[ccp4bb] PNCC Screening Access Mechanism

[Kjirsten Wheeler]

Hello CryoEM Researchers,
Pacific Northwest CryoEM Center is offering a mechanism developed to help 
laboratories with limited or no cryo-EM resources enter the field of cryo-EM. 
PNCC's "Screening Access Mechanism" will provide users on-site access to 
state-of-the-art cryo-EM resources and expertise to carry out sample 
preparation and optimization under close supervision of trained cryo-EM 
specialists.
Our goal is to help users identify cryo-grid conditions that will be successful 
for transitioning to data collection activities provided by PNCC's General 
Access mechanism or to establish the technical feasibility and provide guidance 
on the next states of the project. We hope this new mechanism will enable 
investigators lacking access to local cryo-EM resources and help jump-start 
investigators interested in entering the field of cryo-EM.
For more information about our "Screening Access Mechanism", go 
here. The next application 
deadline for this new proposal type is August 1st at 11:59pm (Pacific) in our 
portal here. Step-by-step instructions on how 
to submit a proposal to PNCC can be found 
here.
We request your help by disseminating this information to colleagues who may be 
interested in engaging in the field of cryo-EM!"
_
Kjirsten Wheeler
PNCC Administrative Coordinator
Pacific Northwest Cryo-EM Center
a PNNL and OHSU affiliation
Website
PNCC 
Twitter

wheel...@ohsu.edu




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Re: [ccp4bb] How to calculate experimental residual electron density map

[Tim Gruene]

Dear Amkur K Singh,

every refinement program (buster, refmac5, phenix.refine, SHELXL)
produces coefficients for the electron density map, that you name
"2Fmo-dFc", as well es the residual electron density map. That's named
'difference map'. Unless I misunderstand, that is what you are looking
for. As you are familiar with MoPro, SHELXL might be easier for you
than the other refinement programs listed above. With 'pdb2ins', you
can easily generate ins- and hkl-file from a PDB-entry.
Best wishes,
Tim



On Mon, 24 Jul 2023 11:26:07 + Ankur Kumar Singh
 wrote:

> Dear Members,
> I am trying to generate an experimental residual electron density map
> for a protein structure resolved at 1.1 Angstrom. One way to do this
> is by refining the structure using an aspherical model of charge
> distribution (Multipole density proposed by Hansen and Coppens) in
> MoPro. However, I cannot take that approach due to resolution
> limitation. Another way to calculate this map is-
> 
> 
>   *   Calculate only the atomic density for each atom in the
> structure.
>   *   Calculate the electron density for the entire structure which
> is 2Fmo-dFc
>   *   Subtract these density to obtain the residual electron density
> map.
> 
> Is this approach correct? Assuming it to be correct, I looked for
> CCP4 tools to perform this job but I couldn't find it. Can anyone
> please suggest or comment on this?
> 
> Thanks in advance.
> 
> --
> Regards,
> Ankur K Singh
> Ph.D Student
> 
> 
> 
> 
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> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Description: OpenPGP digital signature

Re: [ccp4bb] 1990s-style stereo viewer

[Goldman, Adrian]

Yes but this is just classic side by side stereo. I had one until quite 
recently. My memory of the ps300 is that it was fullscreen, not side by side 
with the display synced as another poster said. 

I also feel that the ps300 didn’t flicker because it was a raster display so no 
matter how many lines it still displayed at 30 or 60 hz. Don’t remember. The 
ps2, on the other hand drew each vectors line by line - and my god that 
flickered awfully with “complex” objects. 

Adrian 

Sent from my iPhone

> On 24 Jul 2023, at 18:53, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Alastair
> 
> YES! Those are the ones.
> 
> Many thanks
> 
> Harry
> 
>> On 24 Jul 2023, at 16:46, Alastair MC EWEN  wrote:
>> 
>> Hi Harry,
>> 
>> Are these the ones you mean? 
>> 
>> Best,
>> Alastair
>> 
>> ~
>> Alastair McEwen, PhD
>> Integrated Structural Biology Platform
>> IGBMC
>> 1 rue Laurent Fries
>> 67404 ILLKIRCH - FRANCE
>> tel: +33 (0)3 69 48 52 82
>> From: CCP4 bulletin board  on behalf of Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
>> Sent: 24 July 2023 16:58:26
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] 1990s-style stereo viewer
>> 
>> Hi folks
>> 
>> I was wondering if anyone has a photo of the old-style head-mounted stereo 
>> viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
>> don’t mean the ones that were used to view the side-by-side stereo images 
>> that once appeared in printed journals, but the ones that were used for 
>> advanced computer graphics machines like E PS300.
>> 
>> From my somewhat dim memory, they had an adjustable mirror on one side so 
>> that the two views could be coalesced (with the adjustment knob on the top 
>> of the box).
>> 
>> More in hope than expectation…
>> 
>> Harry
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>> https://www.jiscmail.ac.uk/policyandsecurity/
>> 
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>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> <20230724_174436.jpg>
> 
> 
> 
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Re: [ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Hi Alastair

YES! Those are the ones.

Many thanks

Harry

> On 24 Jul 2023, at 16:46, Alastair MC EWEN  wrote:
> 
> Hi Harry,
> 
> Are these the ones you mean? 
> 
> Best,
> Alastair
> 
> ~
> Alastair McEwen, PhD
> Integrated Structural Biology Platform
> IGBMC
> 1 rue Laurent Fries
> 67404 ILLKIRCH - FRANCE
> tel: +33 (0)3 69 48 52 82
> From: CCP4 bulletin board  on behalf of Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> Sent: 24 July 2023 16:58:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 1990s-style stereo viewer
>  
> Hi folks
> 
> I was wondering if anyone has a photo of the old-style head-mounted stereo 
> viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
> don’t mean the ones that were used to view the side-by-side stereo images 
> that once appeared in printed journals, but the ones that were used for 
> advanced computer graphics machines like E PS300.
> 
> From my somewhat dim memory, they had an adjustable mirror on one side so 
> that the two views could be coalesced (with the adjustment knob on the top of 
> the box).
> 
> More in hope than expectation…
> 
> Harry
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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> <20230724_174436.jpg>



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Re: [ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Can’t have been a PS300 in that case!

I’ve since been reminded that they were made of wood (the stereo viewers, not 
the Evans and Sutherland. But I’m probably wrong about that as well…)

Harry

> On 24 Jul 2023, at 16:03, Wim Burmeister  wrote:
> 
> Hi,
> the E PS300 already used LCD-based shutter glasses connected with a wire 
> although awfully flickering with a switching frequency in the 8 Hz range!
> Wim
> 
> - Mail original -
> De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> À: "CCP4BB" 
> Envoyé: Lundi 24 Juillet 2023 16:58:26
> Objet: [ccp4bb] 1990s-style stereo viewer
> 
> Hi folks
> 
> I was wondering if anyone has a photo of the old-style head-mounted stereo 
> viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
> don’t mean the ones that were used to view the side-by-side stereo images 
> that once appeared in printed journals, but the ones that were used for 
> advanced computer graphics machines like E PS300.
> 
> From my somewhat dim memory, they had an adjustable mirror on one side so 
> that the two views could be coalesced (with the adjustment knob on the top of 
> the box).
> 
> More in hope than expectation…
> 
> Harry
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
> -- 
> Wim Burmeister 
> Professor 
> Institut de Biologie Structurale (IBS) CIBB 
> 71 avenue des Martyrs / CS 20192 
> 38044 Grenoble Cedex 9, FRANCE 
> E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
> Mobile: +33 (0) 7 50 49 19 91 
> [ 
> http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
>  | website ]
> 
> 
> 
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Re: [ccp4bb] 1990s-style stereo viewer

[Wim Burmeister]

Hi,
the E PS300 already used LCD-based shutter glasses connected with a wire 
although awfully flickering with a switching frequency in the 8 Hz range!
Wim

- Mail original -
De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
À: "CCP4BB" 
Envoyé: Lundi 24 Juillet 2023 16:58:26
Objet: [ccp4bb] 1990s-style stereo viewer

Hi folks

I was wondering if anyone has a photo of the old-style head-mounted stereo 
viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
don’t mean the ones that were used to view the side-by-side stereo images that 
once appeared in printed journals, but the ones that were used for advanced 
computer graphics machines like E PS300.

>From my somewhat dim memory, they had an adjustable mirror on one side so that 
>the two views could be coalesced (with the adjustment knob on the top of the 
>box).

More in hope than expectation…

Harry


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-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ]



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[ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Hi folks

I was wondering if anyone has a photo of the old-style head-mounted stereo 
viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
don’t mean the ones that were used to view the side-by-side stereo images that 
once appeared in printed journals, but the ones that were used for advanced 
computer graphics machines like E PS300.

From my somewhat dim memory, they had an adjustable mirror on one side so that 
the two views could be coalesced (with the adjustment knob on the top of the 
box).

More in hope than expectation…

Harry


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Re: [ccp4bb] How to calculate experimental residual electron density map

[Eleanor Dodson]

You would hope it would show some hydrogen positions..
Eleanor

On Mon, 24 Jul 2023 at 13:47, Ankur Kumar Singh  wrote:

> Dear Prof. Eleanor Dodson,
> Thank you for the response. I will try generating difference map as told
> and will update.
>
> -
> Regards,
> Ankur K Singh
> Ph.D. Student
>
> --
> *From:* Eleanor Dodson 
> *Sent:* Monday, July 24, 2023 5:31 PM
> *To:* Ankur Kumar Singh 
> *Cc:* CCP4BB@jiscmail.ac.uk 
> *Subject:* Re: [ccp4bb] How to calculate experimental residual electron
> density map
>
> External Email
>
> hy not calculate structure factors without hydrogen atoms and look at the
> difference map?
> Eleanor
>
> On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh <
> a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear Members,
> I am trying to generate an experimental residual electron density map for
> a protein structure resolved at 1.1 Angstrom. One way to do this is by
> refining the structure using an aspherical model of charge distribution
> (Multipole density proposed by Hansen and Coppens) in MoPro. However, I
> cannot take that approach due to resolution limitation. Another way to
> calculate this map is-
>
>
>- Calculate only the atomic density for each atom in the structure.
>- Calculate the electron density for the entire structure which is
>2Fmo-dFc
>- Subtract these density to obtain the residual electron density map.
>
> Is this approach correct? Assuming it to be correct, I looked for CCP4
> tools to perform this job but I couldn't find it. Can anyone please suggest
> or comment on this?
>
> Thanks in advance.
>
> --
> Regards,
> Ankur K Singh
> Ph.D Student
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] How to calculate experimental residual electron density map

[Ankur Kumar Singh]

Dear Prof. Eleanor Dodson,
Thank you for the response. I will try generating difference map as told and 
will update.

-
Regards,
Ankur K Singh
Ph.D. Student


From: Eleanor Dodson 
Sent: Monday, July 24, 2023 5:31 PM
To: Ankur Kumar Singh 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] How to calculate experimental residual electron density 
map

External Email

hy not calculate structure factors without hydrogen atoms and look at the 
difference map?
Eleanor

On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh 
>
 wrote:
Dear Members,
I am trying to generate an experimental residual electron density map for a 
protein structure resolved at 1.1 Angstrom. One way to do this is by refining 
the structure using an aspherical model of charge distribution (Multipole 
density proposed by Hansen and Coppens) in MoPro. However, I cannot take that 
approach due to resolution limitation. Another way to calculate this map is-


  *   Calculate only the atomic density for each atom in the structure.
  *   Calculate the electron density for the entire structure which is 2Fmo-dFc
  *   Subtract these density to obtain the residual electron density map.

Is this approach correct? Assuming it to be correct, I looked for CCP4 tools to 
perform this job but I couldn't find it. Can anyone please suggest or comment 
on this?

Thanks in advance.

--
Regards,
Ankur K Singh
Ph.D Student




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Re: [ccp4bb] How to calculate experimental residual electron density map

[Eleanor Dodson]

hy not calculate structure factors without hydrogen atoms and look at the
difference map?
Eleanor

On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh <
a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Members,
> I am trying to generate an experimental residual electron density map for
> a protein structure resolved at 1.1 Angstrom. One way to do this is by
> refining the structure using an aspherical model of charge distribution
> (Multipole density proposed by Hansen and Coppens) in MoPro. However, I
> cannot take that approach due to resolution limitation. Another way to
> calculate this map is-
>
>
>- Calculate only the atomic density for each atom in the structure.
>- Calculate the electron density for the entire structure which is
>2Fmo-dFc
>- Subtract these density to obtain the residual electron density map.
>
> Is this approach correct? Assuming it to be correct, I looked for CCP4
> tools to perform this job but I couldn't find it. Can anyone please suggest
> or comment on this?
>
> Thanks in advance.
>
> --
> Regards,
> Ankur K Singh
> Ph.D Student
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] How to calculate experimental residual electron density map

[Ankur Kumar Singh]

Dear Members,
I am trying to generate an experimental residual electron density map for a 
protein structure resolved at 1.1 Angstrom. One way to do this is by refining 
the structure using an aspherical model of charge distribution (Multipole 
density proposed by Hansen and Coppens) in MoPro. However, I cannot take that 
approach due to resolution limitation. Another way to calculate this map is-


  *   Calculate only the atomic density for each atom in the structure.
  *   Calculate the electron density for the entire structure which is 2Fmo-dFc
  *   Subtract these density to obtain the residual electron density map.

Is this approach correct? Assuming it to be correct, I looked for CCP4 tools to 
perform this job but I couldn't find it. Can anyone please suggest or comment 
on this?

Thanks in advance.

--
Regards,
Ankur K Singh
Ph.D Student




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