly desirable.



The appointment is available initially for three years contingent on
satisfactory research progress. Funding starts in Fall 2018, and salary
will commensurate with qualifications. To Apply, please email a cover
letter, CV and contact information for three references to Professor Peter
Qin, p...@usc.edu

*(PS.  Please do not reply to this email, I post this job for Dr. Peter
Qin, please directly contact with Dr. Peter Qin)*



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Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

I see. Thanks Eleanor!

On Thu, Dec 7, 2017 at 4:33 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:

> Rf_used is the R factor for the non-free reflections.
>
> If you do the plot the 4SSQ/L**2 is converted to As..
>
> E
>
> On 7 December 2017 at 11:50, Xiao Lei <xiaolei...@gmail.com> wrote:
>
>> Thanks Eleanor, yes, I looked at that table and tried to find out the
>> Rfree and R, I know the 4SSQ/LL means column means resolution bins but I
>> did not know what column means Rfac (The Rf_free means Rfree I guess).
>>
>>
>> On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Dont you look at the graphs from the log file?
>>>
>>> This table gives you all sorts of information including R and Rfree in
>>> resolution shells..
>>>
>>> Eleanor
>>> Things for loggraph, R factor and
>>> others
>>>
>>>
>>> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
>>> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
>>> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
>>> :Cycle   11. % observed v. resln :N:1,3:
>>> $$
>>> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
>>> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
>>> $$
>>>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2
>>> 539.4  0.59  0.62
>>>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5
>>> 412.9  0.57  0.58
>>>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6
>>> 431.4  0.57  0.57
>>>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3
>>> 455.8  0.59  0.59
>>>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2
>>> 354.8  0.55  0.54
>>>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1
>>> 304.8  0.57  0.54
>>>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5
>>> 229.6  0.60  0.58
>>>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8
>>> 195.7  0.52  0.50
>>>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4
>>> 170.1  0.59  0.56
>>>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1
>>> 144.9  0.61  0.57
>>>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1
>>> 115.1  0.57  0.53
>>>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5
>>> 110.5  0.60  0.58
>>>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.4
>>> 96.3  0.54  0.53
>>>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.4
>>> 84.0  0.55  0.53
>>>  0.2147427  99.1887.670.9  0.53  0.52 40088.9
>>> 71.3  0.53  0.52
>>>  0.2297702  98.6877.361.2  0.52  0.52 39580.2
>>> 61.7  0.54  0.53
>>>  0.2447963  98.9265.652.3  0.48  0.48 42865.5
>>> 53.7  0.54  0.54
>>>  0.2588198  98.48    56.844.6  0.46  0.46 43753.5
>>> 43.6  0.49  0.49
>>>  0.2738375  98.6647.737.5  0.43  0.43 42848.0
>>> 37.6  0.47  0.48
>>>  0.2888611  98.2440.932.1  0.42  0.42 45041.8
>>> 32.1  0.50  0.50
>>> $$
>>>
>>>
>>>
>>> On 7 December 2017 at 01:07, Bernhard Rupp <hofkristall...@gmail.com>
>>> wrote:
>>>
>>>> You can find these numbers in the header of the output model coordinate
>>>> file.
>>>>
>>>>
>>>>
>>>> BR
>>>>
>>>>
>>>>
>>>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>>> Of *Xiao Lei
>>>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>>>> resolution bin in Refmac 5?
>>>>
>>>>
>>>>
>>>> Dear All,
>>>>
>>>> I am asking how to find the Rfree and R in the highest resolution bin
>>>> in Refmac 5 output?
>>>>
>>>> I used Refmac5 in refinement of protein structure at 3A resolution.
>>>> Output of Refmac5 gives Rfee and R as:
>>>>
>>>>   InitialFinal
>>>>
>>>>R factor0.2900   0.2052
>>>>
>>>>  R free0.3015   0.2639
>>>>
>>>>
>>>> I'd also like to see the Rfree and R in the highest resolution bin. I
>>>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>>>> with columns of Rf_free and WR_free, I searched in internet and still could
>>>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>>>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>>>> value in the parenthesis).
>>>>
>>>>
>>>>
>>>> thanks ahead.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

Thanks Eleanor, yes, I looked at that table and tried to find out the Rfree
and R, I know the 4SSQ/LL means column means resolution bins but I did not
know what column means Rfac (The Rf_free means Rfree I guess).

On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dont you look at the graphs from the log file?
>
> This table gives you all sorts of information including R and Rfree in
> resolution shells..
>
> Eleanor
> Things for loggraph, R factor and
> others
>
>
> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
> :Cycle   11. % observed v. resln :N:1,3:
> $$
> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
> $$
>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2   539.4
> 0.59  0.62
>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5   412.9
> 0.57  0.58
>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6   431.4
> 0.57  0.57
>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3   455.8
> 0.59  0.59
>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2   354.8
> 0.55  0.54
>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1   304.8
> 0.57  0.54
>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5   229.6
> 0.60  0.58
>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8   195.7
> 0.52  0.50
>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4   170.1
> 0.59  0.56
>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1   144.9
> 0.61  0.57
>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1   115.1
> 0.57  0.53
>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5   110.5
> 0.60  0.58
>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.496.3
> 0.54  0.53
>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.484.0
> 0.55  0.53
>  0.2147427  99.1887.670.9  0.53  0.52 40088.971.3
> 0.53  0.52
>  0.2297702  98.6877.361.2  0.52  0.52 39580.261.7
> 0.54  0.53
>  0.2447963  98.9265.652.3  0.48  0.48 42865.553.7
> 0.54  0.54
>  0.2588198  98.4856.844.6  0.46  0.46 43753.543.6
> 0.49  0.49
>  0.2738375  98.6647.737.5  0.43  0.43 42848.037.6
> 0.47  0.48
>  0.2888611  98.2440.932.1  0.42  0.42 45041.832.1
> 0.50  0.50
> $$
>
>
>
> On 7 December 2017 at 01:07, Bernhard Rupp <hofkristall...@gmail.com>
> wrote:
>
>> You can find these numbers in the header of the output model coordinate
>> file.
>>
>>
>>
>> BR
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Xiao Lei
>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>> resolution bin in Refmac 5?
>>
>>
>>
>> Dear All,
>>
>> I am asking how to find the Rfree and R in the highest resolution bin in
>> Refmac 5 output?
>>
>> I used Refmac5 in refinement of protein structure at 3A resolution.
>> Output of Refmac5 gives Rfee and R as:
>>
>>   InitialFinal
>>
>>R factor0.2900   0.2052
>>
>>  R free0.3015   0.2639
>>
>>
>> I'd also like to see the Rfree and R in the highest resolution bin. I
>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>> with columns of Rf_free and WR_free, I searched in internet and still could
>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>> value in the parenthesis).
>>
>>
>>
>> thanks ahead.
>>
>>
>>
>>
>>
>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

This works. Thanks a lot Bernhard.

On Wed, Dec 6, 2017 at 5:07 PM, Bernhard Rupp <hofkristall...@gmail.com>
wrote:

> You can find these numbers in the header of the output model coordinate
> file.
>
>
>
> BR
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Wednesday, December 6, 2017 2:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] How to find the Rfree and R in the highest resolution
> bin in Refmac 5?
>
>
>
> Dear All,
>
> I am asking how to find the Rfree and R in the highest resolution bin in
> Refmac 5 output?
>
> I used Refmac5 in refinement of protein structure at 3A resolution.
> Output of Refmac5 gives Rfee and R as:
>
>   InitialFinal
>
>R factor0.2900   0.2052
>
>  R free0.3015   0.2639
>
>
> I'd also like to see the Rfree and R in the highest resolution bin. I
> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
> with columns of Rf_free and WR_free, I searched in internet and still could
> not understand the Rf_free and WR_free label meaning.  I'd like to find
> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
> value in the parenthesis).
>
>
>
> thanks ahead.
>
>
>
>
>

[ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

Dear All,

I am asking how to find the Rfree and R in the highest resolution bin in
Refmac 5 output?

I used Refmac5 in refinement of protein structure at 3A resolution.
Output of Refmac5 gives Rfee and R as:

  InitialFinal

   R factor0.2900   0.2052

 R free0.3015   0.2639


I'd also like to see the Rfree and R in the highest resolution bin. I
checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
with columns of Rf_free and WR_free, I searched in internet and still could
not understand the Rf_free and WR_free label meaning.  I'd like to find
something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
value in the parenthesis).

thanks ahead.

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Xiao Lei]

Dear All,

Thanks. I tried PDBemotif, indeed, it works very well!

On Thu, Oct 26, 2017 at 10:04 AM, Andrew Lovering <
andrewleelover...@googlemail.com> wrote:

> The backbone psi phi angle option in pdbemotif should limit hits to a
> particular secondary structure.
>
> Good luck!
> Andy
>
> On 26 Oct 2017 5:54 pm, "xiaolei...@gmail.com" 
> wrote:
>
>> Dear All,
>>
>> Thanks for the suggestions!  I tried MPI pattern search, MOTIF2 as Andrew
>> suggested, they worked fine to pull out of the PDB containing short
>> sequences. What I need to do is a little bit more, I'd also like to know my
>> hit region's secondary structure (helix, sheet, or loop), MPI and MOTIF2
>> usually pulls out tons of sequences, then at this stage I have to manually
>> go to each PDB, check the hit region's secondary structure. I wonder if
>> there is a tool to do both, i.e., let's say I could search for short
>> sequences in only helix region or loop region of PDB files?
>>
>>
>>
>> On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering 
>> wrote:
>>
>>> I would guess that you want to search PDB for a small motif you've
>>> observed in a structure of yours, looking to find examples of it used in
>>> same context?
>>>
>>> If that's true, I would recommend PDBemotif, put the sequence in, and
>>> then use the backbone psi phi angles of your motif as a secondary
>>> constraint in the search, increasing/decreasing the angle tolerance as
>>> appropriate.
>>>
>>> If I’m incorrect, and you just want to find examples of a short motif,
>>> this webserver is awesome – you can also limit it by taxonomy:
>>>
>>> http://www.genome.jp/tools/motif/MOTIF2.html
>>>
>>>
>>>
>>> Best
>>>
>>> Andy
>>>
>>>
>>>
>>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>> Of *xiaolei...@gmail.com
>>> *Sent:* 26 October 2017 04:40
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [ccp4bb] blast pdb for a very short sequence (3 amino acids)
>>>
>>>
>>>
>>> Dear CCP4BB members,
>>>
>>>
>>>
>>> Sorry this post is off-topic. I am asking is there a way to blast pdb
>>> for a very short sequence like 2 or 3 amino acids?  I tried this for a
>>> positive control in pdb database but returned that "Your search parameters
>>> were adjusted to search for a short input sequence."  and "No significant
>>> similarity found. ".
>>>
>>>
>>>
>>>
>>>
>>
>>

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Xiao Lei]

Dear All,

Thanks for the suggestions!  I tried MPI pattern search, MOTIF2 as Andrew
suggested, they worked fine to pull out of the PDB containing short
sequences. What I need to do is a little bit more, I'd also like to know my
hit region's secondary structure (helix, sheet, or loop), MPI and MOTIF2
usually pulls out tons of sequences, then at this stage I have to manually
go to each PDB, check the hit region's secondary structure. I wonder if
there is a tool to do both, i.e., let's say I could search for short
sequences in only helix region or loop region of PDB files?



On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering 
wrote:

> I would guess that you want to search PDB for a small motif you've
> observed in a structure of yours, looking to find examples of it used in
> same context?
>
> If that's true, I would recommend PDBemotif, put the sequence in, and then
> use the backbone psi phi angles of your motif as a secondary constraint in
> the search, increasing/decreasing the angle tolerance as appropriate.
>
> If I’m incorrect, and you just want to find examples of a short motif,
> this webserver is awesome – you can also limit it by taxonomy:
>
> http://www.genome.jp/tools/motif/MOTIF2.html
>
>
>
> Best
>
> Andy
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> xiaolei...@gmail.com
> *Sent:* 26 October 2017 04:40
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] blast pdb for a very short sequence (3 amino acids)
>
>
>
> Dear CCP4BB members,
>
>
>
> Sorry this post is off-topic. I am asking is there a way to blast pdb for
> a very short sequence like 2 or 3 amino acids?  I tried this for a positive
> control in pdb database but returned that "Your search parameters were
> adjusted to search for a short input sequence."  and "No significant
> similarity found. ".
>
>
>
>
>

[ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Xiao Lei]

Dear CCP4BB members,

Sorry this post is off-topic. I am asking is there a way to blast pdb for a
very short sequence like 2 or 3 amino acids?  I tried this for a positive
control in pdb database but returned that "Your search parameters were
adjusted to search for a short input sequence."  and "No significant
similarity found. ".

[ccp4bb] How to search 2 models (ensembles) in Molrep

[Xiao Lei]

Dear Crystallographers,

How to search 2 models (ensembles) in Molrep for molecular replacement?  It
seems there is just one model input place in Molrep GUI.  In Phaser MR,
this can be done with clicking the "add ensemble" button to add another
ensemble, but I am not sure how to do it in Molrep.

[ccp4bb] align structure in Pymol based on dsDNA helix

[Xiao Lei]

Dear All,

I was wondering in Pymol is there a way to align various NCS protein dsDNA
complex structure in asymmetric unit based on the double helix of DNA?

I can do the align with the protein part with action-->align--> to molecule
or to selection. But this way does not work out if I select dsDNA and do
the align to selection. I also tried to used command align obj 01 and chain
X, obj 02 and chain Y to align dsDNA, but still failed with message
"invalid selection for alignment".

thanks ahead for any input.

Re: [ccp4bb] Coot label on symmetric residue not working consistent

[Xiao Lei]

Thanks Paul,

I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
   (or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)

coot>>

On Mon, Apr 10, 2017 at 11:05 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:

> On 10/04/17 18:39, Xiao Lei wrote:
>
>> Hi All,
>>
>> I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate symmetric
>> molecule by Draw---> Cell & Symmetry.  I found double click a residue in
>> symmetric molecules will give me a label sometime but not always. I do not
>> know if anyone has similar experience.
>>
>>
>>
> Try applying the solution described for Missing Symmetry in the manual
> (4.11.1).
>
> Paul.
>
>

[ccp4bb] Coot label on symmetric residue not working consistent

[Xiao Lei]

Hi All,

I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate symmetric
molecule by Draw---> Cell & Symmetry.  I found double click a residue in
symmetric molecules will give me a label sometime but not always. I do not
know if anyone has similar experience.

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Hi All,

I summarized my Coot and Pymol 3D experience here. Monitor is from Asus 24
or 27 inch 3D monitor. Monitor works with Nvidia 3D kit. Refresh rate set
120 HZ. Please first download and install Nvidia 3D kit driver and Asus
monitor driver and install first when working with Windows 7 or 10 (you can
find drivers from official website).  Even after install drivers, 3D is not
automatically working in Windows, you need to follow
http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html#mozTocId906434
and do some settings.

1. Windows 7 with Quadro M4000, Display port (DP) on PC to DP on Monitor,
Works very stable with Coot and Pymol. No 3-D mini DIN cable needed.

2. Window 7 with Quadro 5000, DVI-D dual link on PC to DVI-D dual link on
Monitor. Works very stable with Coot and Pymol. No 3-D mini DIN cable
needed.

3. Fedora 24 with Quadro 5000, DVI-D dual link on PC to DVI-D dual link on
Monitor. Works very stable with Coot and Pymol. 3-D mini DIN cable is
needed in this case. Do not dnf update kernel, as most of the time you have
to re-install Nvidia driver again after kernel updated.

4. Ubuntu Mate with Quadro 5000, DVI-D dual link on PC to DVI-D dual link
on Monitor. Works very stable with Coot and Pymol. 3-D mini DIN cable is
needed in this case. In Ubuntu Mate, the installation of Nvidia driver can
be automatically fetch by the system (install proprietary driver), no need
to type command as in Fedora.

5. Windows 10 with Quadro M4000, Display port (DP) on PC to DP on Monitor,
Works with Pymol 3D but Not Coot in my case. No 3-D mini DIN cable needed.
Not stable even with Pymol 3D, I need to reset every parameter after update
and reset refresh rate to 120hz.. This is the worst option in my case!
Because Win10 keeps giving us problem I switch back to Win7 and everything
works great!




On Thu, Mar 2, 2017 at 4:15 PM, Xiao Lei <xiaolei...@gmail.com> wrote:

> Hi All,
>
> Just share my experience, Windows 10 works for pymol 3D under Quadro M4000
> with Nvidia 3D kit (no need to connect the 3 pin MINI DIN, Quadro M4000
> does not have 3 pin Mini DIN connections). I use Asus 24 inch 3D monitor,
> connect the monitor with display port to display port of Quadro M4000, no
> active DP to DVI needed in my case. We have a problem for Coot 3D works
> even when Pymol 3D works ok, we are trying to figure out the problem but
> Windows 10 does work for pymol 3D under DP to DP port.
>
> On Tue, Jan 31, 2017 at 6:39 AM, Yong Wang <wang_yon...@lilly.com> wrote:
>
>> Xiao,
>>
>>
>>
>> I had a direct connection from display port to display port that had
>> worked for several years (Windows 7).  Since last year I have been losing
>> the stereo.  Often the control panel won’t show the 120 Hz like what you
>> saw.  Sometimes I was able to forcefully add a 120 Hz resolution (using the
>> “Customize …” menu).  But it was not stable, i.e. the stereo would stay for
>> some time then disappear and go back to the state of not having 120 Hz.  I
>> have not had time to investigate further into this but I suspect a driver
>> issue here.  You may want to check the drivers for both the graphics card
>> and the monitor.
>>
>>
>>
>> Yong
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Xiao Lei
>> *Sent:* Monday, January 30, 2017 11:50 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>>
>> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
>> under Windows 10
>>
>>
>>
>> Taka,
>>
>>
>>
>> I really appreciate this information! I do have Displayport cable and can
>> connect the card and Asus VG248QE both via the DP cable, somehow on the
>> Nvidia control panel in Windows 10, I do not have an option of choosing
>> "120HZ" or "144Hz", I only have option choosing "60Hz" or below, which
>> sounds weird to me. Windows 10 should make things easier not harder. If
>> CentOS 6 works then Windows 10 should work, I guess I have to go back to
>> Windows 7 if needed, but as I already ordered the DP to DVI active cable,
>> I'll test this cable first and update CCP4bb later.
>>
>>
>>
>> On Mon, Jan 30, 2017 at 7:50 PM, <fukami...@chugai-pharm.co.jp> wrote:
>>
>> Xiao,
>>
>>
>>
>> If you connect the board and monitor by DisplayPort cable directly, it
>> should work.
>>
>> I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not
>> tested on Windows.
>>
>>
>>
>> Taka
>>
>>
>>
>> *From:* Xiao Lei [mailto:xiaolei...@gmail.com]
>> *Sent:* Tuesday, January 31, 2017 10:08 AM
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Su

Re: [ccp4bb] Large number of outliers in the dataset

[Xiao Lei]

This case is encouraging to me that a structure can be solved with such
high mosaicity (in your report is 1.9). I wonder how the diffraction looks
like (I imagine spots smearing or streak). With such high mosaicity, the
unit cell dimension and space group determination is highly likely not
accurate. I usually lose hope of a dataset with average mosaicity above 1.3
and I would not process any high mosaic data, but from your case it seems
2.6A cutoff you get a very nice solution.  It seems the  data processing
software (Imosflm or XDS) nowadays can handle with high mosaic data well.





On Wed, Mar 29, 2017 at 11:00 AM, Gianluca Santoni  wrote:

> In addition to what Nicolas has pointed out, is it quite suspicious to me
> that you have the same multiplicity in the high resolution shell as in the
> low resolution.
>
> On Mar 29, 2017 18:17, Nicolas FOOS  wrote:
>
> Dear Juliana,
>
> all the statistics presented here looks good in terms of resolution cut
> (maybe I will be less sever). For me the point is about the mosaicity you
> report 1.90 it's high in my opinion. How looks you images? I am wondering
> if the indexation is really right. And maybe the complain of Xtriage about
> outlier is due to this high mosaicity. What is the diagnostic of Xtriage in
> terms of possible twinning? I am also wondering about a pseudo translation.
> Maybe try to re-processed your data in this direction.
>
> Hope to help.
>
> Nicolas
>
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9+33 (0)6 76 88 14 87 <+33%206%2076%2088%2014%2087>+33 
> (0)4 76 88 45 19 <+33%204%2076%2088%2045%2019>
>
> On 29/03/2017 17:56, Mark J van Raaij wrote:
>
> To be really convinced I think you should also compare the maps at 2.6 and
> 2.3 Å. If the 2.3 Å map looks better, go for it. If it doesn’t look better,
> perhaps you are adding noise, but the I/sigma and CC1/2 values suggest you
> aren’t.
> Perhaps try 2.5 and 2.4 Å also.
> And perhaps remove a well-ordered aa from the input model, refine at
> different resolutions and compare the difference maps for that aa. Or
> calculate omit maps at different resolutions and compare those.
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016>
> http://wwwuser.cnb.csic.es/~mjvanraaij
>
> On 29 Mar 2017, at 17:44, Phil Evans  wrote:
>
> It is not clear to me why you believe that cutting the resolution of the
> data would improve your model (which after all is the aim of refinement).
> At the edge CC(1/2) and I/sigI are perfectly respectable, and there doesn’t
> seem to be anything wrong with the Wilson plot. Th R-factor will of course
> be higher if you include more weak data, but minimising R is _not_ the aim
> of refinement. You should keep all the data
>
> I don’t know what xtriage means by “large number of outliers”: perhaps
> someone else can explain
>
> Phil
>
>
>
> On 29 Mar 2017, at 14:54, Juliana Ferreira de Oliveira <
> juliana.olive...@lnbio.cnpem.br> wrote:
>
> Hello,
> I have one dataset at 2.3 Å (probably it can be better, I/σ = 2.1 and
> CC1/2 = 0.779, the summary data is below), but when I perform Xtriage
> analysis it says that “There are a large number of outliers in the data”.
> The space group is P212121. When I refine the MR solution the Rfree stops
> around 30% and it doesn´t decrease (in fact if I continue refining it
> starts to increase).
> The Wilson plot graph is not fitting very well between 2.3 and 2.6 Å:
>
> 
>
> So I decided to cut the data at 2.6A and Xtriage analysis doesn’t notify
> about outliers anymore. I could refine the MR solution very well, the final
> Rwork is 0.2427 and Rfree = 0.2730 and validation on Phenix results in a
> good structure.
> I run Zanuda to confirm the space group and it says that the space group
> assignment seems to be correct.
> Do you think that I can improve my structure and solve it at 2.3 Å or
> better? Or I can finish it with 2.6 Å? To publish at 2.6 Å I need to
> justify the resolution cut, right? What should I say?
> Thank you for your help!
> Regards,
> Juliana
>
> Summary data:
> OverallInnerShell  OuterShell
> Low resolution limit  51.51  51.51
>   2.42
> High resolution limit  2.30 7.27
>2.30
> Rmerge   0.147
>   0.054   0.487
> Rmerge in top intensity bin0.080   -
>  -
> Rmeas (within I+/I-)  0.155   0.057
>   0.516
> Rmeas (all I+ & I-)0.155   0.057
>   0.516
> Rpim (within I+/I-)   

Re: [ccp4bb] Coot render tool missing

[Xiao Lei]

Hi All,

With Bernhard's help, I fixed this issue of render tool in Coot in Win7. I
summarize what I did here:

1.* - add C:\yourccp4installationdirectory\bin to PATH in the coot startup
script (runwincoot.bat in C:\yourwincootinstallationdirectory) *

 I use Notepad to open the .bat file and do edit:
set PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\libexec;%COOT_PREFIX%\
python27;%PATH%;*C:\CCP4-7\7.**0\bin*). My CCP4 installation folder is
C:\CCP4-7\7.0\bin. To locate files, I just simply use Win7 search file from
the start menu.







*2. - edit the raster3d.py file
(C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\)
from (line 44 or so):r3d_exe = find_exe("render", "PATH")tor3d_exe =
find_exe("render", "CCP4_BIN", "PATH")*

After I did this, Coot can find Raster3D PATH, but I still have an error of
"Some errors in Raster3D"  in terminal windows and fail to render.

*3. Download:*



*https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py
<https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py>and
replace the same file (maybe make a backup first) in
C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\*

*4. Done. Works!*


Thanks Bernhard!



On Wed, Mar 29, 2017 at 11:58 AM, Xiao Lei <xiaolei...@gmail.com> wrote:

> Hello B.,
>
> Works.Thank you very much!
>
> On Wed, Mar 29, 2017 at 8:14 AM, B.Lohkamp <b.lohk...@gmail.com> wrote:
>
>>
>> Hello,
>>
>> I see. Sorry. Now I remember this and I fixed this elsewhere too. Please
>> try the following. Download:
>>
>> https://raw.githubusercontent.com/bernhardcl/coot/master/pyt
>> hon/raster3d.py
>>
>> and replace the same file (maybe make a backup first) in
>> C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\
>>
>> This should work.
>>
>> Bernhard
>>
>> Hi B. ,
>>>
>>> I followed your suggestions and now Wincoot can find render.exe, but it
>>> has a warning message of "this copy of render was not built with tiff
>>> support BL Warning: some error in rester3D" .
>>>
>>> I attach the picture here. I'd appreciate if you have any idea of how to
>>> fix it.
>>>
>>> Thanks a lot.
>>>
>>> Inline image 1
>>>
>>> On Tue, Mar 28, 2017 at 12:54 AM, B.Lohkamp <b.lohk...@gmail.com
>>> <mailto:b.lohk...@gmail.com>> wrote:
>>>
>>>
>>> remove the % around the ccp4 path and you are set.
>>>
>>> B
>>>
>>> Hi Bernhard,
>>>
>>> Thank you for your help. I attach my runwincoot.bat below. My
>>> render.exe
>>> path is "C:\CCP4-7\7.0\bin". What should I do to add to the
>>> PATH? I
>>> could not understand the grammar well, should I add as :
>>> set
>>> PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\libexec;%COOT_PREFIX%\p
>>> ython27;%PATH%;%C:\CCP4-7\7.0\bin%
>>>   ?
>>> 
>>> 
>>> --
>>> @set LANG=en
>>> title WinCoot
>>>
>>>
>>> set COOT_PREFIX=C:\WinCoot
>>> set COOT_GUILE_PREFIX=C:/WinCoot
>>>
>>> set COOT_HOME=%COOT_PREFIX%
>>> set COOT_BACKUP_DIR=%COOT_PREFIX%\coot-backup
>>>
>>> set COOT_SHARE=%COOT_PREFIX%\share
>>> if not exist "%CLIBD_MON%" (
>>>   echo no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
>>>   set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
>>> )
>>> set COOT_SCHEME_DIR=%COOT_SHARE%/coot/scheme
>>> set COOT_STANDARD_RESIDUES=%COOT_SHARE%\coot\standard-residues.p
>>> db
>>> set COOT_PIXMAPS_DIR=%COOT_SHARE%\coot\pixmaps
>>> set COOT_RESOURCES_FILE=%COOT_SHARE%\coot\cootrc
>>> set COOT_DATA_DIR=%COOT_SHARE%\coot
>>> set COOT_REF_STRUCTS=%COOT_SHARE%\coot\reference-structures
>>> set COOT_PYTHON_DIR=%COOT_PREFIX%\python27\lib\site-packages\coo
>>> t
>>> set COOT_REF_SEC_STRUCTS=%COOT_SHARE%\coot\ss-reference-structur
>>> es
>>>
>>> set PYTHONHOME=%COOT_PREFIX%\python27
>>>
>>> set
>>> GUILE_LOAD_PATH=%COOT_GUILE_PREFIX%/share/guile/1.8;%COOT_GU
>>> I

Re: [ccp4bb] Coot render tool missing

[Xiao Lei]

Hi Ethan,

Thank you for the information. I have ccp4i installed on the same PC, the
error from Coot is "Couldn't find render in default path and PATH Shall we
search the whole disk?" If I click "Yes", then Coot freezes forever and I
need to force close it.

On Mon, Mar 27, 2017 at 2:18 PM, Ethan A Merritt <merr...@u.washington.edu>
wrote:

> On Monday, 27 March, 2017 22:12:22 Paul Emsley wrote:
> > On 27/03/17 21:55, Xiao Lei wrote:
> > >
> > >
> > > Because the picture quality from Coot>>Draw>>Screenshot>>Simple is
> > > very low, I tried Coot>>Draw>>Screenshot>>Povray or Raster3D to export
> > > high quality picture, but I had an error of "render tool missing" and
> > > Coot tried automatically find the render tool but failed. I use
> > > Wincoot 0.8 version in Win7. I do know if any of you have similar
> > > experience.
> > >
> > >
> >
> > The render program is part of Ethan Merritt's Raster3D package/suite.
> > The build system in coot that attempts to compile it is a bit fragile.
> >
> > http://skuld.bmsc.washington.edu/raster3d/
>
> That is the source package, yes.
>
> The Raster3D programs are now in the CCP4 bundle also.
> If render is not being found, you may have a PATH error.
> Is your Coot finding other CCP4 programs?
>
> Ethan
>
>
> >
> > Paul.
> >
> > p.s. Draw -> Additional Representation -> Ball & Stick makes things a
> > bit nicer, as does Extensions -> Representation -> Highlight Interesting
> > Site (still not as nice as a proper molecular graphics program though).
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
>

[ccp4bb] Coot render tool missing

[Xiao Lei]

Hi All,

Because the picture quality from Coot>>Draw>>Screenshot>>Simple is very
low, I tried Coot>>Draw>>Screenshot>>Povray or Raster3D to export high
quality picture, but I had an error of "render tool missing" and Coot tried
automatically find the render tool but failed. I use Wincoot 0.8 version in
Win7. I do know if any of you have similar experience.

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Xiao Lei]

Thanks Pavel,  is there a command that can tell secondary structure
assignment based on Rama plot of each residue beside phi and psi? for
example :
 A   2  ASN:56.93:-60.58:141.19:Favored:General   alpha helix
 A   3  ASN:48.44:-119.25:125.15:Favored:General  alpha helix

On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine  wrote:

> Trivial using command line. Example:
>
> - get a file from PDB:
>
> phenix.fetch_pdb 1yjp
>
> - get all phi/psi for all residues:
>
> phenix.ramalyze 1yjp.pdb
> residue:score%:phi:psi:evaluation:type
>  A   2  ASN:56.93:-60.58:141.19:Favored:General
>  A   3  ASN:48.44:-119.25:125.15:Favored:General
>  A   4  GLN:16.23:-126.16:112.81:Favored:General
>  A   5  GLN:55.13:-114.98:126.76:Favored:General
>  A   6  ASN:6.17:-116.42:97.69:Favored:General
> SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A where
> applicable)
> SUMMARY: 0.00% outliers (Goal: < 0.2%)
> SUMMARY: 100.00% favored (Goal: > 98%)
>
> Pavel
>
>
> On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty 
> wrote:
>
>> Alex
>>
>> It seems that nobody has answered your question. I'm not sure what you
>> can do in CCP4, but if I understand your question correctly, you can
>> perform a comprehensive validation in Phenix complete with Ramachandran
>> plot including clickable points relating to your residues which allow you
>> to see the residues in Coot.
>>
>> Happen to help further on the PHENIXBB or off-line.
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>
>> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee 
>> wrote:
>>
>>> Dear All,
>>>
>>> Is there a tool or software which can give Ramachandran information of
>>> individual residues in a plot?
>>>
>>> I used Coot to check for Ramachandran plots, but it shows all the
>>> residues in a coordinate I put in Coot, not individual one. I also use
>>> "residue info" in coot, it tells Ramachandran "phi psi" angles of
>>> individual residue, but it does not show it in a plot, only numbers.
>>>
>>> Thanks ahead for any input.
>>>
>>>
>>
>

Re: [ccp4bb] Positive densities map on selective residues on Coot

[Xiao Lei]

Hi Paul,

Thanks for the instructions! Works in my case.

On Mon, Mar 20, 2017 at 6:05 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:

> On 17/03/17 14:41, Xiao Lei wrote:
> >
> > In Coot, I could adjust the densities of map (2Fo-Fc in my case)
> > radius, but I'd like to show the density on selective residues, not
> > on the unselected part of structure, is there a way to do it?
>
> Yes.  Extensions -> Maps -> Mask Map by Atom Selection...
>
> After selecting your  model molecule, you will be asked about an Atom
> Selection
>
> use (for example)
>
> //A/20-30
>
> to mean residues 20 to 30 (inclusive) in the A chain.
>
> You will want to click the "Invert Masking" checkbutton.
>
> Masked maps often scroll "slowly" so increase (say to 0.5) the r.m.s.d.
> step in the Map Properties.
>
> Paul.
>
>

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Xiao Lei]

Hi Martin,

I followed your instructions and everything works. Thank you for your
illustration!

On Mon, Mar 20, 2017 at 3:52 AM, Martin Montgomery <m...@mrc-mbu.cam.ac.uk>
wrote:

> Hello,
>
> You need to tell pymol what to do with the map.
>
> Load your pdb file
> Load the map
>
> create an object with residues you wish to display the map around.  You
> can use the create command to do this or you can click on all the residues
> that you want to use in the main window then go to the object called (sele)
> in the right hand sidebar, click A and then copy to object.  This will
> create an object called obj01 with the selected residues.  You can rename
> this if you wish.
>
> Then you need to use the isomesh command to display the map.
>
>
> isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0
>
> mapname is the name you want to appear in the right hand sidebar for the
> mesh (can be the same as the mapfilename if you wish)
>
> mapfilename would be D83Vchimmap1 (from your screen shot).
>
> 2.5 is the sigma setting and carve=2.0 means the mesh is created within
> 2.0 Å of the selected atoms.  Adjust these values to suit.
>
> You might want to go back to go back and check your FFT log and look at
> the grid settings.  It is a good idea to re run the FFT job but double the
> grid values from the original job.
>
> It is all covered here:
>
> https://pymolwiki.org/index.php/Display_CCP4_Maps
>
> Regards
>
> MGM
>
> Martin G Montgomery
> ATP Synthase Group
> Medical Research Council Mitochondrial Biology Unit
> University of Cambridge
> Wellcome Trust/MRC Building
> Cambridge Biomedical Campus
> Hills Road
> Cambridge
> Great Britain
> CB2 0XY
>
> www.mrc-mbu.cam.ac.uk
>
>
>
>
>
>
> On 18 Mar 2017, at 10:43, Eleanor Dodson <eleanor.dod...@york.ac.uk>
> wrote:
>
> I think CCP4MG does this very selectively?
>
> Eleanor Dodson
>
> On 17 March 2017 at 17:03, Xiao Lei <xiaolei...@gmail.com> wrote:
>
>> Dear All,
>>
>> Thanks for the information.
>> I tried the way suggested by pymol wiki, but pymol fail to display the
>> map.
>> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map
>> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the
>> file extension .map.ccp4 to the generated output map. After open by pymol,
>> only a unit cell sign is shown (I attach here), no map is displayed.. I
>> use Pymol 1.8.X in Win7.
>>
>> Any further input is appreciated.
>>
>>
>>
>> .
>>
>>
>>
>>
>> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei <xiaolei...@gmail.com> wrote:
>>
>>> Dear All,
>>>
>>> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
>>> but I'd like to show the density on selective residues, not on the
>>> unselected part of structure, is there a way to do it? I am using WinCoot
>>> 0.81.
>>>
>>> In addition, could Pymol do it?
>>>
>>> Thanks ahead!
>>>
>>
>>
>
>

[ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Xiao Lei]

Dear All,

In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
but I'd like to show the density on selective residues, not on the
unselected part of structure, is there a way to do it? I am using WinCoot
0.81.

In addition, could Pymol do it?

Thanks ahead!

[ccp4bb] Refmac twin refine works for Amplitude based but not Intensity based

[Xiao Lei]

Dear CCP4bb members,

I have a dataset of 3A, twinned data (twin fraction 0.15) set of space
group P6222, I solved the structure by phaser (TFZ>10, LLG>1000) with space
group P32 and build model to Rfree/R 30% 26%.  I then tried twin refinement
in Refmac, after I tried amplitude based refine the Rfree/R drops to 24%
17% with output files of .mtz map, .pdb and .cif. Everything is normal in
amplitude based refine.

I also tried intensity based twin refine, the log of Refmac shows the
process is successful (I attach below) but only .cif is in output, I could
not find .mtz and .pdb (I even check the path but I still could not find
the files), in addition, there is no report of Rfree/R in the results panel:

**

* Information from CCP4Interface script

***

Writing final coordinates (XYZOUT) to XXX.pdb

***

***

* Information from CCP4Interface script

***

Writing final phases (HKLOUT) to XXX.mtz

***

#CCP4I TERMINATION STATUS 1

#CCP4I TERMINATION TIME 02 Mar 2017  18:10:04

#CCP4I TERMINATION OUTPUT_FILES  XXX.cif

#CCP4I MESSAGE Task completed successfully


Is this a bug? I use CCP4 7.0.030 in ubuntu.

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Hi All,

Just share my experience, Windows 10 works for pymol 3D under Quadro M4000
with Nvidia 3D kit (no need to connect the 3 pin MINI DIN, Quadro M4000
does not have 3 pin Mini DIN connections). I use Asus 24 inch 3D monitor,
connect the monitor with display port to display port of Quadro M4000, no
active DP to DVI needed in my case. We have a problem for Coot 3D works
even when Pymol 3D works ok, we are trying to figure out the problem but
Windows 10 does work for pymol 3D under DP to DP port.

On Tue, Jan 31, 2017 at 6:39 AM, Yong Wang <wang_yon...@lilly.com> wrote:

> Xiao,
>
>
>
> I had a direct connection from display port to display port that had
> worked for several years (Windows 7).  Since last year I have been losing
> the stereo.  Often the control panel won’t show the 120 Hz like what you
> saw.  Sometimes I was able to forcefully add a 120 Hz resolution (using the
> “Customize …” menu).  But it was not stable, i.e. the stereo would stay for
> some time then disappear and go back to the state of not having 120 Hz.  I
> have not had time to investigate further into this but I suspect a driver
> issue here.  You may want to check the drivers for both the graphics card
> and the monitor.
>
>
>
> Yong
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Monday, January 30, 2017 11:50 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> Taka,
>
>
>
> I really appreciate this information! I do have Displayport cable and can
> connect the card and Asus VG248QE both via the DP cable, somehow on the
> Nvidia control panel in Windows 10, I do not have an option of choosing
> "120HZ" or "144Hz", I only have option choosing "60Hz" or below, which
> sounds weird to me. Windows 10 should make things easier not harder. If
> CentOS 6 works then Windows 10 should work, I guess I have to go back to
> Windows 7 if needed, but as I already ordered the DP to DVI active cable,
> I'll test this cable first and update CCP4bb later.
>
>
>
> On Mon, Jan 30, 2017 at 7:50 PM, <fukami...@chugai-pharm.co.jp> wrote:
>
> Xiao,
>
>
>
> If you connect the board and monitor by DisplayPort cable directly, it
> should work.
>
> I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not
> tested on Windows.
>
>
>
> Taka
>
>
>
> *From:* Xiao Lei [mailto:xiaolei...@gmail.com]
> *Sent:* Tuesday, January 31, 2017 10:08 AM
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> I changed my mind, I should order the usb- powered DP to DVI dual link...
>
>
>
> On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee <chr...@gmail.com> wrote:
>
> Hi Xiao,
>
>
>
> I can confirm you need to buy an active adapter if you want to convert the
> display port on the graphics card to DVI. The one that they supply with the
> graphics card is passive and won't work. I was in the same boat about a
> year ago. I bought a USB powered active adapter which allowed 120htz. My
> monitor only had DVI input so I didn't try a direct display port
> connection. I can't comment on why that didn't work.
>
>
>
> Cheers
>
> Christine
>
>
>
> Sent from my iPhone
>
>
> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami <fukami...@chugai-pharm.co.jp>
> wrote:
>
> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *Xiao Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>
>
>
>
>

[ccp4bb] Phaser MR pairwise percent packing criterion

[Xiao Lei]

Dear CCP4bb members,

I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7),
there is no "allow maximal clash..." option anymore. There are only two
options "pairwise percent packing" and "accept all solutions".  I used to
increase the number in the "allow maximal clash" (let's say from 100 to
200) to do MR and this works fine in a couple of cases.

With the new Phaser version, I could not do this anymore, can I understand
that I just need to increase the pairwise percent packing cutoff (let's say
from 5% to 10%) to loose the tight packing criteria and allow more clashes
in finding solutions?

Re: [ccp4bb] iMosflm twist large variance and specific space group scale output

[Xiao Lei]

Dr. Harry,

Thank you very much for the illustration!

On Wed, Feb 15, 2017 at 2:07 PM, Harry Powell <ha...@mrc-lmb.cam.ac.uk>
wrote:

> Hi
>
> First things first...
>
> 2. I am not sure if iMosflm can be set to output the scale of specific
> space group. For example, in my data set even though the integration is
> done at P321 space group, after click "quick symm" or "quick scale" it
> seems the program automatically choose what it thinks the most likely space
> group P6222, not P321, I know in HKL2000 there is an option to choose
> specific group and scale it, how to do this in iMosflm? I'd like to scale
> the data to P321 and some subgroups in P3 but not P6222.
>
>
> Yes, easily done. In the Indexing task, at the bottom left where iMosflm
> chooses the space group for you, there's a drop-down where you can pick any
> of the chiral trigonal or hexagonal space groups. You could even, if you
> wanted, type in any of the achiral space groups and that would work too.
>
> HOWEVER, unless you are using the Strategy option, I really wouldn't
> bother doing this (most of the time). The *measured* reflections for both
> trigonal and hexagonal space groups are the in the same places and the
> extra symmetry you would have from hexagonal is ignored in the integration.
> The QuickScale option will let Pointless do its job and give you a better
> analysis of the true symmetry and also apply the symmetry to your MTZ file
> (Pointless will use the intensities in its calculations, which is not
> something that Mosflm does).
>
> Importing the output MTZ file from iMosflm (if you haven't run QuickScale)
> into either ccp4i or ccp4i2 will also run Pointless and try to sort out
> your symmetry for you.
>
> Does  this mean if I see twist variance greater than "1" then I need to
> fix both "tilt' and "twist" value before integration in imosflm?
>
>
> Yes, generally speaking if you fix tilt you would probably want to fix
> twist as well.
>
> In my case the variance is greater than 0.5 but less than 1, do I still
> need to fix both "tilt" and "twist" value
>
>
> Maybe, probably. It's hard to be definitive without seeing the graphs from
> integration or the full log file output.
>
> Try it and see if the merging stats look better...
>
> Harry
> --
> Dr Harry Powell
> Chairman of International Union of Crystallography Commission on
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
> On 15 Feb 2017, at 16:36, Xiao Lei <xiaolei...@gmail.com> wrote:
>
> Dear CCP4bb members,
>
> I have two questions about imosflm integration and scaling process (my
> data is 3A resolution and 0.5 degree mosaicity):
>
> 1. I have warnings after integration saying the twist variance is too
> large (from -0.26 to 0.33, which is larger than 0.5), suggesting that cell
> parameters may be wrong, and reindex to the right space group may be
> needed. After I read the imosflm tutorials from internet, the tutorials
> says "For weak images the tilt and twist may not be well defined, and might
> refine to large values (greater than one degree). In such cases these
> parameters should be fixed. It is not generally recommended to fix any
> other detector parameters."
>
> Does  this mean if I see twist variance greater than "1" then I need to
> fix both "tilt' and "twist" value before integration in imosflm?   In my
> case the variance is greater than 0.5 but less than 1, do I still need to
> fix both "tilt" and "twist" value?
>
> 2. I am not sure if iMosflm can be set to output the scale of specific
> space group. For example, in my data set even though the integration is
> done at P321 space group, after click "quick symm" or "quick scale" it
> seems the program automatically choose what it thinks the most likely space
> group P6222, not P321, I know in HKL2000 there is an option to choose
> specific group and scale it, how to do this in iMosflm? I'd like to scale
> the data to P321 and some subgroups in P3 but not P6222.
>
>
> Thanks for any inputs.
>
>
>

[ccp4bb] iMosflm twist large variance and specific space group scale output

[Xiao Lei]

Dear CCP4bb members,

I have two questions about imosflm integration and scaling process (my data
is 3A resolution and 0.5 degree mosaicity):

1. I have warnings after integration saying the twist variance is too large
(from -0.26 to 0.33, which is larger than 0.5), suggesting that cell
parameters may be wrong, and reindex to the right space group may be
needed. After I read the imosflm tutorials from internet, the tutorials
says "For weak images the tilt and twist may not be well defined, and might
refine to large values (greater than one degree). In such cases these
parameters should be fixed. It is not generally recommended to fix any
other detector parameters."

Does this mean if I see twist variance greater than "1" then I need to fix
both "tilt' and "twist" value before integration in imosflm?   In my case
the variance is greater than 0.5 but less than 1, do I still need to fix
both "tilt" and "twist" value?

2. I am not sure if iMosflm can be set to output the scale of specific
space group. For example, in my data set even though the integration is
done at P321 space group, after click "quick symm" or "quick scale" it
seems the program automatically choose what it thinks the most likely space
group P6222, not P321, I know in HKL2000 there is an option to choose
specific group and scale it, how to do this in iMosflm? I'd like to scale
the data to P321 and some subgroups in P3 but not P6222.


Thanks for any inputs.

Re: [ccp4bb] Coot and pymol 3D for Centos 7?

[Xiao Lei]

for Linux you need the 3-pin mini Din connectors

On Tue, Jan 31, 2017 at 8:29 AM, Jun Dong  wrote:

> I have made coot and pymol 3D work with NVIDIA Quadro K5200 under Windows
> 7 but I could not make it work under Centos 7. WinCoot was not able to load
> big virus maps, it crashed all the time. I really want to make coot 3D work
> under Centos 7. Has anybody succeeded at running coot 3D in Centos 7?
> Jun
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Taka,

I really appreciate this information! I do have Displayport cable and can
connect the card and Asus VG248QE both via the DP cable, somehow on the
Nvidia control panel in Windows 10, I do not have an option of choosing
"120HZ" or "144Hz", I only have option choosing "60Hz" or below, which
sounds weird to me. Windows 10 should make things easier not harder. If
CentOS 6 works then Windows 10 should work, I guess I have to go back to
Windows 7 if needed, but as I already ordered the DP to DVI active cable,
I'll test this cable first and update CCP4bb later.

On Mon, Jan 30, 2017 at 7:50 PM, <fukami...@chugai-pharm.co.jp> wrote:

> Xiao,
>
>
>
> If you connect the board and monitor by DisplayPort cable directly, it
> should work.
>
> I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not
> tested on Windows.
>
>
>
> Taka
>
>
>
> *From:* Xiao Lei [mailto:xiaolei...@gmail.com]
> *Sent:* Tuesday, January 31, 2017 10:08 AM
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> I changed my mind, I should order the usb- powered DP to DVI dual link...
>
>
>
> On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee <chr...@gmail.com> wrote:
>
> Hi Xiao,
>
>
>
> I can confirm you need to buy an active adapter if you want to convert the
> display port on the graphics card to DVI. The one that they supply with the
> graphics card is passive and won't work. I was in the same boat about a
> year ago. I bought a USB powered active adapter which allowed 120htz. My
> monitor only had DVI input so I didn't try a direct display port
> connection. I can't comment on why that didn't work.
>
>
>
> Cheers
>
> Christine
>
>
>
> Sent from my iPhone
>
>
> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami <fukami...@chugai-pharm.co.jp>
> wrote:
>
> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *Xiao Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

I changed my mind, I should order the usb- powered DP to DVI dual link...

On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee <chr...@gmail.com> wrote:

> Hi Xiao,
>
> I can confirm you need to buy an active adapter if you want to convert the
> display port on the graphics card to DVI. The one that they supply with the
> graphics card is passive and won't work. I was in the same boat about a
> year ago. I bought a USB powered active adapter which allowed 120htz. My
> monitor only had DVI input so I didn't try a direct display port
> connection. I can't comment on why that didn't work.
>
> Cheers
> Christine
>
>
> Sent from my iPhone
>
> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami <fukami...@chugai-pharm.co.jp>
> wrote:
>
> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *Xiao Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

OK thanks, I'll update!

On Mon, Jan 30, 2017 at 4:57 PM,  wrote:

> Dear Xiao,
>
>
>
> I think it would work, though I'm not sure because it's smaller and
> cheaper than what I used (https://www.amazon.co.uk/
> Dell-BizLink-DisplayPort-Adapter-Powered/dp/B003XYBA72), which have
> worked well since I bought them 5 years ago, though some of them broke in 2
> or 3 years.
>
>
>
> Please let us know if you succeed with the cheaper one.
>
>
>
> Regards,
>
>
>
>
>
> *Sent:* Tuesday, January 31, 2017 9:41 AM
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> Dear Taka,
>
>
>
> Thank you for the information! For the active converter from DP to DVI, is
> it something like  StarTech.com DisplayPort to DVI Active Adapter (
> https://www.amazon.com/StarTech-com-DP2DVIS-DisplayPort-Active-Adapter/dp/
> B004SUO1GM) ?
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Dear Taka,

Thank you for the information! For the active converter from DP to DVI, is
it something like  StarTech.com DisplayPort to DVI Active Adapter (
https://www.amazon.com/StarTech-com-DP2DVIS-DisplayPort-Active-Adapter/dp/B004SUO1GM)
?

On Mon, Jan 30, 2017 at 4:25 PM, <fukami...@chugai-pharm.co.jp> wrote:

> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>

[ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Dear All,

I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
M4000 graphics card, the card has four displayport. I also has a Asus 24
inch 3D monitor. I tried to connect  the graphics card with the monitor
through displayport to displayport connection and displayport to DVI-D dual
link connection but failed to set the monitor run on 120Hz. It seems I have
to follow the old way of using  DVI-D dual link connection for both graphic
card and monitor, but the problem is that the graphics card does not have a
DVI-D dual link socket, it only have displayport.

I appreciate any suggestions.

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Xiao Lei]

Thanks Nicolas and Paul!  I am using active 3D with Quadro 5000 graphics
card and Nvidia 3D kit in Fedora system (Fedora 23). Everytime I update the
kernel (dnf update), I lost the 3D in both the updated new kernel and the
old kernel, I have to reinstall the driver again, but can not make every
reinstallation to the newest kernel successful. It seems Ubuntu Mate and
Xubuntu will be very good alternatives.

On Tue, Dec 20, 2016 at 8:33 AM, Nicolas FOOS  wrote:

> Dear Paul,
>
> I am currently not working under Ubuntu OS, so I can't try your fix.
>
> But if my memory is still good, it was exactly the problem (the dynamic
> menus). And I am sure that some ccp4bb reader will be happy to find and try
> this solution.
>
> Thank you.
>
> Nicolas
>
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9
> +33 (0)6 76 88 14 87
> +33 (0)4 76 88 45 19
>
> On 20/12/2016 17:26, Paul Emsley wrote:
>
>> On 20/12/16 16:21, Nicolas FOOS wrote:
>>
>>> Dear Lei,
>>>
>>> I already try :
>>>
>>> Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had
>>> problem with coot due to unity desktop).
>>>
>>
>> A shot in the dark, but maybe your problem is with dynamic menus?
>>
>> If so, try this:
>>
>>
>> $ export UBUNTU_MENUPROXY=0
>>
>> before running coot.
>>
>>
>> Paul
>>
>

[ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Xiao Lei]

Hi All,

I am asking if anyone used Ubuntu Mate operating system and is this system
good for Pymol and Coot 3D?

Re: [ccp4bb] Refmac5 update water option

[Xiao Lei]

Got it. Thank you very much Christian!

On Fri, Dec 16, 2016 at 12:14 PM, Christian Roth <christianroth...@gmail.com
> wrote:

> Hi,
>
> the adding water option is basically a COOT script to find waters, which
> get subsequently refined. There is no automatic evaluation and deletion of
> waters based on certain criteria. That you have to do manually. You can
> always try to automatically add new waters, which is done by this option in
> later refinement runs of course, but that doesn't "touch" the waters
> previously added to the model.
>
> Cheers
>
> Christian
>
> Am 16.12.2016 um 19:50 schrieb Xiao Lei:
>
> Dear CCP4bb members,
>
> Does Refmac5 in CCP4i have an option of adding waters to the refined
> structure (the input coordinate does not have any water)?  I see in Phenix
> refine there is an option of "update water", I tried to look for this
> option in Refmac5 but I could not find it. I am using CCP4i 7.0.025 version.
>
>
>

[ccp4bb] Refmac5 update water option

[Xiao Lei]

Dear CCP4bb members,

Does Refmac5 in CCP4i have an option of adding waters to the refined
structure (the input coordinate does not have any water)?  I see in Phenix
refine there is an option of "update water", I tried to look for this
option in Refmac5 but I could not find it. I am using CCP4i 7.0.025 version.

[ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

[Xiao Lei]

Hi All,


I have an x ray diffraction dataset of protein and dna complex processed
with pointless and I am trying to get the resolution cut for this data, the
result is below, I do not know why in the N=23 (Dmid=3.68) bin, there is no
statistic of CC(1/2), N_cc, CCfit, etc?  The program just put a "-" sign
into it.  I guess if this means something bad probably I have to cut the
resolution to 3.7A.


$TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution:

$GRAPHS:Resolution estimate 3.89A:0.000213587|0.0981986x0|1:2,4,6,7,9:

 $$

  N  1/d^2Dmid CC(1/2)   N_CC   CCfit  Mn(I/sigI)  N (I/sigI)/10   $$ $$

  1  0.0018  23.27   0.939 51   0.990   92.43142   9.243

  2  0.0051  13.99   0.993210   0.987   72.33607   7.233

  3  0.0084  10.92   0.984323   0.984   61.77937   6.177

  4  0.0116   9.27   0.974344   0.981   54.77   1030   5.477

  5  0.0149   8.19   0.969486   0.976   29.98   1412   2.998

  6  0.0182   7.42   0.961491   0.971   13.24   1459   1.324

  7  0.0214   6.83   0.879535   0.9648.75   1558   0.875

  8  0.0247   6.36   0.885597   0.9566.70   1755   0.670

  9  0.0280   5.98   0.939693   0.9477.16   2003   0.716

 10  0.0312   5.66   0.807697   0.9354.97   2042   0.497

 11  0.0345   5.38   0.815757   0.9215.53   2195   0.553

 12  0.0378   5.15   0.910878   0.9046.08   2547   0.608

 13  0.0410   4.94   0.913890   0.8847.49   2582   0.749

 14  0.0443   4.75   0.906934   0.8617.42   2710   0.742

 15  0.0476   4.58   0.824976   0.8345.06   2695   0.506

 16  0.0508   4.44   0.812   1010   0.8025.32   2859   0.532

 17  0.0541   4.30   0.843   1099   0.7675.25   3126   0.525

 18  0.0574   4.17   0.862   1030   0.7274.49   2790   0.449

 19  0.0606   4.06   0.752   1115   0.6833.04   2927   0.304

 20  0.0639   3.96   0.675439   0.6362.53   1117   0.253

 21  0.0672   3.86   0.139176   0.5861.64393   0.164

 22  0.0704   3.77   0.734   1082   0.5342.65   2641   0.265

 23  0.0737   3.68- -----

 24  0.0770   3.60   0.489681   0.4292.20   1633   0.220

 25  0.0802   3.53   0.358   1430   0.3781.85   3248   0.185

 26  0.0835   3.46  -0.428 12   0.3301.38 22   0.138

 27  0.0868   3.39   0.390663   0.2851.73   1404   0.173

 28  0.0900   3.33   0.128   1443   0.2441.39   2946   0.139

 29  0.0933   3.27   0.149   1372   0.2071.37   2835   0.137

 30  0.0966   3.22   0.183   1578   0.1751.40   3202   0.140


Thanks ahead.

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

[Xiao Lei]

We are using Fedora system for pymol and coot 3D. I prefer Mac OSX, but I
have no way of making 3D environment for pymol and coot 3D, I'd like to
know if any lab make the 3D environment work for Mac OS X system.

On Sat, Oct 15, 2016 at 7:45 AM, Robert Oeffner  wrote:

> We build Phenix on all three platforms, i.e. Windows, Linux and MacOSX.
> Microsoft provides great C/C++compilers for free on Windows. One minor
> issue though is that since our software uses Python 2.7 binary
> compatibility with the python2.7 installer requires that the rest of Phenix
> is built with the older VS2008 compiler. That edition doesn't support the
> latest bells and whistles of esoteric C++ language features but this is not
> a showstopper.
>
> Rob
>
>
> Subject:  Re: Structural biology software that does not run on Windows or
> gives important Windows-specific problems
> From:  Patrick Loll 
> Date:  Fri, 14 Oct 2016 12:31:54 -0400
>
> How about the ability to compile code? Are there decent compilers readily
> available for Windows? I like being able to write & compile the occasional
> fortran program {hic sunt dinosaurs}, and it’s easy to do this on a
> unix-based platform like OSX.
>
> If your reasoned arguments fail, I have found that many institutions'
> information technology administrators are easily intimidated by a few
> random references to unix (Rsync! Grep! Bash!). Such words seem to function
> as charms that keep evil spirits (i.e. IT administrators) at bay.
>
> > On 14 Oct 2016, at 11:14 AM, Mark J van Raaij 
> wrote:
> >
> > Dear All,
> >
> > our institution requires me to provide a reasoning not to buy a Windows
> computer (I want to buy a new MacOSX system), so I am looking for software
> that does not run or is limited on Windows.
> >
> > Not available:
> > (Auto)SHARP
> > ARPWARP
> >
> > Available on Windows but with significant limitations
> > Phenix (no MR-Rosetta, no parallelization)
> > CCP4 (limitations on file-names)
> >
> > Please correct me if pertinent and provide additional examples if
> possible.
> >
> > Gratefully yours,
> >
> > Mark
> >
> > Mark J van Raaij
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > calle Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://wwwuser.cnb.csic.es/~mjvanraaij
>

[ccp4bb] Alternative ways to get electron density map other than EDS server

[Xiao Lei]

Hi All,

I am trying to get electron density map of some pdb structures, I know
there is a database called Electron density server (EDS
http://eds.bmc.uu.se/eds). But somehow these days I can not connect to the
website and I keep getting the This webpage is not available message in
my browser (Internet connection is ok).  I also tried to go to PDB
databank, search a structure and click EDS link, but this did not connect
to the server neither.

Are there other ways to get electron density maps?

Thanks.


Xiao

Re: [ccp4bb] OS X yosemite

[Xiao Lei]

Hi Mirek,

I have to reinstall xquartz to get my ccp4 and coot working after upgrading
to Yosemite from Mavericks.

Xiao

On Tue, Mar 17, 2015 at 4:30 PM, Cygler, Miroslaw miroslaw.cyg...@usask.ca
wrote:

  Hi,
 I am thinking of upgrading the os on my mac to Yosemite. Are there any
 known issues for crystallographic software that I should pay attention to?
 Thanks,

 Mirek

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

[Xiao Lei]

Hi Marc,

I have a Macbook pro Mid 2009 model (with integrated graphics card) and I
can run coot and pymol without any problem ( I haven't tested on Chimera),
I do not think a discrete graphics is needed. However, for pymol I can not
use the stereo function. I do not know if the discrete graphic card is
needed for this function.

Xiao

On Tue, Mar 17, 2015 at 1:12 PM, Marc Graille 
marc.grai...@polytechnique.edu wrote:

 Hello,

 I would like to buy a MacBook Pro laptop that will allow me among others
 to solve structures, build models and visualize electron density maps using
 Pymol, Coot or Chimera.
 I have the choice between between Intel Iris Pro (5200 series) and Intel Iris
 Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is
 fine for the programs I want to run.
 Can some of you share advices/feedback with me?

 Thanks a lot for your answer.

 Best wishes,

 Marc


 Dr Marc GRAILLE

 Directeur de recherche CNRS

 Team: Translation and degradation of eukaryotic mRNAs

 Team supported by the ATIP-Avenir CNRS program

 Laboratoire de Biochimie

 ECOLE POLYTECHNIQUE - UMR7654 CNRS

 91128 PALAISEAU CEDEX

 Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09

 Office 033012B

 Email: marc.grai...@polytechnique.edu

 http://bioc.polytechnique.fr/spip.php?rubrique117

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

[Xiao Lei]

Hi Randy,
Thank you very much for the advice. I use CCP4 version 6.4.0 on my Mac OS X
10.10.1, after my updating my Mac OS X to 10.10.1 three weeks ago, I did
have a issue to open CCP4, I have to re-install X-Quartz and after that I
can open CCP4 well. I haven't updated CCP4 to 6.5, maybe I should update to
6.5 because of somehow I may have a bug on my CCP4 as you said.

Xiao


On Tue, Jan 13, 2015 at 1:04 AM, Randy Read rj...@cam.ac.uk wrote:

 Hi,

 Since you posted the whole data set to the BB (a link to a file-sharing
 website might have been better), I took a look at it with other tools.
 Perhaps I’m running a later version of phenix.xtriage, as in my hands a
 moderate amount of anisotropy is found.  Similarly, Phaser finds a moderate
 amount of anisotropy.

 I suspect what you have uncovered here is a bug in the version of
 ctruncate that you were using, leading to the negative eigenvalues.  Your
 data set is relatively incomplete, and the incompleteness itself is highly
 anisotropic, which can be seen for instance with hklview in CCP4.  However,
 I’m not getting the same results, using version 1.15.10 of ctruncate from
 CCP4-6.4 on a Mac (I haven’t updated yet to 6.5).  Which version of
 ctruncate and which operating system were you using?

 Best wishes,

 Randy Read

 -
 Randy J. Read
 Department of Haematology, University of Cambridge
 Cambridge Institute for Medical ResearchTel: +44 1223 336500
 Wellcome Trust/MRC Building Fax: +44 1223 336827
 Hills Road
 E-mail: rj...@cam.ac.uk
 Cambridge CB2 0XY, U.K.
 www-structmed.cimr.cam.ac.uk

 On 13 Jan 2015, at 00:34, Xiao Lei xiaolei...@gmail.com wrote:

  Hi Eleanor,
 
  Thank you for the advice.  The .sca file is here. The data may not be
 useful as you said, but the anisotropic analysis for this data is
 confusing. From the phenix xtriage output, it seems the data has no
 anisotropic issue (I may interpret wrong the log file, I attach part of the
 xtriage log file here). But from CCP4, I know the data has anisotropic
 problem (Negative Eigenvalues).
 
  Below is part of log file from Phenix.
 
  Anisotropy analyses 
 
  Anisotropy( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) :  3.233e-01
Anisotropic ratio p-value :  0.000e+00
 
   The p-value is a measure of the severity of anisotropy as observed
 in the PDB.
   The p-value of 0.000e+00 indicates that roughly 100.0 % of datasets
 available in the PDB have
   an anisotropy equal to or worse than this dataset.
 
  Xiao
 
  On Sun, Jan 11, 2015 at 7:51 AM, Eleanor Dodson 
 eleanor.dod...@york.ac.uk wrote:
  Well - I really need to see the output.sca file with the reflection list
 to test the problem properly, but this log file does show your reflections
 at the highest resolution are very weak, and maybe not useful. Try cutting
 the resolute a bit and see what happens.
  Eleanor
 
  On 11 January 2015 at 00:08, Xiao Lei xiaolei...@gmail.com wrote:
  Hi Eleanor,
 
  Thanks for the input, I attach the scale log file here.
 
  On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson 
 eleanor.dod...@york.ac.uk wrote:
  Certainly a negative eigen value is bad - can you attach the data? There
 may be some obvious problem..
  Eleanor
 
  On 10 January 2015 at 04:42, Xiao Lei xiaolei...@gmail.com wrote:
  Dear All,
 
  I tried to convert my x-ray diffraction sca data from HKL200 (.sca file)
 to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should
 I supposed to do next to correct the problem, any suggestions are
 appreciated. I pasted the message from part of log file below:
 
 
  ANISOTROPY ANALYSIS (using intensities):
 
 
  Eigenvalues: -0.5668 0.1479 0.3584
 
  Eigenvalue ratios: -1.5815 0.4128 1.
 
  ctruncate: Anisotropy correction failed - negative eigenvalue.
 
  Times: User: 0.4s System: 0.0s Elapsed: 0:00
 
 
 ***
 
  * Information from CCP4Interface script
 
 
 ***
 
  The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate
 -hklin /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp -hklout
 /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp -colin
 /*/*/\[IMEAN,SIGIMEAN\] -colout P1_12
 
  has failed with error message
 
  ctruncate: Anisotropy correction failed - negative eigenvalue.
 
  ObjectCache: Leaked 0005 refs to
 
 
 ***
 
 
 
  #CCP4I TERMINATION STATUS 0  ctruncate:  Anisotropy correction failed -
 negative eigenvalue. ObjectCache: Leaked 0005 refs to
 
  
 
  #CCP4I TERMINATION TIME 09 Jan 2015  19:55:50
 
  #CCP4I MESSAGE Task failed
 
 
 
 
 
 
  P1_12_P1_rej2.6_output.sca

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

[Xiao Lei]

Hi Evans,

Thank you very much for the suggestions! I'll post my data on an online
file sharing system from now on.

Xiao

On Tue, Jan 13, 2015 at 5:21 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:

 It is hard to tell without having the unmerged data (don't post that to
 the BB), but running the data through Pointless, Aimless ctruncate (though
 I had to fix Aimless) suggests

 1. the data are not very good
 2. the space group may be C2
 3. it may be twinned (or just some spot overlap with the long 288A c axis)

 Phil

 On 13 Jan 2015, at 00:34, Xiao Lei xiaolei...@gmail.com wrote:

  Hi Eleanor,
 
  Thank you for the advice.  The .sca file is here. The data may not be
 useful as you said, but the anisotropic analysis for this data is
 confusing. From the phenix xtriage output, it seems the data has no
 anisotropic issue (I may interpret wrong the log file, I attach part of the
 xtriage log file here). But from CCP4, I know the data has anisotropic
 problem (Negative Eigenvalues).
 
  Below is part of log file from Phenix.
 
  Anisotropy analyses 
 
  Anisotropy( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) :  3.233e-01
Anisotropic ratio p-value :  0.000e+00
 
   The p-value is a measure of the severity of anisotropy as observed
 in the PDB.
   The p-value of 0.000e+00 indicates that roughly 100.0 % of datasets
 available in the PDB have
   an anisotropy equal to or worse than this dataset.
 
  Xiao
 
  On Sun, Jan 11, 2015 at 7:51 AM, Eleanor Dodson 
 eleanor.dod...@york.ac.uk wrote:
  Well - I really need to see the output.sca file with the reflection list
 to test the problem properly, but this log file does show your reflections
 at the highest resolution are very weak, and maybe not useful. Try cutting
 the resolute a bit and see what happens.
  Eleanor
 
  On 11 January 2015 at 00:08, Xiao Lei xiaolei...@gmail.com wrote:
  Hi Eleanor,
 
  Thanks for the input, I attach the scale log file here.
 
  On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson 
 eleanor.dod...@york.ac.uk wrote:
  Certainly a negative eigen value is bad - can you attach the data? There
 may be some obvious problem..
  Eleanor
 
  On 10 January 2015 at 04:42, Xiao Lei xiaolei...@gmail.com wrote:
  Dear All,
 
  I tried to convert my x-ray diffraction sca data from HKL200 (.sca file)
 to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should
 I supposed to do next to correct the problem, any suggestions are
 appreciated. I pasted the message from part of log file below:
 
 
  ANISOTROPY ANALYSIS (using intensities):
 
 
  Eigenvalues: -0.5668 0.1479 0.3584
 
  Eigenvalue ratios: -1.5815 0.4128 1.
 
  ctruncate: Anisotropy correction failed - negative eigenvalue.
 
  Times: User: 0.4s System: 0.0s Elapsed: 0:00
 
 
 ***
 
  * Information from CCP4Interface script
 
 
 ***
 
  The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate
 -hklin /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp -hklout
 /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp -colin
 /*/*/\[IMEAN,SIGIMEAN\] -colout P1_12
 
  has failed with error message
 
  ctruncate: Anisotropy correction failed - negative eigenvalue.
 
  ObjectCache: Leaked 0005 refs to
 
 
 ***
 
 
 
  #CCP4I TERMINATION STATUS 0  ctruncate:  Anisotropy correction failed -
 negative eigenvalue. ObjectCache: Leaked 0005 refs to
 
  
 
  #CCP4I TERMINATION TIME 09 Jan 2015  19:55:50
 
  #CCP4I MESSAGE Task failed
 
 
 
 
 
 
  P1_12_P1_rej2.6_output.sca

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

[Xiao Lei]

Hi Vaheh,

Thank you for point out this. You are right, the crystal is a plate and
somehow at certain angles the frames even failed index, I see a lot of
rejection spots when integration. From all the suggestions I got so far, I
think I have to grow better crystals and try better collecting data
strategies next time.

Xiao

On Tue, Jan 13, 2015 at 6:35 AM, Oganesyan, Vaheh oganesy...@medimmune.com
wrote:

  I might be completely wrong here but doesn’t it bother that the number
 of rejected reflections shown in log file is ~83000? It shows, at least to
 me, that either indexing step is far from being correct or crystal is not
 really good enough due to defects.







 *Vaheh Oganesyan*

 *www.medimmune.com http://www.medimmune.com*



 *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
 Lei
 *Sent:* Saturday, January 10, 2015 7:08 PM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction
 failed



 Hi Eleanor,



 Thanks for the input, I attach the scale log file here.



 On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson eleanor.dod...@york.ac.uk
 wrote:

 Certainly a negative eigen value is bad - can you attach the data? There
 may be some obvious problem..

 Eleanor



 On 10 January 2015 at 04:42, Xiao Lei xiaolei...@gmail.com wrote:

 Dear All,



 I tried to convert my x-ray diffraction sca data from HKL200 (.sca file)
 to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should
 I supposed to do next to correct the problem, any suggestions are
 appreciated. I pasted the message from part of log file below:




 ANISOTROPY ANALYSIS (using intensities):


 Eigenvalues: -0.5668 0.1479 0.3584

 Eigenvalue ratios: -1.5815 0.4128 1.

 ctruncate: Anisotropy correction failed - negative eigenvalue.

 Times: User: 0.4s System: 0.0s Elapsed: 0:00

 ***

 * Information from CCP4Interface script

 ***

 The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate
 -hklin /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp -hklout
 /LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp -colin
 /*/*/\[IMEAN,SIGIMEAN\] -colout P1_12

 has failed with error message

 ctruncate: Anisotropy correction failed - negative eigenvalue.

 ObjectCache: Leaked 0005 refs to

 ***



 #CCP4I TERMINATION STATUS 0  ctruncate:  Anisotropy correction failed -
 negative eigenvalue. ObjectCache: Leaked 0005 refs to

 

 #CCP4I TERMINATION TIME 09 Jan 2015  19:55:50

 #CCP4I MESSAGE Task failed








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[ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

[Xiao Lei]

Dear All,

I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) to
mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should I
supposed to do next to correct the problem, any suggestions are
appreciated. I pasted the message from part of log file below:


ANISOTROPY ANALYSIS (using intensities):


Eigenvalues: -0.5668 0.1479 0.3584

Eigenvalue ratios: -1.5815 0.4128 1.

ctruncate: Anisotropy correction failed - negative eigenvalue.

Times: User: 0.4s System: 0.0s Elapsed: 0:00

***

* Information from CCP4Interface script

***

The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate -hklin
/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp -hklout
/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp -colin
/*/*/\[IMEAN,SIGIMEAN\] -colout P1_12

has failed with error message

ctruncate: Anisotropy correction failed - negative eigenvalue.

ObjectCache: Leaked 0005 refs to

***



#CCP4I TERMINATION STATUS 0  ctruncate:  Anisotropy correction failed -
negative eigenvalue. ObjectCache: Leaked 0005 refs to



#CCP4I TERMINATION TIME 09 Jan 2015  19:55:50

#CCP4I MESSAGE Task failed